match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	TIGR01884	203	170	100.0	3.3E-29	[------------------------------------------       ]	cas_HTH	CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
2	cd09655	198	168	99.9	1.4E-25	[------------------------------------------       ]	CasRa_I-A	CRISPR/Cas system-associated transcriptional regulator CasRa. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system
3	cd00090	78	57	98.9	2E-09	[                           --------------        ]	HTH_ARSR	Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
4	pfam01022	47	46	98.8	8.8E-09	[                           ------------          ]	HTH_5	Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
5	COG2512	258	62	98.8	8.8E-09	[                          ---------------        ]	COG2512	Uncharacterized membrane protein
6	pfam13412	48	45	98.6	1.4E-07	[                           -----------           ]	HTH_24	Winged helix-turn-helix DNA-binding.
7	pfam01978	68	53	98.5	2.6E-07	[                           -------------         ]	TrmB	Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
8	COG1846	126	64	98.5	3.1E-07	[                           ----------------      ]	MarR	DNA-binding transcriptional regulator, MarR family
9	pfam12802	61	50	98.4	6.3E-07	[                           ------------          ]	MarR_2	MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
10	COG3355	126	54	98.4	3.8E-07	[                          --------------         ]	COG3355	Predicted transcriptional regulator
11	pfam12840	61	53	98.4	6.9E-07	[                           -------------         ]	HTH_20	Helix-turn-helix domain. This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.
12	COG1522	154	49	98.4	5.9E-07	[                          ------------           ]	Lrp	DNA-binding transcriptional regulator, Lrp family
13	pfam01047	59	50	98.4	1E-06	[                           ------------          ]	MarR	MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
14	pfam13404	42	41	98.3	1.2E-06	[                           ----------            ]	HTH_AsnC-type	AsnC-type helix-turn-helix domain.
15	COG4742	260	63	98.2	7E-07	[                           ----------------      ]	COG4742	Predicted transcriptional regulator, contains HTH domain
16	pfam13463	68	60	98.1	8.5E-06	[                           ---------------       ]	HTH_27	Winged helix DNA-binding domain.
17	pfam09339	52	45	98.0	1.2E-05	[                            -----------          ]	HTH_IclR	IclR helix-turn-helix domain.
18	COG1321	154	64	98.0	7.6E-06	[                           ----------------      ]	MntR	Mn-dependent transcriptional regulator, DtxR family
19	cd00092	67	44	97.9	2E-05	[                              -----------        ]	HTH_CRP	helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
20	COG1414	246	55	97.8	3E-05	[                            -------------        ]	IclR	DNA-binding transcriptional regulator, IclR family
21	COG2345	218	67	97.8	3E-05	[                          -----------------      ]	COG2345	Predicted transcriptional regulator, ArsR family
22	pfam08279	52	39	97.7	8.7E-05	[                             ---------           ]	HTH_11	HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
23	cd00569	42	38	97.7	9.2E-05	[                           ---------             ]	HTH_Hin_like	Helix-turn-helix domain of Hin and related proteins. This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.
24	pfam08220	57	47	97.7	6.4E-05	[                            ------------         ]	HTH_DeoR	DeoR-like helix-turn-helix domain.
25	pfam13730	55	47	97.6	0.00018	[                           -----------           ]	HTH_36	Helix-turn-helix domain.
26	COG1349	253	50	97.5	0.00012	[                            ------------         ]	GlpR	DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family
27	COG1733	120	59	97.3	0.00035	[                            ---------------      ]	HxlR	DNA-binding transcriptional regulator, HxlR family
28	pfam01325	58	45	97.3	0.00047	[                            -----------          ]	Fe_dep_repress	Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
29	COG0640	110	55	97.3	0.00079	[                           -------------         ]	ArsR	DNA-binding transcriptional regulator, ArsR family
30	pfam03965	115	57	97.2	0.00074	[                           --------------        ]	Penicillinase_R	Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
31	pfam04967	53	43	97.2	0.0012	[                           -----------           ]	HTH_10	HTH DNA binding domain.
32	pfam14947	77	58	97.1	0.00077	[                            ---------------      ]	HTH_45	Winged helix-turn-helix. This winged helix-turn-helix domain contains an extended C-terminal alpha helix which is responsible for dimerization of this domain.
33	pfam03444	79	61	97.1	0.00079	[                           ---------------       ]	HrcA_DNA-bdg	Winged helix-turn-helix transcription repressor, HrcA DNA-binding. This domain is always found with a pair of CBS domains pfam00571.
34	PRK04172	489	64	97.1	0.00076	[                           ----------------      ]	pheS	phenylalanyl-tRNA synthetase subunit alpha; Provisional
35	pfam13936	44	41	97.1	0.0014	[                           ----------            ]	HTH_38	Helix-turn-helix domain. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
36	COG1378	247	60	97.0	0.0013	[                          ---------------        ]	TrmB	Sugar-specific transcriptional regulator TrmB
37	COG0735	145	55	97.0	0.0014	[                          --------------         ]	Fur	Fe2+ or Zn2+ uptake regulation protein
38	pfam00126	60	54	96.9	0.0019	[                            --------------       ]	HTH_1	Bacterial regulatory helix-turn-helix protein, lysR family.
39	cd06170	57	40	96.9	0.0022	[                           ----------            ]	LuxR_C_like	C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.
40	pfam01638	91	59	96.8	0.0019	[                            ---------------      ]	HxlR	HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.
41	COG1497	260	62	96.8	0.0025	[                           ---------------       ]	COG1497	Predicted transcriptional regulator
42	COG4189	308	67	96.8	0.0025	[                          -----------------      ]	COG4189	Predicted transcriptional regulator
43	COG3413	215	47	96.8	0.0025	[                          ------------           ]	COG3413	Predicted DNA binding protein, contains HTH domain
44	cd07153	116	47	96.8	0.0017	[                            ------------         ]	Fur_like	Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.
45	pfam13601	80	57	96.8	0.0017	[                            --------------       ]	HTH_34	Winged helix DNA-binding domain.
46	pfam13518	52	39	96.8	0.0039	[                            ----------           ]	HTH_28	Helix-turn-helix domain. This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.
47	COG3398	240	57	96.7	0.003	[                           --------------        ]	COG3398	Predicted transcriptional regulator, containsd two HTH domains
48	cd07377	66	31	96.6	0.0019	[                               --------          ]	WHTH_GntR	Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.
49	COG2771	65	47	96.6	0.0081	[                           -----------           ]	CsgD	DNA-binding transcriptional regulator, CsgD family
50	TIGR04176	105	59	96.6	0.0051	[                           ---------------       ]	MarR_EPS	EPS-associated transcriptional regulator, MarR family. Members of this family of MarR-family transcriptional regulators are associated with long genomic loci consisting of genes encoding enzymes for the biosynthesis of exopolysaccharides. These genes include glycosyl transferases, sugar modifying enzymes (epimerases, isomerases, methyltransferases, aminotransferases, etc.), and exopolysaccharide polymerases (wzx, wzy). In Leptospira interrogans, borgpeterenii and biflexa, this gene is observed first in unidirectional EPS biosynthesis loci as long as 90 genes. MarR genes (pfam01407) are known to bind to DNA regions with palindromic or pseudopalindromic sequences as homodimers, and to bind small molecules as triggers for conformational changes controlling on/off states.
51	pfam13384	50	40	96.5	0.01	[                            ----------           ]	HTH_23	Homeodomain-like domain.
52	pfam00196	58	47	96.5	0.0078	[                           -----------           ]	GerE	Bacterial regulatory proteins, luxR family.
53	COG1654	79	33	96.4	0.0072	[                              --------           ]	BirA	Biotin operon repressor
54	COG2524	294	66	96.4	0.0049	[                           ----------------      ]	COG2524	Predicted transcriptional regulator, contains C-terminal CBS domains
55	pfam13545	70	42	96.3	0.0065	[                               ----------        ]	HTH_Crp_2	Crp-like helix-turn-helix domain. This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.
56	pfam09012	69	42	96.3	0.0079	[                              ----------         ]	FeoC	FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a
57	PRK15090	257	54	96.3	0.0066	[                            -------------        ]	PRK15090	DNA-binding transcriptional regulator KdgR; Provisional
58	PRK00215	205	52	96.3	0.0083	[                           -------------         ]	PRK00215	LexA repressor; Validated
59	COG1386	184	59	96.3	0.0073	[                          ----------------       ]	ScpB	Chromosome segregation and condensation protein ScpB
60	PRK11886	319	55	96.2	0.0071	[                            -------------        ]	PRK11886	bifunctional biotin--
61	pfam14394	171	53	96.2	0.0088	[                             -------------       ]	DUF4423	Domain of unknown function (DUF4423). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 170 amino acids in length.
62	COG3682	123	54	96.1	0.017	[                           -------------         ]	COG3682	Predicted transcriptional regulator
63	pfam02796	45	39	96.0	0.012	[                           ----------            ]	HTH_7	Helix-turn-helix domain of resolvase.
64	pfam08281	54	43	95.8	0.026	[                           ----------            ]	Sigma70_r4_2	Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
65	TIGR00331	337	68	95.8	0.013	[                           --------------------- ]	hrcA	heat shock gene repressor HrcA. HrcA represses the class I heat shock operons groE and dnaK; overproduction prevents induction of these operons by heat shock while deletion allows constitutive expression even at low temperatures. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
66	pfam02082	83	41	95.8	0.017	[                               ----------        ]	Rrf2	Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
67	pfam08461	66	54	95.8	0.019	[                             -------------       ]	HTH_12	Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
68	pfam02002	105	55	95.8	0.025	[                          --------------         ]	TFIIE_alpha	TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the pre-initiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
69	TIGR02431	248	54	95.7	0.018	[                            --------------       ]	pcaR_pcaU	beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
70	COG3432	95	63	95.7	0.0056	[                           ----------------      ]	COG3432	Predicted transcriptional regulator
71	COG2865	467	91	95.7	0.043	[                -----------------------          ]	COG2865	Predicted transcriptional regulator, contains HTH domain
72	PRK09834	263	58	95.7	0.012	[                            --------------       ]	PRK09834	DNA-binding transcriptional activator MhpR; Provisional
73	COG1725	125	44	95.7	0.014	[                               -----------       ]	YhcF	DNA-binding transcriptional regulator YhcF, GntR family
74	COG2197	211	46	95.7	0.022	[                           -----------           ]	CitB	DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains
75	pfam10007	93	54	95.6	0.036	[                           -------------         ]	DUF2250	Uncharacterized protein conserved in archaea (DUF2250). Members of this family of hypothetical archaeal proteins have no known function.
76	pfam00325	32	30	95.6	0.02	[                               -------           ]	Crp	Bacterial regulatory proteins, crp family.
77	COG1693	325	61	95.5	0.026	[                           ---------------       ]	COG1693	Repressor of nif and glnA expression
78	pfam09202	82	59	95.4	0.044	[                           ---------------       ]	Rio2_N	Rio2, N-terminal. Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains.
79	PRK11050	152	63	95.4	0.029	[                           ----------------      ]	PRK11050	manganese transport regulator MntR; Provisional
80	PRK00082	339	71	95.3	0.022	[                           --------------------- ]	hrcA	heat-inducible transcription repressor; Provisional
81	PRK11179	153	65	95.3	0.0087	[                           ----------------      ]	PRK11179	DNA-binding transcriptional regulator AsnC; Provisional
82	COG4190	144	63	95.3	0.026	[                         ---------------         ]	COG4190	Predicted transcriptional regulator
83	COG1959	150	45	95.2	0.027	[                               -----------       ]	IscR	DNA-binding transcriptional regulator, IscR family
84	COG0583	297	62	95.2	0.015	[                           ----------------      ]	LysR	DNA-binding transcriptional regulator, LysR family
85	pfam14493	91	36	95.2	0.047	[                             ---------           ]	HTH_40	Helix-turn-helix domain. This presumed domain is found at the C-terminus of a large number of helicase proteins.
86	pfam09651	136	68	95.2	0.056	[        -----------------                        ]	Cas_APE2256	CRISPR-associated protein (Cas_APE2256). This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.
87	pfam07848	70	40	95.1	0.028	[                                ----------       ]	PaaX	PaaX-like protein. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolizm of phenylacetic acid. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058).
88	PRK06266	178	47	95.0	0.044	[                           ------------          ]	PRK06266	transcription initiation factor E subunit alpha; Validated
89	pfam01475	120	61	95.0	0.058	[                          ---------------        ]	FUR	Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
90	pfam04079	158	99	95.0	0.048	[          -----------------------------          ]	DUF387	Putative transcriptional regulators (Ypuh-like). This family of conserved bacterial proteins are thought to possibly be helix-turn-helix type transcriptional regulators.
91	COG3398	240	52	95.0	0.046	[                           -------------         ]	COG3398	Predicted transcriptional regulator, containsd two HTH domains
92	TIGR02937	158	43	94.9	0.047	[                           ----------            ]	sigma70-ECF	RNA polymerase sigma factor, sigma-70 family. This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
93	cd09742	183	64	94.9	0.084	[          ----------------                       ]	Csm6_III-A	CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems; also known as APE2256 family
94	pfam00392	64	34	94.9	0.027	[                               ---------         ]	GntR	Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolizm and development in Streptomyces coelicolor.
95	pfam04545	50	41	94.8	0.095	[                           ----------            ]	Sigma70_r4	Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
96	COG3177	348	47	94.8	0.036	[                            ------------         ]	COG3177	Fic family protein
97	pfam04182	74	45	94.7	0.064	[                           -----------           ]	B-block_TFIIIC	B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
98	COG1777	217	58	94.7	0.09	[                             --------------      ]	COG1777	Predicted transcriptional regulator
99	TIGR02337	118	66	94.7	0.065	[                          -----------------      ]	HpaR	homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
100	pfam01726	63	48	94.7	0.1	[                           ------------          ]	LexA_DNA_bind	LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
101	pfam05043	87	43	94.6	0.077	[                            -----------          ]	Mga	Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
102	cd06171	55	41	94.6	0.096	[                           ----------            ]	Sigma70_r4	Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
103	PRK11169	164	48	94.6	0.044	[                           -----------           ]	PRK11169	leucine-responsive transcriptional regulator; Provisional
104	PRK13509	251	46	94.6	0.048	[                             -----------         ]	PRK13509	transcriptional repressor UlaR; Provisional
105	pfam05732	165	42	94.5	0.043	[                               -----------       ]	RepL	Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
106	pfam06969	66	52	94.2	0.15	[                             -------------       ]	HemN_C	HemN C-terminal domain. Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX, one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (pfam04055) suggest it may be a substrate binding domain.
107	TIGR00122	69	41	94.1	0.053	[                            ----------           ]	birA_repr_reg	BirA biotin operon repressor domain. This model represents the amino-terminal helix-turn-helix repressor region of the biotin--acetyl-CoA-carboxylase ligase/biotin operon repressor bifunctional protein BirA. In many species, the biotin--acetyl-CoA-carboxylase ligase ortholog lacks this DNA-binding repressor region and therefore is not equivalent to the well-characterized BirA of E. coli. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
108	COG1510	177	39	94.0	0.074	[                              ----------         ]	GbsR	DNA-binding transcriptional regulator GbsR, MarR family
109	TIGR02702	203	44	94.0	0.045	[                            -----------          ]	SufR_cyano	iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
110	COG4565	224	129	93.9	0.14	[     ---------------------------------           ]	CitB	Response regulator of citrate/malate metabolism
111	TIGR00637	99	62	93.9	0.1	[                           ----------------      ]	ModE_repress	ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
112	pfam03551	75	39	93.8	0.043	[                                 ----------      ]	PadR	Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolizm.
113	pfam05225	45	36	93.8	0.15	[                            ---------            ]	HTH_psq	helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
114	TIGR02944	130	59	93.5	0.16	[                           ---------------       ]	suf_reg_Xantho	FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
115	COG1339	214	49	93.3	0.07	[                               ------------      ]	Rfk	Archaeal CTP-dependent riboflavin kinase
116	COG1675	176	51	93.2	0.13	[                           -------------         ]	TFA1	Transcription initiation factor IIE, alpha subunit
117	pfam08222	60	34	93.1	0.094	[                               --------          ]	HTH_CodY	CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
118	COG2188	236	46	93.0	0.086	[                             -----------         ]	MngR	DNA-binding transcriptional regulator, GntR family
119	TIGR00738	132	48	93.0	0.16	[                              ------------       ]	rrf2_super	Rrf2 family protein. This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
120	TIGR00281	186	56	93.0	0.19	[                           --------------        ]	TIGR00281	segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
121	pfam13542	51	34	93.0	0.25	[                            ---------            ]	HTH_Tnp_ISL3	Helix-turn-helix domain of transposase family ISL3.
122	PRK05638	442	65	92.9	0.12	[                           ----------------      ]	PRK05638	threonine synthase; Validated
123	COG1420	346	49	92.9	0.19	[                           ------------          ]	HrcA	Transcriptional regulator of heat shock response
124	COG3388	101	56	92.6	0.06	[                            --------------       ]	COG3388	Predicted transcriptional regulator
125	pfam13309	64	37	92.5	0.072	[                           ---------             ]	HTH_22	HTH domain. This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.
126	pfam02001	100	45	92.5	0.37	[                          -----------            ]	DUF134	Protein of unknown function DUF134. This family of archaeal proteins has no known function.
127	PRK14165	217	58	92.4	0.11	[                            --------------       ]	PRK14165	winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
128	pfam13551	109	38	92.3	0.29	[                             ---------           ]	HTH_29	Winged helix-turn helix. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
129	COG3327	291	43	92.1	0.12	[                                ----------       ]	PaaX	DNA-binding transcriptional regulator PaaX (phenylacetic acid degradation)
130	COG3415	138	39	92.1	0.27	[                             ---------           ]	COG3415	Transposase
131	TIGR03879	73	33	92.1	0.083	[                              --------           ]	near_KaiC_dom	probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
132	COG5340	269	45	92.0	0.34	[                              -----------        ]	COG5340	Transcriptional regulator, predicted component of viral defense system
133	COG1695	138	62	92.0	0.15	[                            ---------------      ]	PadR	DNA-binding transcriptional regulator, PadR family
134	pfam14502	48	36	91.9	0.16	[                               ---------         ]	HTH_41	Helix-turn-helix domain.
135	pfam09862	113	58	91.9	0.34	[                        --------------           ]	DUF2089	Protein of unknown function (DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function. This domain is a zinc-ribbon.
136	COG2390	321	33	91.9	0.28	[                              --------           ]	DeoR	DNA-binding transcriptional regulator LsrR, DeoR family
137	pfam12728	52	27	91.2	0.22	[                               --------          ]	HTH_17	Helix-turn-helix domain. This domain is a DNA-binding helix-turn-helix domain.
138	pfam04218	53	41	91.1	0.59	[                           ----------            ]	CENP-B_N	CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
139	COG3888	321	33	91.1	0.43	[                              --------           ]	COG3888	Predicted transcriptional regulator
140	pfam07900	220	46	91.1	0.4	[                           -----------           ]	DUF1670	Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
141	pfam08784	103	47	90.7	0.6	[                           -----------           ]	RPA_C	Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
142	pfam08280	59	39	90.6	0.73	[                            ---------            ]	HTH_Mga	M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.
143	COG1342	99	67	90.4	1.2	[                          -------------------    ]	COG1342	Predicted DNA-binding protein, UPF0251 family
144	PRK09249	453	67	90.1	0.3	[                          -----------------      ]	PRK09249	coproporphyrinogen III oxidase; Provisional
145	cd01392	52	19	89.8	0.21	[                                -----            ]	HTH_LacI	Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.
146	pfam02954	42	36	89.7	0.62	[                            ---------            ]	HTH_8	Bacterial regulatory protein, Fis family.
147	pfam07638	185	40	89.7	0.63	[                          ----------             ]	Sigma70_ECF	ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
148	COG2186	241	42	89.6	0.34	[                              ----------         ]	FadR	DNA-binding transcriptional regulator, FadR family
149	cd04761	49	27	89.6	0.39	[                               --------          ]	HTH_MerR-SF	Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
150	PRK13777	185	51	89.6	0.24	[                              -------------      ]	PRK13777	transcriptional regulator Hpr; Provisional
151	COG2005	130	65	89.5	0.32	[                          -----------------      ]	ModE	DNA-binding transcriptional regulator ModE (molybdenum-dependent)
152	COG1595	182	43	89.3	0.74	[                          -----------            ]	RpoE	DNA-directed RNA polymerase specialized sigma subunit, sigma24 family
153	pfam13613	53	29	89.3	1.5	[                              -------            ]	HTH_Tnp_4	Helix-turn-helix of DDE superfamily endonuclease. This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.
154	cd04789	102	44	89.2	0.22	[                               ----------------- ]	HTH_Cfa	Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
155	PRK09333	150	57	88.9	0.45	[                             --------------      ]	PRK09333	30S ribosomal protein S19e; Provisional
156	COG0478	304	63	88.8	1	[                          ----------------       ]	RIO2	RIO-like serine/threonine protein kinase fused to N-terminal HTH domain
157	COG5625	113	56	88.8	0.65	[                          --------------         ]	COG5625	Predicted DNA-binding transcriptional regulator, contains HTH domain
158	pfam13443	63	30	88.8	0.56	[                             -------             ]	HTH_26	Cro/C1-type HTH DNA-binding domain. This is a helix-turn-helix domain that probably binds to DNA.
159	pfam00356	46	23	88.4	0.43	[                               ------            ]	LacI	Bacterial regulatory proteins, lacI family.
160	PRK10434	256	44	88.3	0.77	[                            ----------           ]	srlR	DNA-bindng transcriptional repressor SrlR; Provisional
161	COG1802	230	41	88.2	0.52	[                             ----------          ]	GntR	DNA-binding transcriptional regulator, GntR family
162	pfam04157	218	45	88.2	1	[                           -----------           ]	EAP30	EAP30/Vps36 family. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity.
163	COG1568	354	57	87.8	0.59	[                            ---------------      ]	COG1568	Predicted methyltransferase
164	pfam01527	75	42	87.7	1.6	[                           ----------            ]	HTH_Tnp_1	Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
165	pfam01418	77	50	87.4	1.1	[                          ------------           ]	HTH_6	Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is Escherichia coli rpiR, a regulator of the expression of rpiB gene.
166	COG4109	432	48	87.3	0.34	[                              ------------       ]	YtoI	Predicted transcriptional regulator containing CBS domains
167	PRK06474	178	51	87.1	0.97	[                            ------------         ]	PRK06474	hypothetical protein; Provisional
168	COG3284	606	76	87.0	2.5	[                 --------------------            ]	AcoR	Transcriptional regulator of acetoin/glycerol metabolism
169	TIGR00498	199	54	87.0	1.2	[                           -------------         ]	lexA	SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
170	PRK03635	294	62	86.7	0.37	[                           ----------------      ]	PRK03635	chromosome replication initiation inhibitor protein; Validated
171	COG1710	139	45	86.6	1.3	[                          -----------            ]	COG1710	Uncharacterized protein
172	PRK10651	216	50	86.4	0.62	[                           ------------          ]	PRK10651	transcriptional regulator NarL; Provisional
173	COG2378	311	48	85.8	1.5	[                            ------------         ]	YafY	Predicted DNA-binding transcriptional regulator YafY, contains an HTH and WYL domains
174	TIGR03642	124	42	85.8	1.4	[          ----------                             ]	cas_csx14	CRISPR-associated protein, Csx14 family. This model describes a protein N-terminal protein sequence domain strictly associated with CRISPR and CRISPR-associated protein systems. This model and TIGR02584 identify two separate clades from a larger homology domain family, both CRISPR-associated, while other homologs are found that may not be. Members are found in bacteria that include Pelotomaculum thermopropionicum SI, Thermoanaerobacter tengcongensis MB4, and Roseiflexus sp. RS-1, and in archaea that include Thermoplasma volcanium, Picrophilus torridus, and Methanospirillum hungatei. The molecular function is unknown.
175	PRK09954	362	58	85.7	2	[                            ---------------      ]	PRK09954	putative kinase; Provisional
176	COG2238	147	56	85.6	0.58	[                             --------------      ]	RPS19A	Ribosomal protein S19E (S16A)
177	pfam06971	49	32	85.4	1.7	[                            --------             ]	Put_DNA-bind_N	Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
178	PRK11639	169	60	85.3	1.5	[                          ---------------        ]	PRK11639	zinc uptake transcriptional repressor; Provisional
179	COG1318	182	33	85.1	0.72	[                              --------           ]	COG1318	Predicted transcriptional regulator
180	cd00592	100	27	84.8	0.97	[                               --------          ]	HTH_MerR-like	Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
181	pfam07453	37	21	84.8	0.48	[                               -----             ]	NUMOD1	NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
182	pfam04703	61	48	84.6	2.2	[                            ------------         ]	FaeA	FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
183	cd04775	102	32	84.5	0.63	[                               ---------         ]	HTH_Cfa-like	Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
184	pfam00376	38	26	84.5	1.1	[                               --------          ]	MerR	MerR family regulatory protein.
185	PRK09775	442	35	84.4	1.3	[                             --------            ]	PRK09775	putative DNA-binding transcriptional regulator; Provisional
186	cd09723	132	42	84.3	1.8	[          ----------                             ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as csx13 family
187	COG0789	124	32	84.3	0.96	[                               ---------         ]	SoxR	DNA-binding transcriptional regulator, MerR family
188	PRK03902	142	60	84.3	1.8	[                            --------------       ]	PRK03902	manganese transport transcriptional regulator; Provisional
189	PRK13348	294	62	84.1	1.1	[                           ----------------      ]	PRK13348	chromosome replication initiation inhibitor protein; Provisional
190	cd04762	49	21	84.0	1.1	[                               -----             ]	HTH_MerR-trunc	Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
191	COG1542	593	66	83.4	1.9	[                          ----------------       ]	COG1542	Uncharacterized protein
192	TIGR02010	135	45	83.2	2.4	[                             -----------         ]	IscR	iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
193	pfam01371	88	36	83.2	1.7	[                            ---------            ]	Trp_repressor	Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
194	PRK11753	211	93	83.1	1.5	[     ---------------------------------           ]	PRK11753	DNA-binding transcriptional dual regulator Crp; Provisional
195	COG4901	107	47	83.0	1.7	[                             -----------         ]	RPS25	Ribosomal protein S25
196	COG5631	199	61	82.7	2.6	[                           ---------------       ]	COG5631	Predicted transcription regulator, contains HTH domain, MarR family
197	COG2964	220	41	82.5	1.1	[                            ----------           ]	YheO	Predicted transcriptional regulator YheO, contains PAS and DNA-binding HTH domains
198	TIGR00373	158	52	82.5	4.5	[                          -------------          ]	TIGR00373	transcription factor E. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
199	TIGR04543	331	57	82.2	1.8	[                             --------------      ]	ketoArg_3Met	2-ketoarginine methyltransferase. This SAM-dependent C-methyltransferase performs the middle step of a three step conversion from arginine to beta-methylarginine. It performs a C-methylation at position 3 of 5-guanidino-2-oxopentanoic acid (keto-arginine). An aminotransferase converts arginine to 5-guanidino-2-oxopentanoic acid, and later converts 5-guanidino-3-methyl-2-oxopentanoic acid to beta-methylarginine.
200	PRK11924	179	42	82.1	2.6	[                          -----------            ]	PRK11924	RNA polymerase sigma factor; Provisional
201	TIGR02607	78	23	82.0	1.4	[                               -----             ]	antidote_HigA	addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
202	cd00093	58	29	82.0	2.4	[                             -------             ]	HTH_XRE	Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
203	TIGR01889	109	51	81.0	5	[                           ------------          ]	Staph_reg_Sar	staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam01047.
204	TIGR01764	49	22	81.0	1.7	[                               -----             ]	excise	DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
205	pfam07022	65	30	80.8	2.4	[                             -------             ]	Phage_CI_repr	Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
206	COG2963	116	50	80.4	4.2	[                            ------------         ]	InsE	Transposase and inactivated derivatives
207	COG1609	333	23	80.4	1.3	[                               ------            ]	PurR	DNA-binding transcriptional regulator, LacI/PurR family
208	pfam04458	591	66	80.0	2.7	[                          ----------------       ]	DUF505	Protein of unknown function (DUF505). Family of uncharacterized prokaryotic proteins.
209	COG2826	318	42	79.5	2.2	[                           ----------            ]	Tra8	Transposase and inactivated derivatives, IS30 family
210	TIGR02698	130	53	79.5	4.8	[                           -------------         ]	CopY_TcrY	copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
211	pfam04492	100	55	79.3	4.1	[                          --------------         ]	Phage_rep_O	Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
212	pfam09681	121	45	79.0	3.2	[                              -----------        ]	Phage_rep_org_N	N-terminal phage replisome organizer (Phage_rep_org_N). This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.
213	PRK08898	394	55	79.0	1.4	[                             --------------      ]	PRK08898	coproporphyrinogen III oxidase; Provisional
214	COG1737	281	50	78.4	2.7	[                          ------------           ]	RpiR	DNA-binding transcriptional regulator, MurR/RpiR family, contains HTH and SIS domains
215	pfam04552	160	37	78.2	2.1	[                               ------------      ]	Sigma54_DBD	Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
216	COG2469	284	66	78.0	0.56	[                          -----------------      ]	COG2469	Uncharacterized protein, contains HTH domain
217	pfam03428	177	32	77.8	3.3	[                                --------         ]	RP-C	Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication.
218	PRK11569	274	45	77.7	3.4	[                            -----------          ]	PRK11569	transcriptional repressor IclR; Provisional
219	COG3877	122	57	77.5	5.4	[                          --------------         ]	COG3877	Uncharacterized protein, DUF2089 family
220	TIGR02985	161	41	77.3	5.2	[                           ----------            ]	Sig70_bacteroi1	RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
221	pfam13660	228	85	77.1	3.6	[       ------------------------------            ]	DUF4147	Domain of unknown function (DUF4147). This domain is frequently found at the N-terminus of proteins carrying the glycerate kinase-like domain MOFRL, pfam05161.
222	PRK04217	110	43	77.0	3.9	[                           ----------            ]	PRK04217	hypothetical protein; Provisional
223	pfam08221	62	46	76.9	8.5	[                           -----------           ]	HTH_9	RNA polymerase III subunit RPC82 helix-turn-helix domain. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix.
224	TIGR02787	251	48	76.8	3.8	[                           ------------          ]	codY_Gpos	GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
225	pfam01381	55	25	76.7	2.9	[                              ------             ]	HTH_3	Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the Neisseria gonorrhoeae phage associated protein NGO0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family.
226	COG0664	214	33	76.6	4.4	[                               --------          ]	Crp	cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases
227	pfam01090	140	63	76.6	1.6	[                           ---------------       ]	Ribosomal_S19e	Ribosomal protein S19e.
228	TIGR03298	292	62	76.6	2.7	[                           ----------------      ]	argP	transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity.
229	pfam10668	60	32	76.5	3.8	[                            --------             ]	Phage_terminase	Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
230	TIGR03338	212	34	76.5	2.3	[                                --------         ]	phnR_burk	phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
231	cd04781	120	27	76.3	2.7	[                               --------          ]	HTH_MerR-like_sg6	Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
232	PRK10141	117	61	76.0	3.1	[                          ---------------        ]	PRK10141	DNA-binding transcriptional repressor ArsR; Provisional
233	pfam00440	47	27	75.6	2.8	[                               ------            ]	TetR_N	Bacterial regulatory proteins, tetR family.
234	PRK13347	453	67	75.6	3.4	[                          -----------------      ]	PRK13347	coproporphyrinogen III oxidase; Provisional
235	pfam14338	92	29	74.9	1.2	[                                    -------      ]	Mrr_N	Mrr N-terminal domain. This domain is found at the N-terminus of the Mrr restriction endonuclease catalytic domain, pfam04471. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition.
236	pfam02295	61	46	74.9	12	[                             -----------         ]	z-alpha	Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
237	PRK06811	189	24	74.6	3.1	[                               ------            ]	PRK06811	RNA polymerase factor sigma-70; Validated
238	TIGR02325	238	32	74.6	3.6	[                                --------         ]	C_P_lyase_phnF	phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
239	COG4566	202	47	74.1	6.6	[                          ------------           ]	FixJ	Two-component response regulator, FixJ family, consists of REC and HTH domains
240	PRK09334	86	47	74.0	5.8	[                             -----------         ]	PRK09334	30S ribosomal protein S25e; Provisional
241	TIGR02999	183	43	74.0	6.1	[                          -----------            ]	Sig-70_X6	RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
242	PRK00118	104	45	73.9	6.5	[                          -----------            ]	PRK00118	putative DNA-binding protein; Validated
243	PRK12515	189	74	73.7	7.1	[                  ------------------             ]	PRK12515	RNA polymerase sigma factor; Provisional
244	PRK12528	161	27	73.7	3.3	[                              -------            ]	PRK12528	RNA polymerase sigma factor; Provisional
245	PRK09492	315	26	73.5	1.8	[                              ------             ]	treR	trehalose repressor; Provisional
246	pfam02650	85	45	73.5	11	[                           -----------           ]	HTH_WhiA	WhiA C-terminal HTH domain. This domain is found at the C-terminus of the sporulation regulator WhiA. It is predicted to form a DNA-binding helix-turn-helix structure. The WhiA protein also contains two N-terminal domains that are distant homologues of LAGLIDADG homing endonucleases.
247	COG2522	119	30	73.3	4.2	[                             -------             ]	COG2522	Predicted transcriptional regulator
248	COG2344	211	39	73.3	5.6	[                            ----------           ]	Rex	NADH/NAD ratio-sensing transcriptional regulator Rex
249	COG3373	108	77	73.1	0.85	[                          ---------------------  ]	COG3373	Predicted transcriptional regulator, contains HTH domain
250	pfam03297	105	46	73.0	5	[                             -----------         ]	Ribosomal_S25	S25 ribosomal protein.
251	COG1309	201	27	72.8	3.1	[                               ------            ]	AcrR	DNA-binding transcriptional regulator, AcrR family
252	COG2739	105	45	72.6	5.7	[                          -----------            ]	YlxM	Predicted DNA-binding protein YlxM, UPF0122 family
253	TIGR02952	170	47	72.5	6.1	[                          ------------           ]	Sig70_famx2	RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
254	COG4465	261	48	72.5	5	[                           ------------          ]	CodY	GTP-sensing pleiotropic transcriptional regulator CodY
255	pfam00046	57	36	72.5	5.7	[                           --------              ]	Homeobox	Homeobox domain.
256	PRK01381	99	36	72.5	2.4	[                            ---------            ]	PRK01381	Trp operon repressor; Provisional
257	pfam13411	69	29	72.2	4.1	[                               --------          ]	MerR_1	MerR HTH family regulatory protein.
258	pfam13556	56	31	71.9	8.2	[                              --------           ]	HTH_30	PucR C-terminal helix-turn-helix domain. This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators and is likely to be DNA-binding.
259	pfam13814	191	51	71.9	4.8	[                              -------------      ]	Replic_Relax	Replication-relaxation. This family includes proteins which are essential for plasmid replication and plasmid DNA relaxation.
260	PRK05660	378	50	71.9	3.8	[                              -------------      ]	PRK05660	HemN family oxidoreductase; Provisional
261	COG1191	247	42	71.4	8.2	[                           ----------            ]	FliA	DNA-directed RNA polymerase specialized sigma subunit
262	COG4754	157	58	71.1	8.5	[                            ---------------      ]	COG4754	Uncharacterized protein
263	TIGR02063	709	50	71.0	8	[                              -------------      ]	RNase_R	ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
264	pfam01498	72	33	70.5	8.2	[                             --------            ]	HTH_Tnp_Tc3_2	Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements.
265	cd00086	59	38	69.7	12	[                          ----------             ]	homeodomain	Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
266	PRK05472	213	40	68.9	7.3	[                            ----------           ]	PRK05472	redox-sensing transcriptional repressor Rex; Provisional
267	pfam12964	96	43	68.8	3.3	[                              -------------      ]	DUF3853	Protein of unknown function (DUF3853). A family of uncharacterized proteins found by clustering human gut metagenomic sequences.
268	pfam12116	82	34	68.5	8	[                            --------             ]	SpoIIID	Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
269	pfam13693	78	32	68.5	6.2	[                             --------            ]	HTH_35	Winged helix-turn-helix DNA-binding.
270	COG0758	350	49	68.5	8.6	[                            ------------         ]	Smf	Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake
271	pfam04760	52	29	68.4	6.1	[                               -------           ]	IF2_N	Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
272	COG1167	459	32	68.0	5.4	[                               --------          ]	ARO8	DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain
273	TIGR02277	280	41	67.8	3.8	[                                ----------       ]	PaaX_trns_reg	phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
274	PRK11013	309	58	67.7	8	[                           ---------------       ]	PRK11013	DNA-binding transcriptional regulator LysR; Provisional
275	pfam04079	158	48	67.7	12	[                              ---------------    ]	DUF387	Putative transcriptional regulators (Ypuh-like). This family of conserved bacterial proteins are thought to possibly be helix-turn-helix type transcriptional regulators.
276	pfam01316	70	44	67.1	12	[                              ------------       ]	Arg_repressor	Arginine repressor, DNA binding domain.
277	TIGR02395	429	36	66.9	4.2	[                               ------------      ]	rpoN_sigma	RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., ). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
278	TIGR02221	218	81	66.8	15	[--------------------                             ]	cas_TM1812	CRISPR-associated protein, TM1812 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1812 of Thermotoga maritima, is found also in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, a large plasmid of Synechocystis sp. PCC 6803, and Fibrobacter succinogenes S85.
279	pfam08535	93	25	66.7	7.1	[                               ------            ]	KorB	KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
280	pfam09397	67	47	66.4	19	[                             -----------         ]	Ftsk_gamma	Ftsk gamma domain. This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
281	PRK09645	173	46	66.1	11	[                           -----------           ]	PRK09645	RNA polymerase sigma factor SigL; Provisional
282	TIGR03418	291	60	66.0	9.4	[                           ----------------      ]	chol_sulf_TF	putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
283	PRK09483	217	58	65.7	7.5	[                          ----------------       ]	PRK09483	response regulator; Provisional
284	COG3311	70	26	65.3	5.5	[                               ------            ]	AlpA	Predicted DNA-binding transcriptional regulator AlpA
285	PRK00135	188	50	65.2	14	[                          -------------          ]	scpB	segregation and condensation protein B; Reviewed
286	COG4344	175	45	65.1	11	[                            -----------          ]	COG4344	Predicted transciptional regulator, contains HTH domain
287	TIGR00538	455	67	65.1	6.8	[                          -----------------      ]	hemN	oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT
288	PRK11512	144	63	65.0	7.9	[                           ---------------       ]	PRK11512	DNA-binding transcriptional repressor MarR; Provisional
289	COG3711	491	36	65.0	15	[                             --------            ]	BglG	Transcriptional antiterminator
290	PRK04140	317	101	64.8	7.7	[        ----------------------------             ]	PRK04140	hypothetical protein; Provisional
291	cd06571	90	29	64.8	8.8	[                              -------            ]	Bac_DnaA_C	C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
292	TIGR02036	302	51	64.7	10	[                              -------------      ]	dsdC	D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
293	pfam04297	101	46	64.6	11	[                          ------------           ]	UPF0122	Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.
294	PRK09726	88	35	64.6	12	[                           ---------             ]	PRK09726	antitoxin HipB; Provisional
295	cd14322	39	22	64.4	4.1	[-----                                            ]	UBA_LATS	UBA domain found in serine/threonine-protein kinase LATS and similar proteins. The LATS proteins family consists of two isoforms, LATS1 and LATS2, both of which are mammalian homologs of the Drosophila tumor suppressor gene lats/warts. LATS1, also called large tumor suppressor homolog 1, or WARTS protein kinase (warts), is a serine/threonine-protein kinase that highly conserved from fly to human. LATS2, also called kinase phosphorylated during mitosis protein, or large tumor suppressor homolog 2, or serine/threonine-protein kinase KPM, or Warts-like kinase, inhibits the G1/S transition and is essential for embryonic development, proliferation control and genomic integrity. LATS proteins contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain.
296	TIGR02404	233	35	63.7	8.7	[                               ---------         ]	trehalos_R_Bsub	trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
297	pfam05158	315	56	63.6	10	[                          --------------         ]	RNA_pol_Rpc34	RNA polymerase Rpc34 subunit. Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment.
298	TIGR00180	187	101	63.5	8.4	[           --------------------------            ]	parB_part	ParB/RepB/Spo0J family partition protein. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
299	PRK10086	311	66	63.0	13	[                           ----------------      ]	PRK10086	DNA-binding transcriptional regulator DsdC; Provisional
300	cd01109	113	32	62.9	7.8	[                               ---------         ]	HTH_YyaN	Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
301	pfam14090	70	52	62.6	16	[                            --------------       ]	HTH_39	Helix-turn-helix domain. This helix-turn-helix domain is often found in phage proteins and is likely to be DNA-binding.
302	PRK10411	240	43	62.4	15	[                            ----------           ]	PRK10411	DNA-binding transcriptional activator FucR; Provisional
303	PRK03911	260	35	61.5	12	[                              ---------          ]	PRK03911	heat-inducible transcription repressor; Provisional
304	pfam05331	114	47	61.1	9	[                           -----------           ]	DUF742	Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
305	TIGR04548	178	51	60.7	15	[                          ------------           ]	DnaD_Mollicutes	DnaD family protein, Mollicutes type. This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis.
306	PRK11139	297	58	60.5	15	[                            ---------------      ]	PRK11139	DNA-binding transcriptional activator GcvA; Provisional
307	TIGR02147	271	49	59.7	15	[                              ------------       ]	Fsuc_second	TIGR02147 family protein. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85 and a smaller number in Bdellovibrio bacteriovorus HD100. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
308	COG1373	398	68	59.5	11	[                            -----------------    ]	COG1373	Predicted ATPase, AAA+ superfamily
309	pfam11427	50	43	59.3	14	[                          -----------            ]	HTH_Tnp_Tc3_1	Tc3 transposase. Tc3 is transposase with a specific DNA-binding domain which contains three alpha-helices, two of which form a helix-turn-helix motif which makes four base-specific contacts with the major groove. The N-terminus makes contacts with the minor groove. There is a base specific recognition between Tc3 and the transposon DNA. The DNA binding domain forms a dimer in which each monomer binds a separate transposon end. This implicates that the dimer has a role in synapsis and is necessary for the simultaneous cleavage of both transposon termini.
310	pfam04645	181	29	59.2	11	[                              -------            ]	DUF603	Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
311	pfam05491	75	54	59.1	25	[                           -------------         ]	RuvB_C	Holliday junction DNA helicase ruvB C-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.
312	PRK10403	215	44	58.9	13	[                          -----------            ]	PRK10403	transcriptional regulator NarP; Provisional
313	TIGR03541	232	44	58.5	15	[                          -----------            ]	reg_near_HchA	LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
314	TIGR01321	94	36	58.5	12	[                            ---------            ]	TrpR	trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
315	pfam07750	162	43	58.0	13	[                           -----------           ]	GcrA	GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
316	PRK10341	312	57	57.6	7.1	[                            ---------------      ]	PRK10341	DNA-binding transcriptional activator TdcA; Provisional
317	PRK12679	316	61	57.4	6	[                            ---------------      ]	cbl	transcriptional regulator Cbl; Reviewed
318	PRK13824	404	24	57.3	7.2	[                                 -----           ]	PRK13824	replication initiation protein RepC; Provisional
319	PRK04158	256	48	56.8	7.6	[                           ------------          ]	PRK04158	transcriptional repressor CodY; Validated
320	pfam06056	58	33	56.8	12	[                              --------           ]	Terminase_5	Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.
321	pfam09756	189	50	56.3	20	[                             --------------      ]	DDRGK	DDRGK domain. This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.
322	pfam09002	379	49	55.9	17	[        ------------                             ]	DUF1887	Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.
323	TIGR02716	306	60	55.8	15	[                            ---------------      ]	C20_methyl_CrtF	C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
324	cd09747	378	54	55.7	35	[        ---------------                          ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as Cas02710 family
325	pfam07381	90	59	55.2	8.3	[                            ---------------      ]	DUF1495	Winged helix DNA-binding domain (DUF1495). This family consists of several hypothetical archaeal proteins of around 110 residues in length. The structure of this domain possesses a winged helix DNA-binding domain suggesting these proteins are bacterial transcription factors.
326	COG1202	830	30	55.1	8.6	[                                   --------      ]	COG1202	Superfamily II helicase, archaea-specific
327	pfam00486	77	44	55.0	33	[                           ----------            ]	Trans_reg_C	Transcriptional regulatory protein, C terminal.
328	pfam00165	42	26	55.0	21	[                              -------            ]	HTH_AraC	Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.
329	TIGR02405	311	22	55.0	9.3	[                               -----             ]	trehalos_R_Ecol	trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
330	cd00383	95	45	54.6	29	[                          -----------            ]	trans_reg_C	Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
331	pfam14277	162	55	54.4	8.4	[                          -----------------      ]	DUF4364	Domain of unknown function (DUF4364). This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 180 amino acids in length.
332	COG2379	422	88	54.4	18	[       ---------------------------------         ]	GckA	Glycerate-2-kinase
333	pfam11994	72	47	54.2	35	[                           -----------           ]	DUF3489	Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
334	PRK05932	455	37	54.2	9	[                               ------------      ]	PRK05932	RNA polymerase factor sigma-54; Reviewed
335	cd09668	214	77	54.1	80	[ -------------------                             ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TM1812 family
336	TIGR02719	138	37	53.2	5.2	[                                 ---------       ]	repress_PhaQ	poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
337	pfam12844	64	29	52.9	20	[                             -------             ]	HTH_19	Helix-turn-helix domain. Members of this family contains a DNA-binding helix-turn-helix domain.
338	pfam05930	51	22	52.6	15	[                               -----             ]	Phage_AlpA	Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the Escherichia coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
339	PRK09480	194	34	52.5	17	[                            ---------            ]	slmA	division inhibitor protein; Provisional
340	TIGR01610	95	49	52.4	26	[                          ------------           ]	phage_O_Nterm	phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
341	COG3423	82	32	52.2	18	[                             --------            ]	SfsB	Predicted transcriptional regulator, lambda repressor-like DNA-binding domain
342	PRK08558	238	31	52.2	15	[                             -------             ]	PRK08558	adenine phosphoribosyltransferase; Provisional
343	TIGR01453	214	23	51.5	12	[                               ------            ]	grpIintron_endo	group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, pfam01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
344	TIGR03339	279	57	51.4	12	[                            ---------------      ]	phn_lysR	aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
345	COG3829	560	45	51.1	16	[                          -----------            ]	RocR	Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding Fis domains
346	cd04772	99	31	50.9	17	[                               ---------         ]	HTH_TioE_rpt1	First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
347	COG2207	127	32	50.5	44	[                              --------           ]	AraC	AraC-type DNA-binding domain and AraC-containing proteins
348	pfam13560	63	28	50.0	30	[                             -------             ]	HTH_31	Helix-turn-helix domain. This domain is a helix-turn-helix domain that probably binds to DNA.
349	TIGR04285	255	87	49.7	28	[           --------------------------            ]	nucleoid_noc	nucleoid occlusion protein. This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete.
350	pfam06970	76	24	49.7	13	[                               ------            ]	RepA_N	Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
351	cd04773	108	26	49.7	17	[                               -------           ]	HTH_TioE_rpt2	Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
352	PRK12682	309	61	49.2	14	[                            ---------------      ]	PRK12682	transcriptional regulator CysB-like protein; Reviewed
353	pfam09821	120	43	49.2	15	[                                -----------      ]	AAA_assoc_C	C-terminal AAA-associated domain. This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family, pfam00005.
354	cd04776	118	44	49.0	3.7	[                               ------------      ]	HTH_GnyR	Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
355	pfam09670	379	106	48.2	54	[         ----------------------------            ]	Cas_Cas02710	CRISPR-associated protein (Cas_Cas02710). Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
356	PRK12684	313	61	48.2	15	[                            ---------------      ]	PRK12684	transcriptional regulator CysB-like protein; Reviewed
357	COG4006	278	119	47.4	1.1E+02	[        --------------------------------         ]	COG4006	CRISPR/Cas system-associated protein Csm6, COG1517 family
358	cd09741	219	42	47.1	48	[           ----------                            ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family
359	pfam09904	90	36	46.9	39	[                              --------           ]	HTH_43	Winged helix-turn helix. This family, found in various hypothetical prokaryotic proteins, is a probable winged helix DNA-binding domain.
360	cd04786	131	31	46.5	19	[                               ---------         ]	HTH_MerR-like_sg7	Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
361	COG1777	217	42	46.2	24	[                           -----------           ]	COG1777	Predicted transcriptional regulator
362	cd03264	211	75	46.1	1E+02	[        ----------------------                   ]	ABC_drug_resistance_like	ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
363	pfam02387	279	33	46.1	4	[                               --------          ]	IncFII_repA	IncFII RepA protein family. This protein is plasmid encoded and found to be essential for plasmid replication.
364	PRK15431	78	37	45.9	41	[                             ---------           ]	PRK15431	ferrous iron transport protein FeoC; Provisional
365	PRK13182	175	23	45.9	21	[                               ------            ]	racA	polar chromosome segregation protein; Reviewed
366	PRK14606	188	40	45.7	16	[                           ----------            ]	ruvA	Holliday junction DNA helicase RuvA; Provisional
367	TIGR01714	119	46	45.6	31	[                               -----------       ]	phage_rep_org_N	phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
368	pfam09455	372	43	45.5	32	[          ----------                             ]	Cas_DxTHG	CRISPR-associated (Cas) DxTHG family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. The family describes Cas proteins of about 400 residues that include the motif
369	PRK12519	194	38	45.5	38	[                           ---------             ]	PRK12519	RNA polymerase sigma factor; Provisional
370	TIGR03020	247	74	45.3	36	[                  -------------------            ]	EpsA	transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
371	pfam09929	118	58	45.2	35	[                           ---------------       ]	DUF2161	Uncharacterized conserved protein (DUF2161). This domain, found in various hypothetical prokaryotic proteins, has no known function.
372	COG2973	103	36	45.2	23	[                            ---------            ]	TrpR	Trp operon repressor
373	PRK00411	394	95	45.1	19	[                ------------------------         ]	cdc6	cell division control protein 6; Reviewed
374	cd01104	68	19	44.1	20	[                               -----             ]	HTH_MlrA-CarA	Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
375	COG1974	201	31	44.1	22	[                               --------          ]	LexA	SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase)
376	TIGR04094	383	44	43.9	20	[                           -----------           ]	adjacent_YSIRK	YSIRK-targeted surface antigen transcriptional regulator. Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.
377	PRK04172	489	68	43.6	44	[                        -----------------        ]	pheS	phenylalanyl-tRNA synthetase subunit alpha; Provisional
378	PRK07408	256	38	43.2	18	[                           ----------            ]	PRK07408	RNA polymerase sigma factor SigF; Reviewed
379	TIGR02846	227	22	43.2	24	[                               -----             ]	spore_sigmaK	RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
380	PRK11920	153	49	43.2	17	[                            ------------         ]	rirA	iron-responsive transcriptional regulator; Reviewed
381	PRK06930	170	27	42.8	35	[                               ------            ]	PRK06930	positive control sigma-like factor; Validated
382	PRK05803	233	22	42.3	24	[                               -----             ]	PRK05803	sporulation sigma factor SigK; Reviewed
383	TIGR02844	80	34	42.1	36	[                            --------             ]	spore_III_D	sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
384	pfam13635	154	69	42.1	29	[                            -----------------    ]	DUF4143	Domain of unknown function (DUF4143). This domain is almost always found C-terminal to an ATPase core family.
385	pfam12793	115	32	41.9	30	[                               --------          ]	SgrR_N	Sugar transport-related sRNA regulator N-term. Small, non-coding RNA molecules play important regulatory roles in a variety of physiological processes in bacteria. SgrR_N is the N-terminus of a family of proteins which regulate the transcription of these sRNAs, in particular SgrS. SgrR_N contains a helix-turn-helix motif characteristic of winged-helix DNA-binding transcriptional regulators. SgrS is a small RNA required for recovery from glucose-phosphate stress in bacteria. In examining the regulation of sgrR expression it was found that SgrR negatively auto-regulates its own transcription in the presence and absence of stress, and thus SgrR coordinates the response to glucose-phosphate stress by binding specifically to sgrS promoter DNA.
386	COG5566	137	25	41.8	26	[                              -------            ]	COG5566	Transcriptional regulator, Middle operon regulator (Mor) family
387	PRK10216	319	45	41.4	34	[                          -----------            ]	PRK10216	DNA-binding transcriptional regulator YidZ; Provisional
388	cd14400	39	14	41.3	18	[                                   ----          ]	UBA_Gts1p_like	UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins. Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture. Gts1p contains an N-terminal zinc finger motif similar to that of GATA-transcription factors, a ubiquitin-associated (UBA) domain and a C-terminal glutamine-rich strand. The zinc finger is responsible for the binding to the glycolytic enzyme glyceraldehydes-3-phosphate dehydrogenase (GAPDH) which is required for the maintenance of the metabolic oscillations of budding yeast. The polyglutamine sequence is indispensable for the pleiotropy and nuclear localization of Gts1p. It is essential for the transcriptional activation, whereas Gts1p lacks DNA binding activity.
389	pfam09623	225	27	41.3	67	[              -------                            ]	Cas_NE0113	CRISPR-associated protein NE0113 (Cas_NE0113). Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.
390	PRK03573	144	48	41.2	28	[                              ------------       ]	PRK03573	transcriptional regulator SlyA; Provisional
391	cd14435	87	40	41.1	52	[                                ----------       ]	SPO1_TF1_like	Bacteriophage SPO1-encoded TF1 binds and bends DNA. This group contains proteins related to bacillus phage SPO1-encoded transcription factor 1 (TF1), a type II DNA-binding protein related to the DNA sequence specific (IHF) and non-specific (HU) domains. Type II DNA-binding proteins bind and bend DNA as dimers. Like IHF, TF1 binds DNA specifically and bends DNA sharply. Bacteriophage SPO1-encoded TF1 recognizes SPO1 phage DNA containing 5-(hydroxymethyl)-2'-deoxyuridine as opposed to thymine, Related family members includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups).
392	PRK10857	164	38	41.0	39	[                              ----------         ]	PRK10857	DNA-binding transcriptional regulator IscR; Provisional
393	pfam13565	77	38	40.7	60	[                           ---------             ]	HTH_32	Homeodomain-like domain.
394	COG1508	444	36	40.6	22	[                               ------------      ]	RpoN	DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog
395	PRK09802	269	45	40.5	26	[                           -----------           ]	PRK09802	DNA-binding transcriptional regulator AgaR; Provisional
396	cd04780	95	25	40.4	29	[                               -------           ]	HTH_MerR-like_sg5	Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
397	PRK12513	194	39	40.2	61	[                           ---------             ]	PRK12513	RNA polymerase sigma factor; Provisional
398	PRK13413	200	44	39.7	47	[                          -----------            ]	mpi	multiple promoter invertase; Provisional
399	pfam02319	67	43	39.1	52	[                            -----------          ]	E2F_TDP	E2F/DP family winged-helix DNA-binding domain. This family contains the transcription factor E2F and its dimerization partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.
400	TIGR04353	73	46	39.0	74	[                           -----------           ]	PqqD_rel_X	PqqD family protein, HPr-rel-A system. Members of this protein show distant homology to PqqD, and belong to a three-gene cassette that included the HPr kinase related protein family of TIGR04352. The role of the cassette, and of this protein, are unknown.
401	cd00591	85	45	38.9	84	[                                -----------      ]	HU_IHF	DNA sequence specific (IHF) and non-specific (HU) domains. This family includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). Bacillus phage SPO1-encoded transcription factor 1 (TF1) is another related type II DNA-binding protein. Like IHF, TF1 binds DNA specifically and bends DNA sharply.
402	PRK11202	203	37	38.8	24	[                               ---------         ]	PRK11202	DNA-binding transcriptional repressor FabR; Provisional
403	cd04770	123	31	38.7	26	[                               ---------         ]	HTH_HMRTR	Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
404	PRK12683	309	61	38.7	20	[                            ---------------      ]	PRK12683	transcriptional regulator CysB-like protein; Reviewed
405	COG3093	104	38	37.3	51	[                           ---------             ]	VapI	Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain
406	pfam04539	78	27	37.1	65	[                              -------            ]	Sigma70_r3	Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
407	cd08780	90	18	36.9	28	[                                  -----          ]	Death_TRADD	Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
408	cd01108	127	30	36.8	34	[                               ---------         ]	HTH_CueR	Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
409	TIGR02018	230	42	36.4	26	[                             ----------          ]	his_ut_repres	histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
410	COG1961	222	48	36.3	61	[                           -----------           ]	PinE	Site-specific DNA recombinase related to the DNA invertase Pin
411	TIGR02531	87	34	36.2	69	[                            ---------            ]	yecD_yerC	TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
412	PRK03975	141	38	35.8	50	[                          ----------             ]	tfx	putative transcriptional regulator; Provisional
413	PRK09464	254	28	35.7	30	[                                -------          ]	pdhR	transcriptional regulator PdhR; Reviewed
414	PRK10163	271	52	35.6	72	[                            ---------------      ]	PRK10163	DNA-binding transcriptional repressor AllR; Provisional
415	cd01105	88	27	35.6	42	[                               --------          ]	HTH_GlnR-like	Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
416	pfam09114	96	63	35.4	33	[                           ----------------      ]	MotA_activ	Transcription factor MotA, activation domain. Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2.
417	pfam05584	72	34	35.3	33	[                              ---------          ]	Sulfolobus_pRN	Sulfolobus plasmid regulatory protein. This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
418	PRK11716	269	38	35.3	27	[                                  ---------      ]	PRK11716	DNA-binding transcriptional regulator IlvY; Provisional
419	pfam05595	91	29	34.9	81	[                              -------            ]	DUF771	Domain of unknown function (DUF771). Family of uncharacterized ORFs found in Bacteriophage and Lactococcus lactis.
420	PRK05456	172	47	34.8	43	[                               -------------     ]	PRK05456	ATP-dependent protease subunit HslV; Provisional
421	COG4496	100	35	34.4	53	[                            ---------            ]	YerC	Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain
422	TIGR02619	149	68	34.1	1E+02	[        -----------------                        ]	TIGR02619	putative CRISPR-associated protein, APE2256 family. This model represents a conserved domain of about 150 amino acids found in at least five archaeal species and three bacterial species, exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In six of eight species, the member of this family is in the vicinity of a CRISPR/Cas locus.
423	PRK04841	903	68	33.9	42	[                     -----------------           ]	PRK04841	transcriptional regulator MalT; Provisional
424	PRK04338	382	32	33.8	51	[                               -------           ]	PRK04338	N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
425	COG3132	215	38	33.4	31	[                                 ----------      ]	YceH	Uncharacterized conserved protein YceH, UPF0502 family
426	TIGR02989	159	44	32.8	1.1E+02	[                           ----------            ]	Sig-70_gvs1	RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
427	TIGR02959	170	46	32.5	56	[                          -----------            ]	SigZ	RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
428	cd09694	181	72	32.5	99	[        ------------------                       ]	Csm6_III-A	CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems
429	pfam07106	169	50	32.5	1.1E+02	[                             --------------      ]	TBPIP	Tat binding protein 1(TBP-1)-interacting protein (TBPIP). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation.
430	COG3811	85	28	32.3	23	[                                    -------      ]	YjhX	Uncharacterized protein YjhX, UPF0386/DUF2084 family
431	PRK13980	265	37	32.1	86	[                             ---------           ]	PRK13980	NAD synthetase; Provisional
432	TIGR00308	374	41	32.1	37	[                            ----------           ]	TRM1	tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
433	pfam04337	148	23	31.8	45	[                                 ------          ]	DUF480	Protein of unknown function, DUF480. This family consists of several proteins of uncharacterized function.
434	PRK13239	206	36	31.8	98	[                            ---------            ]	PRK13239	alkylmercury lyase; Provisional
435	cd01913	171	47	31.8	43	[                               -------------     ]	protease_HslV	Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases. HslV has a nucleophilic threonine residue at its N-terminus that is exposed after processing of the propeptide and is directly involved in active site catalysis.
436	pfam12836	65	33	31.5	67	[                              --------           ]	HHH_3	Helix-hairpin-helix motif. The HhH domain is a short DNA-binding domain.
437	PRK10225	257	41	31.4	56	[                                ----------       ]	PRK10225	DNA-binding transcriptional repressor UxuR; Provisional
438	pfam00216	90	44	31.4	1.5E+02	[                                -----------      ]	Bac_DNA_binding	Bacterial DNA-binding protein.
439	PRK09391	230	30	31.3	37	[                               -------           ]	fixK	transcriptional regulator FixK; Provisional
440	cd04766	91	35	30.8	1.3E+02	[                          ----------             ]	HTH_HspR	Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
441	pfam08765	107	38	30.7	74	[                            ---------            ]	Mor	Mor transcription activator family. Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N terminal region of Mor is the dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA.
442	TIGR03692	171	47	30.6	53	[                               -------------     ]	ATP_dep_HslV	ATP-dependent protease HslVU, peptidase subunit. The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease.
443	pfam05344	65	35	30.6	84	[                             --------            ]	DUF746	Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons. Structural modelling suggests this domain may bind nucleic acids.
444	pfam09382	92	36	30.5	41	[                                  ---------      ]	RQC	RQC domain. This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain.
445	PRK11074	300	60	30.5	43	[                           ----------------      ]	PRK11074	putative DNA-binding transcriptional regulator; Provisional
446	TIGR02647	77	53	30.5	67	[                            --------------       ]	DNA	TIGR02647 family protein. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
447	pfam09079	85	31	30.3	77	[                                -------          ]	Cdc6_C	CDC6, C terminal. The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.
448	cd14315	43	19	30.2	27	[----                                             ]	UBA1_UBAP1	UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1). UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). Moreover, UBAP-1, together with VPS37A, forms an endosome-specific endosomal sorting complexes I required for transport (ESCRT-I) complex that displays a restricted cellular function, ubiquitin-dependent endosomal sorting and multivesicular body (MVB) biogenesis. UBAP-1 contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and two tandem ubiquitin-associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This model corresponds to UBA1 domain.
449	pfam06163	127	54	30.2	1.7E+02	[                          --------------         ]	DUF977	Bacterial protein of unknown function (DUF977). This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. The function of this family is unknown.
450	PRK10100	216	44	30.1	61	[                          -----------            ]	PRK10100	DNA-binding transcriptional regulator CsgD; Provisional
451	COG2996	287	52	30.0	1.3E+02	[                          -------------          ]	CvfB	Predicted RNA-binding protein, contains S1 domains, virulence factor B family
452	TIGR01111	238	54	29.8	1.1E+02	[  --------------                                 ]	mtrA	N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit A. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase.
453	TIGR03433	100	58	29.7	66	[                            --------------       ]	padR_acidobact	transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
454	COG1386	184	39	29.7	1.4E+02	[                            ---------            ]	ScpB	Chromosome segregation and condensation protein ScpB
455	pfam13022	139	35	29.4	69	[                            --------             ]	HTH_Tnp_1_2	Helix-turn-helix of insertion element transposase. This is a family of largely phage proteins which are likely to be a helix-turn-helix insertion elements.
456	pfam05155	92	19	29.4	46	[                                  ----           ]	Phage_X	Phage X family. This family is the product of Gene X. The function of this protein is unknown.
457	PRK08295	208	44	29.3	69	[                          -----------            ]	PRK08295	RNA polymerase factor sigma-70; Validated
458	TIGR00721	137	37	29.2	93	[                          ----------             ]	tfx	DNA-binding protein, Tfx family. PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
459	cd09660	394	51	28.8	1.5E+02	[          -------------                          ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as MJ1666 family
460	cd13831	86	52	28.8	1.8E+02	[                                --------------   ]	HU	histone-like DNA-binding protein HU. This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). In E. coli, HU binds uniformly to the chromosome, with a preference for damaged or distorted DNA structures and can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Anabaena HU (AHU) shows preference for A/T-rich region in the center of its DNA binding site.
461	COG4861	345	57	28.7	93	[                          --------------         ]	COG4861	Uncharacterized protein
462	cd05644	415	46	28.6	1.3E+02	[                           -----------           ]	M28_like_3	M28 Zn-Peptidases. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They typically have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. Proteins in this subfamily conserve some of the metal-coordinating residues of the typically co-catalytic M28 family, and appear to bind a single metal (Zn) ion.
463	pfam02005	375	40	28.5	55	[                            ----------           ]	TRM	N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
464	COG4800	170	36	28.4	1E+02	[                           ---------             ]	COG4800	Predicted transcriptional regulator with an HTH domain
465	TIGR04381	49	34	28.3	1.6E+02	[                            ---------            ]	HTH_TypR	TyrR family helix-turn-helix domain. This model describes the C-terminal DNA-binding helix-turn-helix domain of several regulators of aromatic amino acid metabolism. Examples include TyrR in Escherichia coli and PhhR in Pseudomonas putida. Most members of this family have a sigma-54 interaction domain.
466	pfam01710	120	39	28.3	81	[                            ----------           ]	HTH_Tnp_IS630	Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
467	COG2150	167	49	28.2	60	[                            ------------         ]	COG2150	Predicted regulator of amino acid metabolism, contains ACT domain
468	PRK09638	176	23	28.2	44	[                               -----             ]	PRK09638	RNA polymerase sigma factor SigY; Reviewed
469	pfam01399	105	33	28.1	88	[                              --------           ]	PCI	PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
470	cd04331	80	67	27.9	1.2E+02	[                       ----------------------    ]	RNAP_E_N	RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
471	PRK10360	196	44	27.9	42	[                          -----------            ]	PRK10360	DNA-binding transcriptional activator UhpA; Provisional
472	PRK03837	241	54	27.6	1.2E+02	[                          --------------         ]	PRK03837	transcriptional regulator NanR; Provisional
473	cd14270	30	15	27.5	36	[---                                              ]	UBA	UBA domain found in proteins involved in ubiquitin-mediated proteolysis. The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains.
474	PRK09637	181	53	27.4	1.2E+02	[                        -------------            ]	PRK09637	RNA polymerase sigma factor SigZ; Provisional
475	cd13832	85	45	27.3	2.2E+02	[                                -----------      ]	IHF	Integration host factor (IHF) and similar proteins. This subfamily includes integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. This subfamily also includes the protein Hbb from tick-borne spirochete Borrelia burgdorferi, responsible for causing Lyme disease in humans. Hbb, a homodimer, shows DNA sequence preferences that are related, yet distinct from those of IHF.
476	PRK00973	446	78	27.3	1.4E+02	[ -------------------                             ]	PRK00973	glucose-6-phosphate isomerase; Provisional
477	pfam06322	64	26	27.3	33	[                                ------           ]	Phage_NinH	Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
478	COG4519	95	33	27.3	68	[                              --------           ]	COG4519	Uncharacterized protein
479	PRK09616	552	137	27.1	57	[---------------------------------------          ]	pheT	phenylalanyl-tRNA synthetase subunit beta; Reviewed
480	PRK11922	231	24	27.0	89	[                               ------            ]	PRK11922	RNA polymerase sigma factor; Provisional
481	PRK10339	327	22	27.0	38	[                               -----             ]	PRK10339	DNA-binding transcriptional repressor EbgR; Provisional
482	COG3655	73	25	26.9	59	[                              ------             ]	YozG	DNA-binding transcriptional regulator, XRE family
483	COG2909	894	41	26.8	71	[                           ----------            ]	MalT	ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT
484	cd03758	193	36	26.6	59	[        ---------                                ]	proteasome_beta_type_2	proteasome beta type-2 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
485	COG3677	129	39	26.3	90	[                            ---------            ]	InsA	Transposase
486	pfam14337	183	50	26.2	82	[                          -------------          ]	DUF4393	Domain of unknown function (DUF4393). This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 254 and 285 amino acids in length.
487	cd14397	41	12	26.2	41	[---                                              ]	UBA_LATS1	UBA domain found in vertebrate serine/threonine-protein kinase LATS1. LATS1, also called large tumor suppressor homolog 1 or WARTS protein kinase (warts), is a serine/threonine-protein kinase that highly conserved from fly to human. It plays a crucial role in the prevention of tumor formation by controlling mitosis progression. Human LATS1 is the mammalian homologs of Drosophila lats/warts gene that could suppress tumor growth and rescue all developmental defects in flies, including embryonic lethality. It forms a regulatory complex with zyxin, a regulator of actin filament assembly. The LATS1/zyxin complex plays a role in controlling mitosis progression on mitotic apparatus. LATS1 is phosphorylated in a cell-cycle-dependent manner and complexes with CDC2 in early mitosis. It can negatively modulates tumor cell growth by inducing G(2)/M cell cycle transition or apoptosis. It also functions as a mitotic exit network kinase interacting with MOB1A, a protein whose homolog in budding yeast associates with kinases involved in mitotic exit. Moreover, LATS1 acts as a novel cytoskeleton regulator that affects cytokinesis by regulating actin polymerization through inhibiting LIMK1. LATS1 can also inhibit transcription regulation and transformation functions of oncogene YAP by inhibiting its nuclear translocation through phosphorylation. In addition, LATS1 can regulate the transcriptional activity of forkhead L2 (FOXL2) via phosphorylation. It also acts as an acting-binding protein that can negatively regulate the actin polymerization. LATS1 contains an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain.
488	pfam09824	160	58	25.9	1.4E+02	[              --------------------               ]	ArsR	ArsR transcriptional regulator. Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
489	cd04774	96	27	25.5	77	[                               --------          ]	HTH_YfmP	Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
490	COG1766	545	84	25.4	73	[                 ------------------------        ]	FliF	Flagellar biosynthesis/type III secretory pathway M-ring protein FliF/YscJ
491	pfam10141	195	61	25.3	59	[                         ---------------         ]	ssDNA-exonuc_C	Single-strand DNA-specific exonuclease, C terminal domain. Members of this set of prokaryotic domains are found in a set of single-strand DNA-specific exonucleases, including RecJ. Their exact function has not, as yet, been determined.
492	PRK06840	339	31	25.2	55	[                              ---------          ]	PRK06840	hypothetical protein; Validated
493	COG0856	203	28	25.1	52	[                              -------            ]	PyrE2	Orotate phosphoribosyltransferase homolog
494	COG5405	178	46	25.0	71	[                               -------------     ]	HslV	ATP-dependent protease HslVU (ClpYQ), peptidase subunit
495	COG1481	308	45	24.5	1.8E+02	[                           -----------           ]	WhiA	DNA-binding transcriptional regulator WhiA, involved in cell division
496	PRK08599	377	49	24.5	1.4E+02	[                              -------------      ]	PRK08599	coproporphyrinogen III oxidase; Provisional
497	COG1438	150	47	24.2	1.5E+02	[                            -------------        ]	ArgR	Arginine repressor
498	COG2042	179	28	24.0	47	[                                    -------      ]	Tsr3	Ribosome biogenesis protein Tsr3 (rRNA maturation)
499	cd14341	52	21	24.0	99	[                                -----            ]	UBA_MELK	UBA domain found in maternal embryonic leucine zipper kinase (MELK) and similar proteins. MELK, also called protein kinase Eg3 (pEg3 kinase), protein kinase PK38 (PK38), or tyrosine-protein kinase MELK, is a cell cycle dependent protein kinase involved in diverse cell processes including stem cell renewal, cell cycle progression, cell proliferation, apoptosis and mRNA processing. It is expressed in normal tissues and especially in cancer cells. It is upregulated in cancer tissues and thus may act as potential anticancer target in diverse tumor entities. MELK comprises an N-terminal protein kinase catalytic domain, followed by an ubiquitin-associated (UBA) domain, and a C-terminal autoinhibitory domain of 5'-AMP-activated protein kinase (AMPK).
500	pfam13413	62	25	23.7	1.2E+02	[                              -------            ]	HTH_25	Helix-turn-helix domain. This domain is a helix-turn-helix domain that probably binds to DNA.