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. |