match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG4951	361	198	99.8	3.4E-19	[ -------------------- ]	COG4951	Uncharacterized protein
2	pfam01896	131	101	98.2	2.6E-06	[ --------- ]	DNA_primase_S	Eukaryotic and archaeal DNA primase small subunit. DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. Bacterial DNA primase adopts a different fold to archaeal and eukaryotic primases.
3	pfam13414	69	64	97.9	8.6E-05	[ ----- ]	TPR_11	TPR repeat.
4	pfam14559	68	60	97.6	9.7E-05	[ ----- ]	TPR_19	Tetratricopeptide repeat.
5	pfam13432	65	56	97.5	0.00056	[ ---- ]	TPR_16	Tetratricopeptide repeat.
6	pfam13424	78	63	96.9	0.0041	[ ------ ]	TPR_12	Tetratricopeptide repeat.
7	cd00525	136	109	96.3	0.039	[ -------------- ]	AE_Prim_S_like	AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro.
8	pfam13431	34	33	96.2	0.0044	[ --- ]	TPR_17	Tetratricopeptide repeat.
9	pfam13428	44	41	95.8	0.023	[ --- ]	TPR_14	Tetratricopeptide repeat.
10	pfam07719	34	34	94.8	0.042	[ --- ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
11	TIGR02521	234	91	94.8	0.21	[-------- ]	type_IV_pilW	type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF and PilW. This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
12	cd04860	232	150	94.2	0.087	[ -------------- ]	AE_Prim_S	AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41.
13	TIGR02521	234	65	93.8	0.13	[ ------ ]	type_IV_pilW	type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF and PilW. This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
14	pfam13181	34	32	93.7	0.099	[ -- ]	TPR_8	Tetratricopeptide repeat.
15	COG3063	250	87	93.5	0.29	[-------- ]	PilF	Tfp pilus assembly protein PilF
16	pfam00515	34	33	93.2	0.13	[ --- ]	TPR_1	Tetratricopeptide repeat.
17	TIGR02917	899	109	93.1	0.82	[--------- ]	PEP_TPR_lipo	putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
18	pfam13371	73	58	92.7	0.34	[ ----- ]	TPR_9	Tetratricopeptide repeat.
19	pfam13429	279	84	92.0	1	[-------- ]	TPR_15	Tetratricopeptide repeat.
20	TIGR02778	245	105	91.9	0.46	[ ----------- ]	ligD_pol	DNA ligase D, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
21	PRK11788	389	67	91.8	0.26	[ ------ ]	PRK11788	tetratricopeptide repeat protein; Provisional
22	pfam13428	44	37	90.9	0.38	[ --- ]	TPR_14	Tetratricopeptide repeat.
23	COG3063	250	64	89.9	0.66	[ ------ ]	PilF	Tfp pilus assembly protein PilF
24	cd04861	227	110	89.7	0.75	[ ----------- ]	LigD_Pol_like	LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.
25	COG2956	389	51	88.7	1.7	[ ---- ]	YciM	Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain
26	COG4235	287	77	87.5	1.1	[ -------- ]	NrfG	Cytochrome c-type biogenesis protein CcmH/NrfG
27	TIGR03939	800	104	86.3	2	[ --------- ]	PGA_TPR_OMP	poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA. Members of this protein family are the poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin PgaA of Gram-negative bacteria. There is no counterpart in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis systems of Gram-positive bacteria such as Staphylococcus epidermidis. The PGA polysaccharide adhesin is a critical determinant of biofilm formation. The conserved C-terminal domain of this outer membrane protein is preceded by a variable number of TPR repeats.
28	pfam00515	34	31	86.3	1.3	[ -- ]	TPR_1	Tetratricopeptide repeat.
29	TIGR00540	367	59	85.9	0.96	[ ------ ]	TPR_hemY_coli	heme biosynthesis-associated TPR protein. Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis.
30	PRK11788	389	47	85.5	1.1	[ ---- ]	PRK11788	tetratricopeptide repeat protein; Provisional
31	pfam13414	69	62	85.2	5.4	[----- ]	TPR_11	TPR repeat.
32	COG3285	299	70	85.0	1.9	[ ------- ]	LigD	Eukaryotic-type DNA primase
33	TIGR02917	899	69	84.8	4.5	[ ------ ]	PEP_TPR_lipo	putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
34	pfam13174	33	31	83.9	1.5	[ -- ]	TPR_6	Tetratricopeptide repeat.
35	cd04864	228	110	83.8	2.2	[ ----------- ]	LigD_Pol_like_1	LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
36	PRK11189	296	90	83.3	2.9	[ -------- ]	PRK11189	lipoprotein NlpI; Provisional
37	pfam13176	36	26	83.3	1.3	[ -- ]	TPR_7	Tetratricopeptide repeat.
38	TIGR02776	552	74	83.1	2.9	[ ------- ]	NHEJ_ligase_prk	DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; it only represents the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
39	pfam07719	34	32	82.9	2.3	[ -- ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
40	TIGR02552	135	95	82.9	8.6	[-------- ]	LcrH_SycD	type III secretion low calcium response chaperone LcrH/SycD. Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
41	COG5010	257	57	82.5	2.6	[ ----- ]	TadD	Flp pilus assembly protein TadD, contains TPR repeats
42	COG4235	287	80	81.2	3.2	[ ------- ]	NrfG	Cytochrome c-type biogenesis protein CcmH/NrfG
43	COG4783	484	100	81.1	3	[ --------- ]	YfgC	Putative Zn-dependent protease, contains TPR repeats
44	cd04862	227	107	80.3	3.5	[ ----------- ]	PaeLigD_Pol_like	PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair.
45	COG2219	363	71	77.0	3.4	[ ------ ]	PRI2	Eukaryotic-type DNA primase, large subunit
46	pfam13181	34	31	75.7	5.2	[ -- ]	TPR_8	Tetratricopeptide repeat.
47	pfam12895	81	43	75.3	10	[ --- ]	Apc3	Anaphase-promoting complex, cyclosome, subunit 3. Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20.
48	pfam13429	279	89	74.6	6.5	[ ---------- ]	TPR_15	Tetratricopeptide repeat.
49	pfam13432	65	63	73.7	21	[----- ]	TPR_16	Tetratricopeptide repeat.
50	COG0457	291	86	73.5	35	[ ------- ]	TPR	Tetratricopeptide (TPR) repeat
51	COG2976	207	70	72.1	6	[ ------ ]	YfgM	Putative negative regulator of RcsB-dependent stress response
52	COG0457	291	57	71.4	29	[ ----- ]	TPR	Tetratricopeptide (TPR) repeat
53	COG5010	257	100	71.1	36	[--------- ]	TadD	Flp pilus assembly protein TadD, contains TPR repeats
54	PRK11447	1157	68	70.9	4.2	[ ----- ]	PRK11447	cellulose synthase subunit BcsC; Provisional
55	COG4785	297	90	69.4	9.8	[ -------- ]	NlpI	Lipoprotein NlpI, contains TPR repeats
56	COG4976	287	57	68.5	7.2	[ ----- ]	COG4976	Predicted methyltransferase, contains TPR repeat
57	pfam14559	68	61	68.3	18	[------ ]	TPR_19	Tetratricopeptide repeat.
58	cd04866	223	83	67.2	20	[ -------- ]	LigD_Pol_like_3	LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
59	TIGR02795	117	56	66.3	21	[ ----- ]	tol_pal_ybgF	tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
60	cd04865	228	89	65.1	14	[ --------- ]	LigD_Pol_like_2	LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
61	TIGR00990	615	65	65.0	11	[ ----- ]	3a0801s09	mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
62	TIGR03939	800	87	63.5	40	[-------- ]	PGA_TPR_OMP	poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA. Members of this protein family are the poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin PgaA of Gram-negative bacteria. There is no counterpart in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis systems of Gram-positive bacteria such as Staphylococcus epidermidis. The PGA polysaccharide adhesin is a critical determinant of biofilm formation. The conserved C-terminal domain of this outer membrane protein is preceded by a variable number of TPR repeats.
63	pfam14561	90	64	62.0	24	[ ------ ]	TPR_20	Tetratricopeptide repeat.
64	cd05804	355	48	61.3	16	[ ----- ]	StaR_like	StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
65	COG3629	280	70	61.0	22	[ ------- ]	DnrI	DNA-binding transcriptional activator of the SARP family
66	PRK05972	860	59	59.8	14	[ ----- ]	ligD	ATP-dependent DNA ligase; Reviewed
67	TIGR02552	135	52	59.4	30	[ ---- ]	LcrH_SycD	type III secretion low calcium response chaperone LcrH/SycD. Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
68	pfam12569	516	69	59.2	25	[ ------ ]	NARP1	NMDA receptor-regulated protein 1. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle.
69	pfam13424	78	32	56.5	14	[ --- ]	TPR_12	Tetratricopeptide repeat.
70	COG1467	341	24	55.3	21	[ -- ]	PRI1	Eukaryotic-type DNA primase, catalytic (small) subunit
71	COG4700	251	85	55.1	99	[-------- ]	COG4700	Uncharacterized protein
72	pfam12688	119	55	54.5	19	[ ---- ]	TPR_5	Tetratrico peptide repeat. BH0479 of Bacillus halodurans is a hypothetical protein which contains a tetratrico peptide repeat (TPR) structural motif. The TPR motif is often involved in mediating protein-protein interactions. This protein is likely to function as a dimer. The first 48 amino acids are not present in the clone construct. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719, pfam07720 and pfam07221 models.
73	cd12212	115	61	54.5	34	[ ----- ]	Fis1	Mitochondrial Fission Protein Fis1, cytosolic domain. Fis1, along with Dnm1 and Mdv1, is an essential protein in mediating mitochondrial fission. Dnm1 and Fis1 are highly conserved, with a common mechanism in disparate species. In mutants of these proteins, mitochondrial fission is impaired, resulting in networks of undivided mitochondria. The Fis1 N-terminus is cytosolic and tethered to the mitochondrial outer membrane via a C-terminal transmembrane domain. Fis1 appears to act via the recruitment of division complexes to the mitochondrial outer membrane, via interactions with Mdv1 or Caf4. Fis1 has tandem Tetratricopeptide repeat (TPR) motifs which are known to mediate protein-protein interactions.
74	pfam07720	34	30	54.5	19	[ -- ]	TPR_3	Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones.
75	pfam14853	53	38	52.7	17	[ --- ]	Fis1_TPR_C	Fis1 C-terminal tetratricopeptide repeat. The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the C-terminal tetratricopeptide repeat
76	PRK02249	343	83	52.6	22	[ ------- ]	PRK02249	DNA primase large subunit; Validated
77	pfam13374	42	28	52.4	26	[ --- ]	TPR_10	Tetratricopeptide repeat.
78	pfam02259	350	68	50.1	45	[ ------ ]	FAT	FAT domain. The FAT domain is named after FRAP, ATM and TRRAP.
79	cd05804	355	70	49.4	34	[ ------ ]	StaR_like	StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
80	PRK14267	253	41	48.4	16	[ --- ]	PRK14267	phosphate ABC transporter ATP-binding protein; Provisional
81	COG1729	262	56	47.9	58	[ ----- ]	YbgF	Periplasmic TolA-binding protein (function unknown)
82	COG2956	389	47	47.5	24	[ ---- ]	YciM	Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain
83	cd02679	79	31	47.2	21	[ --- ]	MIT_spastin	MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
84	pfam00531	81	22	46.4	51	[ -- ]	Death	Death domain.
85	pfam00637	138	47	46.3	39	[ ----- ]	Clathrin	Region in Clathrin and VPS. Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
86	pfam12569	516	45	46.1	36	[ ---- ]	NARP1	NMDA receptor-regulated protein 1. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle.
87	PRK02603	172	54	45.6	50	[ ---- ]	PRK02603	photosystem I assembly protein Ycf3; Provisional
88	cd15832	278	72	45.2	60	[ ------- ]	SNAP	Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family. Members of the soluble NSF attachment protein (SNAP) family are involved in intracellular membrane trafficking, including vesicular transport between the endoplasmic reticulum and Golgi apparatus. Higher eukaryotes contain three isoforms of SNAPs: alpha, beta, and gamma. Alpha-SNAP is universally present in eukaryotes and acts as an adaptor protein between SNARE (integral membrane SNAP receptor) and NSF for recruitment to the 20S complex. Beta-SNAP is brain-specific and shares high sequence identity (about 85%) with alpha-SNAP. Gamma-SNAP is weakly related (about 20-25% identity) to the two other isoforms, and is ubiquitous. It may help regulate the activity of the 20S complex. The X-ray structures of vertebrate gamma-SNAP and yeast Sec17, a SNAP family member, show similar all-helical structures consisting of an N-terminal extended twisted sheet of four Tetratricopeptide repeat (TPR)-like helical hairpins and a C-terminal helical bundle.
89	COG1729	262	56	43.3	52	[ ----- ]	YbgF	Periplasmic TolA-binding protein (function unknown)
90	cd07906	190	65	43.1	16	[ ------- ]	Adenylation_DNA_ligase_LigD_LigC	Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.
91	TIGR00540	367	37	41.0	1.6E+02	[ --- ]	TPR_hemY_coli	heme biosynthesis-associated TPR protein. Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis.
92	PRK15179	694	68	39.9	71	[ ------ ]	PRK15179	Vi polysaccharide biosynthesis protein TviE; Provisional
93	COG3118	304	92	37.4	3.1E+02	[-------- ]	YbbN	Negative regulator of GroEL, contains thioredoxin-like and TPR-like domains
94	TIGR02795	117	60	37.0	97	[ ------ ]	tol_pal_ybgF	tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
95	pfam09986	214	52	35.1	1.4E+02	[ ---- ]	DUF2225	Uncharacterized protein conserved in bacteria (DUF2225). This domain, found in various hypothetical bacterial proteins, has no known function.
96	TIGR03302	235	76	34.2	2.3E+02	[ ------- ]	OM_YfiO	outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
97	PRK11189	296	52	33.8	76	[ ---- ]	PRK11189	lipoprotein NlpI; Provisional
98	PRK10049	765	88	32.0	1.2E+02	[ -------- ]	pgaA	outer membrane protein PgaA; Provisional
99	TIGR00990	615	54	31.9	83	[ ---- ]	3a0801s09	mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
100	pfam12895	81	43	29.9	1.2E+02	[ ---- ]	Apc3	Anaphase-promoting complex, cyclosome, subunit 3. Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20.
101	cd04863	231	76	29.7	92	[ ------- ]	MtLigD_Pol_like	MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.
102	pfam09295	395	82	29.4	3.2E+02	[------- ]	ChAPs	ChAPs (Chs5p-Arf1p-binding proteins). ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialized cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other.
103	pfam11690	112	73	29.4	76	[ ------- ]	DUF3287	Protein of unknown function (DUF3287). This eukaryotic family of proteins has no known function.
104	TIGR02841	140	39	28.2	63	[ --- ]	spore_YyaC	putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
105	pfam09250	160	25	27.3	1.1E+02	[ -- ]	Prim-Pol	Bifunctional DNA primase/polymerase, N-terminal. Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.
106	PRK10049	765	76	27.3	1.4E+02	[ ------- ]	pgaA	outer membrane protein PgaA; Provisional
107	pfam13371	73	62	26.7	3.1E+02	[------ ]	TPR_9	Tetratricopeptide repeat.
108	cd01670	79	53	26.7	1.6E+02	[ ----- ]	Death	Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in animal cells.
109	pfam06967	84	39	26.7	34	[ --- ]	Mo-nitro_C	Mo-dependent nitrogenase C-terminus. This family represents the C-terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria. Note that many family members are hypothetical proteins.
110	COG4783	484	73	26.6	2E+02	[ ------- ]	YfgC	Putative Zn-dependent protease, contains TPR repeats
111	cd08774	225	48	26.4	1.1E+02	[ ---- ]	14-3-3	14-3-3 domain. 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis. More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development.
112	PRK10370	198	54	25.9	1.7E+02	[ ---- ]	PRK10370	formate-dependent nitrite reductase complex subunit NrfG; Provisional
113	pfam02259	350	66	25.7	3.8E+02	[ ------ ]	FAT	FAT domain. The FAT domain is named after FRAP, ATM and TRRAP.
114	cd03210	126	58	25.1	87	[ ------ ]	GST_C_Pi	C-terminal, alpha helical domain of Class Pi Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Pi GST is a homodimeric eukaryotic protein. The human GSTP1 is mainly found in erythrocytes, kidney, placenta and fetal liver. It is involved in stress responses and in cellular proliferation pathways as an inhibitor of JNK (c-Jun N-terminal kinase). Following oxidative stress, monomeric GSTP1 dissociates from JNK and dimerizes, losing its ability to bind JNK and causing an increase in JNK activity, thereby promoting apoptosis. GSTP1 is expressed in various tumors and is the predominant GST in a wide range of cancer cells. It has been implicated in the development of multidrug-resistant tumors.
115	pfam09976	145	52	24.9	1.4E+02	[ ---- ]	TPR_21	Tetratricopeptide repeat. TPR repeat
116	pfam13281	374	65	24.6	88	[----- ]	DUF4071	Domain of unknown function (DUF4071). This domain is found at the N-terminus of many serine-threonine kinase-like proteins.
117	cd00871	175	68	24.6	1.2E+02	[ ------ ]	PI4Ka	Phosphoinositide 4-kinase(PI4K), accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. PI4K phosphorylates hydroxylgroup at position 4 on the inositol ring of phosphoinositide, the first commited step in the phosphatidylinositol cycle.
118	cd04859	152	78	23.6	87	[ --------- ]	Prim_Pol	Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.
119	PRK11447	1157	57	22.9	1.8E+02	[ ----- ]	PRK11447	cellulose synthase subunit BcsC; Provisional
120	PRK10153	517	55	22.8	1.3E+02	[ ----- ]	PRK10153	DNA-binding transcriptional activator CadC; Provisional
121	pfam09976	145	89	22.8	2.7E+02	[-------- ]	TPR_21	Tetratricopeptide repeat. TPR repeat
122	cd02679	79	31	22.3	1.1E+02	[ ---- ]	MIT_spastin	MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
123	cd10395	101	43	21.8	75	[ ---- ]	SH2_RIN3	Src homology 2 (SH2) domain found in Ras and Rab interactor 3 (RIN3)-like proteins. RIN3, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. RIN3 stimulated the formation of GTP-bound Rab31, a Rab5-subfamily GTPase, and formed enlarged vesicles and tubular structures, where it colocalized with Rab31. Transferrin appeared to be transported partly through the RIN3-positive vesicles to early endosomes. RIN3 interacts via its Pro-rich domain with amphiphysin II, which contains SH3 domain and participates in receptor-mediated endocytosis. RIN3, a Rab5 and Rab31 GEF, plays an important role in the transport pathway from plasma membrane to early endosomes. Mutations in the region between the SH2 and RH domain of RIN3 specifically abolished its GEF action on Rab31, but not Rab5. RIN3 was also found to partially translocate the cation-dependent mannose 6-phosphate receptor from the trans-Golgi network to peripheral vesicles and that this is dependent on its Rab31-GEF activity. These data indicate that RIN3 specifically acts as a GEF for Rab31. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
124	PRK06423	73	50	21.6	84	[ ---- ]	PRK06423	phosphoribosylformylglycinamidine synthase; Provisional
125	cd01046	123	103	21.4	1E+02	[ --------- ]	Rubrerythrin_like	rubrerythrin-like, diiron-binding domain. Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins.
126	TIGR04510	814	46	21.3	1.5E+02	[ ---- ]	mod_pep_cyc	putative peptide modification system cyclase. Members of this family show homology to mononucleotidyl cyclases and to tetratricopeptide repeat (TPR) proteins. Members occur in next to two other markers of ribosomal peptide modification systems. One is a dehydrogenase related to SagB proteins from thiazole/oxazole modification systems. The other is the putative precursor, related to the nitrile hydratase-related leader peptide (NHLP) and nitrile hydratase alpha subunit families. These systems occur in many species of Xanthomonas and Stenotrophomonas, among others.
127	pfam08966	72	32	20.9	49	[ -- ]	DUF1882	Domain of unknown function (DUF1882). This domain is found in a set of hypothetical bacterial proteins.
128	cd12261	73	36	20.7	1.5E+02	[ --- ]	RRM1_3_MRN1	RNA recognition motif 1 and 3 in RNA-binding protein MRN1 and similar proteins. This subfamily corresponds to the RRM1 and RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).