match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	TIGR01784	270	66	97.7	0.00026	[                 --------------------------------]	T_den_put_tspse	conserved hypothetical protein (putative transposase or invertase). Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.
2	COG5464	289	83	95.4	0.078	[          ---------------------------------------]	YadD	Predicted transposase YdaD
3	PRK13386	236	14	94.6	0.046	[                                  ------         ]	fliH	flagellar assembly protein H; Provisional
4	PRK13386	236	30	94.0	0.064	[                            ------------         ]	fliH	flagellar assembly protein H; Provisional
5	PRK09956	308	88	92.9	0.7	[       ------------------------------------------]	PRK09956	hypothetical protein; Provisional
6	TIGR01784	270	81	92.0	2.1	[           ------------------------------------  ]	T_den_put_tspse	conserved hypothetical protein (putative transposase or invertase). Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.
7	PRK05687	246	15	91.3	0.79	[                            ------               ]	fliH	flagellar assembly protein H; Validated
8	PRK05687	246	30	91.0	0.46	[                            ------------         ]	fliH	flagellar assembly protein H; Validated
9	pfam09811	39	27	90.9	0.45	[                            -----------          ]	Yae1_N	Essential protein Yae1, N terminal. Members of this family are found in the N terminal region of the essential protein Yae1. Their exact function has not, as yet, been determined. The family DUF1715, pfam08215 has now been merged into this family.
10	pfam09811	39	10	82.5	1.7	[                              ----               ]	Yae1_N	Essential protein Yae1, N terminal. Members of this family are found in the N terminal region of the essential protein Yae1. Their exact function has not, as yet, been determined. The family DUF1715, pfam08215 has now been merged into this family.
11	COG1317	234	26	82.3	3.3	[                            -----------          ]	FliH	Flagellar biosynthesis/type III secretory pathway protein FliH
12	COG2137	174	48	69.4	46	[                           ----------------------]	RecX	SOS response regulatory protein OraA/RecX, interacts with RecA
13	cd14318	40	23	67.8	5.4	[                                       ----------]	UBA_Cbl_like	UBA domain found in casitas B-lineage lymphoma (Cbl) proteins. The Cbl adaptor proteins family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-3. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating the activated tyrosine kinases and targeting them for degradation. Cbl proteins in this family consists of a highly conserved N-terminal half that includes a tyrosine-kinase-binding (TKB) domain and a RING finger domain, both of which are required for Cbl-mediated downregulation of RTKs, and a C-terminal half that includes a ubiquitin-associated (UBA) domain and other protein interaction motifs. The UBA domain contains leucine/isoleucine repeats and may play a role in dimerization of Cbl proteins. In addition, although both c-Cbl and Cbl-b have the C-terminal UBA domain, only the UBA domain from Cbl-b can bind ubiquitin.
14	cd00569	42	32	67.1	3.4	[                                   --------------]	HTH_Hin_like	Helix-turn-helix domain of Hin and related proteins. This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.
15	pfam13606	30	19	63.4	8.8	[                                     --------    ]	Ank_3	Ankyrin repeat. Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities.
16	PRK08944	302	43	62.7	25	[  ------------------                             ]	motB	flagellar motor protein MotB; Reviewed
17	COG1317	234	22	61.8	16	[                        ----------               ]	FliH	Flagellar biosynthesis/type III secretory pathway protein FliH
18	pfam12422	152	38	59.6	6.6	[-----------------                                ]	Condensin2nSMC	Condensin II non structural maintenance of chromosomes subunit. This domain family is found in eukaryotes, and is approximately 150 amino acids in length. This family is part of a non-SMC subunit of condensin II which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II.
19	pfam02631	121	24	50.0	20	[                                      ---------- ]	RecX	RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.
20	pfam00023	33	20	47.9	19	[                                     ---------   ]	Ank	Ankyrin repeat. Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity.
21	pfam02796	45	26	47.4	14	[                                      -----------]	HTH_7	Helix-turn-helix domain of resolvase.
22	pfam02631	121	24	46.5	22	[                                       ----------]	RecX	RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.
23	pfam04695	79	19	45.8	19	[                                         --------]	Pex14_N	Peroxisomal membrane anchor protein (Pex14p) conserved region. Family of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N-terminus of the protein.
24	PRK00117	157	49	45.4	21	[                           ----------------------]	recX	recombination regulator RecX; Reviewed
25	cd14272	38	22	45.3	32	[                                       --------- ]	UBA_AMPK-RKs	UBA domain of AMPK related kinases. The AMPK-RK family comprises AMP-activated protein kinases (AMPKs), MAP/microtubule affinity-regulating kinases (MARKs), Brain-specific kinases (BRSKs), Salt inducible kinases (SIKs), maternal embryonic leucine zipper kinase (MELK), and SNF-related serine/threonine-protein kinase (SNRK). It is the only kinase family in the human genome containing an ubiquitin-associated (UBA) or UBA-like domain which is located immediately C-terminal to their N-terminal protein kinase catalytic domain. In addition, most of family members contain a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK), but some are lack of this region. AMPK-RKs play central roles in metabolic control, energy homeostasis and stress responses in eukaryotes. They require phosphorylation by liver kinase B1 (LKB1) for full activity. Normally, AMPK-RKs appear to exist as heterotrimeric complexes consisting of a catalytic alpha-subunit and regulatory beta- and gamma-subunits. This model corresponds to the catalytic subunit. The UBA domain, previously called SNF1 homology (SNH) domain, regulates the conformation, LKB1-mediated phosphorylation and activation, and localization of the AMPK-RKs, but does not interact with ubiquitin-like molecules. In AMPKalpha subunits, the UBA-like autoinhibitory domain (AID) is responsible for AMPKalpha subunit autoinhibition. Due to the lack of UBA domain, NUAK1 kinase, also called ARK5 (AMPK-related kinase 5), and NUAK2 kinase, also called SNARK (SNF1/AMPK-related kinase), are not included in this family.
26	pfam06179	100	52	45.3	1E+02	[       ----------------------                    ]	Med22	Surfeit locus protein 5 subunit 22 of Mediator complex. This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1. The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organisation is similar in human, mouse and chicken Surfeit locus. The Med22 subunit of Mediator complex is part of the essential core head region.
27	TIGR03825	255	54	44.4	1.8E+02	[           ------------------------              ]	FliH_bacil	flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
28	cd00512	399	34	42.4	45	[                          ---------------        ]	MM_CoA_mutase	Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Examples include Propionbacterium shermanni MCM during propionic acid fermentation, E.coli MCM in a pathway for the conversion of succinate to propionate and Streptomyces MCM in polyketide biosynthesis. P. shermanni and Streptomyces cinnamonensis MCMs are alpha/beta heterodimers, with both subunits being homologous members of this family. It has been shown for P. shermanni MCM that only the alpha subunit binds coenzyme B12 and substrates. Human MCM is a homodimer with two active sites. Mouse and E.coli MCMs are also homodimers. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA (intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis). In humans, impaired activity of MCM results in methylmalonic aciduria, a disorder of propionic acid metabolism.
29	cd09210	143	42	41.6	23	[              --------------------               ]	Riboflavin_synthase_archaeal	archaeal riboflavin synthase (RS); involved in the biosynthesis pathway of riboflavin (vitamin B2). Archaeal RSs are homopentamers catalyzing the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine in riboflavin biosynthesis. Divalent metal ions, preferably manganese or magnesium, are needed for maximum activity. Riboflavin serves as the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), essential cofactors for several oxidoreductases that are indispensable in most living cells. In the final steps of the riboflavin biosynthetic pathway, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), followed by RS which catalyzes a dismutation of DMRL yielding riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. Archaeal RSs share sequence similarity with LSs, both appear to have diverged early in the evolution of archaea from a common ancestor.
30	COG2137	174	23	38.9	31	[                                       ----------]	RecX	SOS response regulatory protein OraA/RecX, interacts with RecA
31	PRK06669	281	28	37.2	2.2E+02	[                        -----------              ]	fliH	flagellar assembly protein H; Validated
32	cd08810	85	54	36.9	93	[    ------------------------                     ]	CARD_BCL10	Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
33	PRK00117	157	23	35.5	71	[                                       ----------]	recX	recombination regulator RecX; Reviewed
34	PRK06669	281	26	35.1	2.4E+02	[                         -----------             ]	fliH	flagellar assembly protein H; Validated
35	cd04778	219	52	34.5	12	[                        ------------------------ ]	HTH_MerR-like_sg2	Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
36	pfam03791	52	28	31.2	1.4E+02	[        ------------                             ]	KNOX2	KNOX2 domain. The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization.
37	pfam11169	103	31	30.8	75	[                            --------------       ]	DUF2956	Protein of unknown function (DUF2956). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
38	pfam13637	54	19	29.7	72	[                                     --------    ]	Ank_4	Ankyrin repeats (many copies).
39	PRK14135	263	30	29.6	1.4E+02	[                                    -------------]	recX	recombination regulator RecX; Provisional
40	PRK06029	185	14	28.7	28	[                                          ------ ]	PRK06029	3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional
41	pfam00627	37	20	27.7	1E+02	[                                       --------- ]	UBA	UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.
42	pfam06925	169	24	27.6	27	[                                       ----------]	MGDG_synth	Monogalactosyldiacylglycerol (MGDG) synthase. This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B.
43	PRK15443	138	53	27.3	97	[       -----------------------                   ]	pduE	propanediol dehydratase small subunit; Provisional
44	pfam11198	181	24	26.9	2E+02	[                                       ----------]	DUF2857	Protein of unknown function (DUF2857). This is a bacterial family of uncharacterized proteins.
45	TIGR01465	247	16	24.3	33	[                                       -------   ]	cobM_cbiF	precorrin-4 C11-methyltransferase. This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products.
46	cd06170	57	19	24.1	86	[                                         --------]	LuxR_C_like	C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.
47	pfam02026	95	16	24.0	45	[                                       ------    ]	RyR	RyR domain. This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
48	COG5012	227	62	23.9	3.5E+02	[                ---------------------------      ]	MtbC1	Methanogenic corrinoid protein MtbC1
49	pfam14748	107	53	23.8	1.6E+02	[        --------------------------               ]	P5CR_dimer	Pyrroline-5-carboxylate reductase dimerization. Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (pfam03807) and a C-terminal dimerization domain. This is the dimerization domain.
50	PRK06937	204	12	21.1	3.8E+02	[          -----                                  ]	PRK06937	type III secretion system protein; Reviewed
51	pfam11387	44	29	20.9	1.5E+02	[                                     ------------]	DUF2795	Protein of unknown function (DUF2795). This family of proteins has no known function.
52	TIGR03825	255	15	20.7	2.8E+02	[                            ------               ]	FliH_bacil	flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
53	pfam03937	74	24	20.4	2E+02	[      ----------                                 ]	Sdh5	Flavinator of succinate dehydrogenase. This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans. Bacterial homologues of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterized as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria. This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true.
54	pfam15168	80	15	20.2	56	[        ------                                   ]	TRIQK	Triple QxxK/R motif-containing protein family. TRIQK member-proteins share a characteristic triple repeat of the sequence QXXK/R, as well as a hydrophobic C-terminal region. Xenopus and mouse triqk genes are broadly expressed throughout embryogenesis, and mtriqk is also generally expressed in mouse adult tissues. TRIQK proteins are localized to the endoplasmic reticulum membrane. This family is found in eukaryotes and members are typically between and 86 amino acids in length.
55	COG2859	237	30	20.0	1.2E+02	[                                  -------------  ]	COG2859	Uncharacterized protein