match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	TIGR02917	899	318	97.5	0.014	[ ----------------------------------              ]	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.
2	TIGR02917	899	406	97.1	0.35	[ -------------------------------------------     ]	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.
3	pfam13414	69	64	96.8	0.0085	[                      ------                     ]	TPR_11	TPR repeat.
4	pfam13424	78	66	96.4	0.011	[                  ------                         ]	TPR_12	Tetratricopeptide repeat.
5	COG0457	291	205	96.1	0.28	[        --------------------                     ]	TPR	Tetratricopeptide (TPR) repeat
6	TIGR02521	234	185	95.5	0.59	[        ----------------------                   ]	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.
7	pfam13424	78	69	94.2	0.24	[                      ------                     ]	TPR_12	Tetratricopeptide repeat.
8	pfam13429	279	234	93.4	2.9	[        --------------------------               ]	TPR_15	Tetratricopeptide repeat.
9	pfam00515	34	27	92.8	0.096	[                      --                         ]	TPR_1	Tetratricopeptide repeat.
10	COG5010	257	180	92.6	2.3	[               ------------------                ]	TadD	Flp pilus assembly protein TadD, contains TPR repeats
11	pfam00515	34	31	92.1	0.17	[                         ---                     ]	TPR_1	Tetratricopeptide repeat.
12	COG3063	250	145	91.7	2.3	[                   ---------------               ]	PilF	Tfp pilus assembly protein PilF
13	TIGR02521	234	159	91.5	1.3	[                ------------------               ]	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	pfam12688	119	82	91.2	0.19	[                      --------                   ]	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.
15	pfam07719	34	31	90.9	0.28	[                         ---                     ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
16	COG3629	280	121	89.9	0.31	[                                      -----------]	DnrI	DNA-binding transcriptional activator of the SARP family
17	pfam13414	69	55	89.8	0.76	[                         -----                   ]	TPR_11	TPR repeat.
18	pfam13432	65	54	89.1	1.2	[                       -----                     ]	TPR_16	Tetratricopeptide repeat.
19	pfam13181	34	31	88.9	0.52	[                         ---                     ]	TPR_8	Tetratricopeptide repeat.
20	COG3063	250	105	88.3	4.5	[ -----------                                     ]	PilF	Tfp pilus assembly protein PilF
21	pfam13176	36	29	87.9	0.4	[                      --                         ]	TPR_7	Tetratricopeptide repeat.
22	TIGR02552	135	74	87.4	0.89	[                     -------                     ]	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.
23	cd00383	95	67	85.1	0.39	[                                      ------     ]	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.
24	pfam14559	68	45	85.1	1.3	[                          -----                  ]	TPR_19	Tetratricopeptide repeat.
25	pfam14559	68	53	84.0	1.8	[                       -----                     ]	TPR_19	Tetratricopeptide repeat.
26	pfam07719	34	30	83.3	1.1	[                      --                         ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
27	pfam13432	65	50	82.0	3.3	[                   -----                         ]	TPR_16	Tetratricopeptide repeat.
28	pfam13428	44	38	82.0	2.7	[        ----                                     ]	TPR_14	Tetratricopeptide repeat.
29	COG2909	894	136	80.9	1.1E+02	[ -------------                                   ]	MalT	ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT
30	PRK11788	389	70	78.6	33	[                   -------                       ]	PRK11788	tetratricopeptide repeat protein; Provisional
31	COG0457	291	96	78.1	21	[                   ---------                     ]	TPR	Tetratricopeptide (TPR) repeat
32	COG0745	229	73	77.6	0.97	[                                     --------    ]	OmpR	DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain
33	COG4783	484	105	76.5	35	[ ------------                                    ]	YfgC	Putative Zn-dependent protease, contains TPR repeats
34	TIGR04510	814	174	74.5	17	[                       --------------------      ]	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.
35	TIGR03939	800	310	73.4	1.6E+02	[ ---------------------------------               ]	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.
36	PRK11788	389	96	73.3	38	[                   ----------                    ]	PRK11788	tetratricopeptide repeat protein; Provisional
37	pfam13429	279	115	73.0	29	[  -----------                                    ]	TPR_15	Tetratricopeptide repeat.
38	PRK11447	1157	301	71.5	2E+02	[ -----------------------------                   ]	PRK11447	cellulose synthase subunit BcsC; Provisional
39	pfam09899	817	24	70.4	3.3	[                                      --         ]	DUF2126	Putative amidoligase enzyme (DUF2126). Members of this family of bacterial domains are predominantly found in transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown, but they are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes).
40	COG2909	894	166	67.8	1.3E+02	[         -----------------                       ]	MalT	ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT
41	pfam12895	81	51	67.4	19	[     -----                                       ]	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.
42	COG3710	148	107	66.1	7.4	[                                     ----------- ]	CadC1	DNA-binding winged helix-turn-helix (wHTH) domain
43	pfam13181	34	30	63.8	6.9	[                      --                         ]	TPR_8	Tetratricopeptide repeat.
44	pfam08195	43	20	63.4	3.7	[                           --                    ]	TRI9	TRI9 protein. Putative gene of 129 bp in the Trichothecene gene cluster of Fusarium sporotrichioides and F. graminearum. Encoding a predicted protein of 43 amino acids which function is unknown.
45	TIGR02174	73	38	61.4	7.5	[                                     -----       ]	CXXU_selWTH	selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
46	COG4783	484	125	61.1	54	[                      ------------               ]	YfgC	Putative Zn-dependent protease, contains TPR repeats
47	pfam13431	34	29	58.6	9	[                            --                   ]	TPR_17	Tetratricopeptide repeat.
48	pfam13428	44	32	58.1	20	[                         ---                     ]	TPR_14	Tetratricopeptide repeat.
49	TIGR00540	367	118	56.9	1.3E+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.
50	TIGR02552	135	63	56.6	96	[                         ------                  ]	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.
51	TIGR04510	814	190	55.7	3.5E+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.
52	COG1654	79	41	55.3	7	[                                        ----     ]	BirA	Biotin operon repressor
53	pfam12895	81	51	53.7	33	[        -----                                    ]	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.
54	pfam06249	152	28	51.5	14	[                                      ---        ]	EutQ	Ethanolamine utilisation protein EutQ. The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear.
55	COG5010	257	125	50.9	71	[                      ------------               ]	TadD	Flp pilus assembly protein TadD, contains TPR repeats
56	COG2956	389	162	49.5	29	[                   ----------------              ]	YciM	Lipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain
57	pfam00486	77	53	48.7	11	[                                       -----     ]	Trans_reg_C	Transcriptional regulatory protein, C terminal.
58	PRK05559	631	53	48.0	29	[                                    -----        ]	PRK05559	DNA topoisomerase IV subunit B; Reviewed
59	pfam09613	156	90	47.1	65	[       --------                                  ]	HrpB1_HrpK	Bacterial type III secretion protein (HrpB1_HrpK). This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
60	pfam13374	42	32	46.2	23	[                  ---                            ]	TPR_10	Tetratricopeptide repeat.
61	COG4766	176	29	45.0	19	[                                      ---        ]	EutQ	Ethanolamine utilization protein EutQ, cupin superfamily (function unknown)
62	PRK04841	903	147	43.9	3.5E+02	[                   ---------------               ]	PRK04841	transcriptional regulator MalT; Provisional
63	PRK02603	172	107	43.5	74	[               -------------                     ]	PRK02603	photosystem I assembly protein Ycf3; Provisional
64	cd01668	60	22	42.6	22	[                                      --         ]	TGS_RelA_SpoT	TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
65	COG1729	262	96	42.4	51	[        ---------                                ]	YbgF	Periplasmic TolA-binding protein (function unknown)
66	TIGR03105	435	96	42.1	21	[                                       --------- ]	gln_synth_III	glutamine synthetase, type III. This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur.
67	cd04791	327	63	41.7	40	[      ------                                     ]	LanC_SerThrkinase	Lanthionine synthetase C-like domain associated with serine/threonine kinases. Some members of this subgroup lack the zinc binding site and the active site residues, and therefore are most likely inactive. The function of this domain is unknown.
68	PRK02603	172	77	41.7	56	[                       -------                   ]	PRK02603	photosystem I assembly protein Ycf3; Provisional
69	TIGR03085	199	40	41.4	13	[                                     ----        ]	TIGR03085	TIGR03085 family protein. This family, like pfam07398 and TIGRFAMs family TIGR03084, belongs to the larger set of probable enzymes defined in family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized.
70	pfam14324	138	22	40.7	21	[                                      --         ]	PINIT	PINIT domain. The PINIT domain is a protein domain that is found in PIAS proteins. The PINIT domain is about 180 amino acids in length.
71	cd00165	70	25	40.3	31	[                                      ---        ]	S4	S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
72	COG3118	304	107	38.8	3.2E+02	[ ----------                                      ]	YbbN	Negative regulator of GroEL, contains thioredoxin-like and TPR-like domains
73	pfam07721	26	22	38.7	50	[        --                                       ]	TPR_4	Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719 and pfam07720 models.
74	cd00413	210	44	38.1	51	[                                     ----        ]	Glyco_hydrolase_16	glycosyl hydrolase family 16. The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues.
75	pfam13174	33	26	38.0	50	[        ---                                      ]	TPR_6	Tetratricopeptide repeat.
76	COG3612	157	72	37.1	30	[                                    --------     ]	COG3612	Uncharacterized protein
77	pfam01846	50	31	36.9	43	[                ----                             ]	FF	FF domain. This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.
78	pfam00630	91	25	36.5	44	[                                     --          ]	Filamin	Filamin/ABP280 repeat.
79	pfam07883	71	22	36.0	36	[                                      --         ]	Cupin_2	Cupin domain. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).
80	PRK14494	229	39	35.9	22	[                                   ----          ]	PRK14494	putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional
81	TIGR02551	298	31	33.9	30	[                                    ---          ]	SpaO_YscQ	type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae.
82	pfam12862	91	36	33.4	29	[                      ---                        ]	Apc5	Anaphase-promoting complex subunit 5. Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction. The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC. This region of the Apc5 member proteins carries a TPR-like motif.
83	pfam03704	146	102	32.8	2.5E+02	[                   ------------                  ]	BTAD	Bacterial transcriptional activator domain. Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR along with the C terminal region is capable of independently directing actinorhodin production. This family contains TPR repeats.
84	PRK05500	477	31	32.0	21	[                                      ---        ]	PRK05500	bifunctional orotidine 5'-phosphate decarboxylase/orotate phosphoribosyltransferase protein; Validated
85	cd12212	115	24	31.8	83	[        ---                                      ]	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.
86	pfam02259	350	193	31.7	5.2E+02	[       -------------------                       ]	FAT	FAT domain. The FAT domain is named after FRAP, ATM and TRRAP.
87	pfam09999	144	61	30.8	91	[                                      ------     ]	DUF2240	Uncharacterized protein conserved in archaea (DUF2240). This domain, found in various hypothetical archaeal proteins, has no known function.
88	pfam14451	81	21	30.5	44	[                                      --         ]	Ub-Mut7C	Mut7-C ubiquitin. This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role.
89	pfam12688	119	89	29.2	2.1E+02	[                   ---------                     ]	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.
90	PRK10049	765	59	28.7	1.1E+02	[                     ------                      ]	pgaA	outer membrane protein PgaA; Provisional
91	cd14417	40	22	27.9	64	[                                --               ]	CUE_DMA_DMRTA1	CUE-like DMA domain found in doublesex- and mab-3-related transcription factor A1 (DMRTA1) and similar proteins. DMRTA1 is encoded by gene DMRT1, a vertebrate equivalent of the Drosophila melanogaster master sex regulator gene, doublesex. In D. melanogaster, doublesex controls the terminal switch of the pathway leading to sex fate choice. DMRT1 may function as regulator of sex differentiation in vertebrate. Especially, it is required for testis differentiation, but is not involved in the gonadal sex fate choice.
92	PRK05529	255	164	27.1	45	[                               ----------------- ]	PRK05529	cell division protein FtsQ; Provisional
93	cd15831	146	100	26.8	3.1E+02	[                   -----------                   ]	BTAD	Bacterial Transcriptional Activation (BTA) domain. The Bacterial Transcriptional Activation (BTA) domain is present in the putative transcriptional regulator Mycobacterium EmbR and the related Streptomyces antibiotic regulatory protein (SARP) family of transcription factors, which includes DnrI and AfsR, among others. Members of this family contain an N-terminal DNA-binding domain, followed by the BTA domain, and many have diverse domains at the C-terminus. EmbR contains an C-terminal forkhead-associated (FHA) domain, which mediates binding to threonine-phosphorylated sites in a sequence-specific manner. The BTA domain of EmbR contains three Tetratricopeptide repeats (TPRs) and two C-terminal helices. The TPR motif typically contains 34 amino acids, and 5 or 6 tandem repeats of the motif generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein.
94	pfam11281	316	27	26.6	56	[                          --                     ]	DUF3083	Protein of unknown function (DUF3083). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
95	TIGR02561	153	70	26.2	2.2E+02	[      -------                                    ]	HrpB1_HrpK	type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
96	pfam01535	31	20	25.3	84	[         -                                       ]	PPR	PPR repeat. This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR.
97	cd03405	249	76	24.2	5.3E+02	[                  --------                       ]	SPFH_HflC	High frequency of lysogenization C (HflC) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prokaryotic HflC (High frequency of lysogenization C). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflC is an integral membrane protein which may localize to the plasma membrane. HflC associates with another SPFH superfamily member (HflK) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection.
98	pfam00250	96	15	24.1	28	[                                             -   ]	Fork_head	Fork head domain.
99	cd12212	115	54	22.9	1.6E+02	[     -----                                       ]	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.
100	pfam10070	783	153	22.0	6.3E+02	[------------------                               ]	DUF2309	Uncharacterized protein conserved in bacteria (DUF2309). Members of this family of hypothetical bacterial proteins have no known function.
101	PRK12863	94	18	21.6	52	[                --                               ]	PRK12863	YciI-like protein; Reviewed
102	cd00059	78	10	21.5	32	[                                            -    ]	FH	Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
103	PRK11447	1157	120	21.1	4.3E+02	[                       ------------              ]	PRK11447	cellulose synthase subunit BcsC; Provisional
104	pfam01479	48	19	21.1	71	[                                      --         ]	S4	S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.