match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam09670	379	109	98.9	3.6E-09	[                   --------------------------    ]	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).
2	cd09747	378	107	98.7	3.4E-08	[                   --------------------------    ]	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
3	TIGR02710	380	116	98.7	7.3E-08	[                   ----------------------------  ]	TIGR02710	CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
4	cd09702	378	119	98.5	3.1E-07	[                   ----------------------------- ]	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 TIGR02710 family
5	pfam09651	136	53	94.6	0.16	[                                 -----------     ]	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.
6	pfam09002	379	111	87.8	1.1	[                     --------------------------- ]	DUF1887	Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.
7	pfam09455	372	103	87.7	2.1	[                   ------------------------      ]	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
8	cd09741	219	116	87.3	5.4	[                    ------------------------     ]	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
9	cd09742	183	102	83.0	3.7	[                     -----------------------     ]	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
10	pfam09623	225	62	82.2	19	[                                ------------     ]	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.
11	TIGR03642	124	94	80.7	11	[                     ---------------------       ]	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.
12	TIGR01884	203	104	80.6	6.4	[                   ------------------------      ]	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.
13	cd09723	132	94	80.0	9	[                     ---------------------       ]	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
14	cd09655	198	102	76.8	9.1	[                   ------------------------      ]	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
15	pfam01034	64	25	74.1	3.5	[          ------                                 ]	Syndecan	Syndecan domain. Syndecans are transmembrane heparin sulfate proteoglycans which are implicated in the binding of extracellular matrix components and growth factors.
16	COG4006	278	55	56.7	26	[                                 -----------     ]	COG4006	CRISPR/Cas system-associated protein Csm6, COG1517 family
17	PRK14477	917	82	53.5	14	[                     ---------------------       ]	PRK14477	bifunctional nitrogenase molybdenum-cofactor biosynthesis protein NifE/NifN; Provisional
18	pfam03853	164	29	53.4	19	[                    -----                        ]	YjeF_N	YjeF-related protein N-terminus. YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions.
19	cd08196	346	80	49.7	33	[                                -----------------]	DHQS-like1	Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. The activity of DHQS requires NAD as cofactor. Proteins of this family share sequence similarity and functional motifs with that of dehydroquinate synthase, but the specific function has not been characterized.
20	COG2949	235	24	49.3	1.4E+02	[                                   -----         ]	SanA	Uncharacterized periplasmic protein SanA, affects membrane permeability for vancomycin
21	PRK07535	261	87	49.0	20	[                   --------------------          ]	PRK07535	methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated
22	TIGR01138	290	71	47.7	30	[                              ---------------    ]	cysM	cysteine synthase B. CysM differs from CysK in that it can also use thiosulfate instead of sulfide, to produce cysteine thiosulfonate instead of cysteine. Alternate name: O-acetylserine (thiol)-lyase
23	pfam04392	292	54	47.3	27	[              -------------                      ]	ABC_sub_bind	ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
24	pfam01118	121	80	43.7	45	[                    --------------------         ]	Semialdhyde_dh	Semialdehyde dehydrogenase, NAD binding domain. This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase
25	cd09732	221	93	42.5	77	[                   -----------------------       ]	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
26	cd06325	281	65	42.5	41	[                   ----------------              ]	PBP1_ABC_uncharacterized_transporter	Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
27	COG3125	111	43	41.8	54	[     ---------                                   ]	CyoD	Heme/copper-type cytochrome/quinol oxidase, subunit 4
28	cd12432	90	47	41.2	26	[                      -------------              ]	RRM_ACINU	RNA recognition motif in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins. This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity.
29	TIGR01478	295	20	41.1	28	[           ----                                  ]	STEVOR	variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
30	TIGR01136	299	49	41.0	52	[                                   ----------    ]	cysKM	cysteine synthase. This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff.
31	cd00423	258	35	40.9	35	[                                -------          ]	Pterin_binding	Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH.
32	pfam06956	183	79	40.0	1E+02	[                                -----------------]	RtcR	Regulator of RNA terminal phosphate cyclase. RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain pfam00158 in the central region of the protein sequence.
33	COG1647	243	66	38.1	41	[                            ----------------     ]	YvaK	Esterase/lipase
34	COG0478	304	49	37.3	68	[                              ---------          ]	RIO2	RIO-like serine/threonine protein kinase fused to N-terminal HTH domain
35	PRK10582	109	44	36.8	72	[     ---------                                   ]	PRK10582	cytochrome o ubiquinol oxidase subunit IV; Provisional
36	cd12094	44	24	35.6	48	[         -----                                   ]	TM_ErbB2	Transmembrane domain of ErbB2, a Protein Tyrosine Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. ErbB2 (HER2, HER2/neu) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. It is activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. ErbB2 does not bind to any known EGFR subfamily ligands, but contributes to the kinase activity of all possible heterodimers. It acts as the preferred partner of other ligand-bound EGFR proteins and functions as a signal amplifier, with the ErbB2-ErbB3 heterodimer being the most potent pair in mitogenic signaling. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of ErbB2 have been associated with increased breast cancer risk. ErbB2 plays an important role in cell development, proliferation, survival and motility. Overexpression of ErbB2 results in its activation and downstream signaling, even in the absence of ligand. ErbB2 overexpression, mainly due to gene amplification, has been shown in a variety of human cancers. Its role in breast cancer is especially well-documented. ErbB2 is up-regulated in about 25% of breast tumors and is associated with increases in tumor aggressiveness, recurrence and mortality. ErbB2 is a target for monoclonal antibodies and small molecule inhibitors, which are being developed as treatments for cancer. The first humanized antibody approved for clinical use is Trastuzumab (Herceptin), which is being used in combination with other therapies to improve the survival rates of patients with HER2-overexpressing breast cancer.
37	PRK06463	255	82	35.3	34	[                     ------------------          ]	fabG	3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
38	PRK00587	99	38	33.9	25	[                               -------           ]	PRK00587	hypothetical protein; Provisional
39	TIGR02705	156	40	33.0	42	[                     ----------                  ]	nudix_YtkD	nucleoside triphosphatase YtkD. The functional assignment to the proteins of this family is contentious, with papers disagreeing in both interpretation and enzyme assay results. This protein belongs to the nudix family and shares some sequence identity with E. coli MutT but appears not to be functionally interchangeable with it.
40	PRK00153	104	43	33.0	57	[                            --------             ]	PRK00153	hypothetical protein; Validated
41	pfam04392	292	48	31.0	1E+02	[                                 ----------      ]	ABC_sub_bind	ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
42	cd01561	291	55	31.0	1E+02	[                                  -----------    ]	CBS_like	CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine.
43	pfam13170	297	29	30.5	45	[                                ------           ]	DUF4003	Protein of unknown function (DUF4003). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 345 amino acids in length.
44	cd09723	132	40	30.4	78	[                                  --------       ]	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
45	pfam00510	258	70	30.2	1E+02	[     --------------                              ]	COX3	Cytochrome c oxidase subunit III.
46	PRK13299	394	60	29.7	22	[                            ------------         ]	PRK13299	tRNA CCA-pyrophosphorylase; Provisional
47	TIGR03010	116	40	29.7	28	[                              ---------          ]	sulf_tusC_dsrF	sulfur relay protein TusC/DsrF. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate.
48	PRK09004	146	65	29.2	45	[                     ----------------            ]	PRK09004	FMN-binding protein MioC; Provisional
49	cd09694	181	66	28.5	1.6E+02	[                              --------------     ]	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
50	pfam03988	55	37	27.6	1.3E+02	[      --------                                   ]	DUF347	Repeat of Unknown Function (DUF347). This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.
51	pfam02575	93	36	27.4	71	[                             -------             ]	YbaB_DNA_bd	YbaB/EbfC DNA-binding family. This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage.
52	TIGR00239	929	34	27.3	68	[                                -------          ]	2oxo_dh_E1	2-oxoglutarate dehydrogenase, E1 component. The 2-oxoglutarate dehydrogenase complex consists of this thiamine pyrophosphate-binding subunit (E1), dihydrolipoamide succinyltransferase (E2), and lipoamide dehydrogenase (E3). The E1 ortholog from Corynebacterium glutamicum is unusual in having an N-terminal extension that resembles the dihydrolipoamide succinyltransferase (E2) component of 2-oxoglutarate dehydrogenase.
53	pfam07095	705	90	27.1	62	[                   -------------------           ]	IgaA	Intracellular growth attenuator protein IgaA. This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the Escherichia coli YrfF and P. mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in S. enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria.
54	cd05144	183	47	27.0	1.4E+02	[                              ---------          ]	RIO2_C	C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase. RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO2 kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K).
55	pfam10073	74	23	25.9	65	[                                 ----            ]	DUF2312	Uncharacterized protein conserved in bacteria (DUF2312). Members of this family of hypothetical bacterial proteins have no known function. Structural modelling suggests this domain may bind nucleic acids.
56	cd10282	256	82	25.9	1.9E+02	[                     -----------------           ]	DNase1	Deoxyribonuclease 1. Deoxyribonuclease 1 (DNase1, EC 3.1.21.1), also known as DNase I, is a Ca2+, Mg2+/Mn2+-dependent secretory endonuclease, first isolated from bovine pancreas extracts. It cleaves DNA preferentially at phosphodiester linkages next to a pyrimidine nucleotide, producing 5'-phosphate terminated polynucleotides with a free hydroxyl group on position 3'. It generally produces tetranucleotides. DNase1 substrates include single-stranded DNA, double-stranded DNA, and chromatin. This enzyme may be responsible for apoptotic DNA fragmentation. Other deoxyribonucleases in this subfamily include human DNL1L (human DNase I lysosomal-like, also known as DNASE1L1, Xib, and DNase X ), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3 (also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and DNase gamma) . DNASE1L3 is implicated in apoptotic DNA fragmentation. DNase I is also a cytoskeletal protein which binds actin. A recombinant form of human DNase1 is used as a mucoactive therapy in patients with cystic fibrosis; it hydrolyzes the extracellular DNA in sputum and reduces its viscosity. Mutations in the gene encoding DNase1 have been associated with Systemic Lupus Erythematosus, a multifactorial autoimmune disease. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.
57	cd13993	267	92	25.7	41	[                            ------------------   ]	STKc_Pat1_like	Catalytic domain of Fungal Pat1-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Schizosaccharomyces pombe Pat1 (also called Ran1), Saccharomyces cerevisiae VHS1 and KSP1, and similar fungal STKs. Pat1 blocks Mei2, an RNA-binding protein which is indispensable in the initiation of meiosis. Pat1 is inactivated and Mei2 activated, which initiates meiosis, under nutrient-deprived conditions through a signaling cascade involving Ste11. Meiosis induced by Pat1 inactivation may show different characteristics than normal meiosis including aberrant positioning of centromeres. VHS1 was identified in a screen for suppressors of cell cycle arrest at the G1/S transition, while KSP1 may be involved in regulating PRP20, which is required for mRNA export and maintenance of nuclear structure. The Pat1-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
58	pfam01580	201	30	25.6	2E+02	[                               -----             ]	FtsK_SpoIIIE	FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from Escherichia coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
59	cd14202	267	47	25.5	76	[                               ---------         ]	STKc_ULK1	Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK1 is required for efficient amino acid starvation-induced autophagy and mitochondrial clearance. It associates with three autophagy-related proteins (Atg13, FIP200 amd Atg101) to form the ULK1 complex. All fours proteins are essential for autophagosome formation. ULK1 is regulated by both mammalian target-of rapamycin complex 1 (mTORC1) and AMP-activated protein kinase (AMPK). mTORC1 negatively regulates the ULK1 complex in a nutrient-dependent manner while AMPK stimulates autophagy by inhibiting mTORC1. ULK1 also plays neuron-specific roles and is involved in non-clathrin-coated endocytosis in growth cones, filopodia extension, neurite extension, and axon branching. The ULK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
60	pfam01102	120	15	25.1	1.1E+02	[           ---                                   ]	Glycophorin_A	Glycophorin A.
61	pfam10911	77	29	24.9	37	[                                ------           ]	DUF2717	Protein of unknown function (DUF2717). Members in this family of proteins are annotated as gene 6.5 protein however currently there is no known function.
62	pfam08869	110	20	24.9	64	[                                   ---           ]	XisI	XisI protein. The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required.
63	COG0031	300	73	24.7	1.6E+02	[                              ---------------    ]	CysK	Cysteine synthase
64	PRK09579	1017	54	24.3	2.2E+02	[                                -----------      ]	PRK09579	multidrug efflux protein; Reviewed
65	TIGR03595	69	31	24.1	99	[                                ------           ]	Obg_CgtA_exten	Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
66	cd07225	306	30	23.7	29	[                                     -------     ]	Pat_PNPLA6_PNPLA7	Patatin-like phospholipase domain containing protein 6 and protein 7. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are 60% identical to each other. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologous to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE hydrolyzes sn-1 esters in lysophosphatidylcholine and lysophosphatidic acid, but shows no lipase activity with substrates like triacylglycerols (TG), cholesteryl esters, retinyl esters (RE), phosphatidylcholine (PC), or monoacylglycerol (MG). This family includes PNPLA6 and PNPLA7 from Homo sapiens, YMF9 from Yeast, and Swiss Cheese protein (sws) from Drosophila melanogaster.
67	COG0718	105	43	23.7	1E+02	[                            --------             ]	YbaB	Conserved DNA-binding protein YbaB (function unknown)
68	PRK09404	924	41	23.7	86	[                            -----------          ]	sucA	2-oxoglutarate dehydrogenase E1 component; Reviewed
69	TIGR02213	411	62	23.5	82	[  --------------                                 ]	lolE_release	lipoprotein releasing system, transmembrane protein LolE. This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in E. coli and related species.
70	cd09746	382	60	23.3	1.6E+02	[                              ------------       ]	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
71	cd10959	187	42	23.2	1.2E+02	[                            ---------            ]	CE4_NodB_like_3	Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases. This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily.
72	pfam00743	532	68	23.1	51	[                        ------------------       ]	FMO-like	Flavin-binding monooxygenase-like. This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases.
73	cd01968	410	86	22.9	77	[                    ----------------------       ]	Nitrogenase_NifE_I	Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
74	cd02016	265	33	22.7	98	[                                -------          ]	TPP_E1_OGDC_like	Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle.
75	COG5336	116	32	22.6	1.3E+02	[--------                                         ]	AtpI2	FoF1-type ATP synthase assembly protein I
76	TIGR03642	124	40	22.6	1.3E+02	[                                  --------       ]	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.
77	PRK00002	358	54	22.5	1.6E+02	[                                 -----------     ]	aroB	3-dehydroquinate synthase; Reviewed
78	PRK11146	412	62	22.5	93	[  --------------                                 ]	PRK11146	outer membrane-specific lipoprotein transporter subunit LolE; Provisional
79	pfam09269	69	31	22.4	1E+02	[                                ------           ]	DUF1967	Domain of unknown function (DUF1967). Members of this family contain a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. They are predominantly found in the bacterial GTP-binding protein Obg, and are still functionally uncharacterized.
80	pfam04156	186	17	22.3	2.8E+02	[           ---                                   ]	IncA	IncA protein. Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA.
81	PRK11199	374	83	21.8	94	[                     ---------------------       ]	tyrA	bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
82	cd08268	328	86	21.8	1.5E+02	[                        --------------------     ]	MDR2	Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines.
83	pfam07245	504	39	21.7	98	[      --------                                   ]	Phlebovirus_G2	Phlebovirus glycoprotein G2. This family consists of several Phlebovirus glycoprotein G2 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi.
84	TIGR01139	298	48	21.7	1.6E+02	[                                   ----------    ]	cysK	cysteine synthase A. This model distinguishes cysteine synthase A (CysK) from cysteine synthase B (CysM). CysM differs in having a broader specificity that also allows the use of thiosulfate to produce cysteine thiosulfonate.
85	pfam13245	72	36	21.7	1E+02	[                                     -------     ]	AAA_19	Part of AAA domain.
86	PRK09546	324	40	21.6	1.2E+02	[     ---------                                   ]	zntB	zinc transporter; Reviewed
87	COG2411	188	94	21.1	80	[                ---------------------            ]	COG2411	Uncharacterized protein
88	pfam05589	64	27	21.0	77	[                                 -----           ]	DUF768	Protein of unknown function (DUF768). This family consists of several uncharacterized hypothetical proteins from Rhizobium loti.
89	PRK10834	239	35	20.5	69	[                                --------         ]	PRK10834	vancomycin high temperature exclusion protein; Provisional
90	COG3518	157	43	20.2	1E+02	[                --------                         ]	COG3518	Predicted component of the type VI protein secretion system
91	cd09728	400	77	20.1	2.6E+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 DxTHG family
92	pfam02705	534	88	20.1	2.9E+02	[    -------------------                          ]	K_trans	K+ potassium transporter. This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members.