match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam02627	84	37	91.4	0.39	[                      -------                    ]	CMD	Carboxymuconolactone decarboxylase family. Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins CMD represents the C-terminal domain, pfam00561 represents the N-terminal domain.
2	PRK01406	476	68	80.6	2.1	[                       -------------             ]	gltX	glutamyl-tRNA synthetase; Reviewed
3	COG0599	124	62	71.8	2.7	[                 ------------                    ]	YurZ	Uncharacterized conserved protein YurZ, alkylhydroperoxidase/carboxymuconolactone decarboxylase family
4	TIGR00350	152	50	66.1	5	[                                ------------     ]	lytR_cpsA_psr	cell envelope-related function transcriptional attenuator common domain. This model describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is proteins psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. Besides the region of strong similarily represented by this model, these proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.
5	TIGR00778	50	23	64.4	11	[                      ----                       ]	ahpD_dom	alkylhydroperoxidase AhpD family core domain. This model represents a 51-residue core region of homology among a family of mostly uncharacterized proteins of 110 to 227 amino acids. Most members of this family contain the motif EXXXXXX
6	COG5644	869	77	63.0	8.1	[               -----------------                 ]	COG5644	U3 small nucleolar RNA-associated protein 14
7	pfam13373	129	26	50.4	12	[                       -----                     ]	DUF2407_C	DUF2407 C-terminal domain. This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.
8	COG2011	222	20	43.0	16	[                      ---                        ]	MetP	ABC-type methionine transport system, permease component
9	pfam13411	69	43	42.1	23	[                  --------                       ]	MerR_1	MerR HTH family regulatory protein.
10	pfam11198	181	23	41.5	18	[                      -----                      ]	DUF2857	Protein of unknown function (DUF2857). This is a bacterial family of uncharacterized proteins.
11	pfam01466	78	34	41.1	28	[                      --------                   ]	Skp1	Skp1 family, dimerization domain.
12	cd00569	42	19	40.9	25	[                      ----                       ]	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.
13	cd14245	114	45	40.5	28	[                                     ---------   ]	DMP12	Putative DNA mimic protein DMP12. The Neisseria sp. protein DMP12 has been shown to interact with the bacterial histone-like protein HU and may do so by acting as a DNA mimic. It is likely to play a regulatory role, but not via direct competition for binding of HU, which is involved in maintenance of the bacterial nucleoid structure.
14	cd13552	266	31	40.0	17	[                                       ------    ]	PBP2_Fbp_like_6	Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
15	pfam10911	77	55	39.2	74	[               ------------                      ]	DUF2717	Protein of unknown function (DUF2717). Members in this family of proteins are annotated as gene 6.5 protein however currently there is no known function.
16	PRK09194	565	41	38.7	20	[                                        -------- ]	PRK09194	prolyl-tRNA synthetase; Provisional
17	pfam12554	48	39	38.4	64	[                 ---------                       ]	MOZART1	Mitotic-spindle organizing gamma-tubulin ring associated. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, this family does not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. MOZART1 is required for gamma-TuRC recruitment to centrosomes.
18	pfam14407	60	20	36.9	36	[                       ----                      ]	Frankia_peptide	Ribosomally synthesized peptide prototyped by Frankia Franean1_4349. Ribosomally synthesized peptide linked to cyclases in chloroflexi. It may have a link to cyclic nucleotide signaling.
19	TIGR01064	472	67	35.0	38	[                           --------------        ]	pyruv_kin	pyruvate kinase. This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars.
20	PRK10792	285	64	33.6	51	[                            -------------        ]	PRK10792	bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
21	PRK10782	217	18	31.8	29	[                      ---                        ]	PRK10782	DL-methionine transporter permease subunit; Provisional
22	cd00530	293	33	29.8	2.1E+02	[                    ------                       ]	PTE	Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active.
23	pfam13348	68	22	28.9	61	[                      ----                       ]	Y_phosphatase3C	Tyrosine phosphatase family C-terminal region.
24	PRK13379	119	22	28.8	47	[                       ----                      ]	PRK13379	protocatechuate 4,5-dioxygenase subunit alpha; Provisional
25	PRK13018	378	51	28.2	32	[------------                                     ]	PRK13018	cell division protein FtsZ; Provisional
26	COG4547	620	32	27.1	31	[                                           ------]	CobT2	Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphorib...
27	PRK11302	284	22	26.9	33	[ ----                                            ]	PRK11302	DNA-binding transcriptional regulator HexR; Provisional
28	cd14310	30	21	26.7	42	[                       ----                      ]	UBA_cnDdi1_like	UBA domain found in Cryptococcus neoformans DNA-damage response protein Ddi1 and similar proteins. The family includes some uncharacterized Ddi and similar proteins which show a high level of sequence similarity with yeast Ddi1. Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in yeast. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (UBL) shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell.
29	COG0618	332	86	26.3	54	[              ------------------                 ]	NrnA	nanoRNase/pAp phosphatase, hydrolyzes c-di-AMP and oligoRNAs
30	PRK11125	480	44	25.5	1.8E+02	[                  ----------                     ]	nrfA	cytochrome c nitrite reductase subunit c552; Provisional
31	pfam13351	84	53	25.3	51	[                       ------------              ]	DUF4099	Protein of unknown function (DUF4099). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. The C-terminal repeat region of this family is DUF4098, pfam13345.
32	pfam07228	192	60	24.9	1.9E+02	[                                 --------------- ]	SpoIIE	Stage II sporulation protein E (SpoIIE). This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments.
33	cd08784	80	17	24.8	54	[                       ----                      ]	Death_DRs	Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
34	pfam02887	117	57	24.7	67	[                             -----------         ]	PK_C	Pyruvate kinase, alpha/beta domain. As well as being found in pyruvate kinase this family is found as an isolated domain in some bacterial proteins.
35	PRK15110	321	45	24.7	35	[                                      ---------  ]	PRK15110	antimicrobial peptide ABC transporter permease SapB; Provisional
36	pfam08963	113	39	24.4	2.4E+02	[                     --------                    ]	DUF1878	Protein of unknown function (DUF1878). This domain is found in a set of hypothetical bacterial proteins.
37	pfam02787	122	18	23.8	1.9E+02	[                       ---                       ]	CPSase_L_D3	Carbamoyl-phosphate synthetase large chain, oligomerization domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
38	cd00779	255	39	23.7	45	[                                        -------  ]	ProRS_core_prok	Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.
39	pfam10979	43	13	23.7	1.2E+02	[                         ---                     ]	DUF2786	Protein of unknown function (DUF2786). This family of proteins has no known function.
40	pfam15601	133	29	23.4	58	[  ------                                         ]	Imm42	Immunity protein 42. A predicted immunity protein with an alpha+beta fold and conserved tyrosine and tryptophan residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-REase-10 family.
41	cd00570	71	43	23.0	64	[  ----------                                     ]	GST_N_family	Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of 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. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK subfamily, a member of the DsbA family). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction and isomerization of certain compounds. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxin 2 and stringent starvation protein A.
42	pfam12327	95	34	22.3	43	[ -------                                         ]	FtsZ_C	FtsZ family, C-terminal domain. This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea.
43	cd08585	237	82	22.1	30	[       -----------------                         ]	GDPD_like_3	Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity with Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
44	pfam00725	97	18	21.9	72	[                       ----                      ]	3HCDH	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain. This family also includes lambda crystallin. Some proteins include two copies of this domain.
45	pfam11268	169	40	21.7	70	[                       -------                   ]	DUF3071	Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
46	pfam00749	314	53	21.6	3E+02	[                ------------                     ]	tRNA-synt_1c	tRNA synthetases class I (E and Q), catalytic domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).
47	pfam03864	328	47	21.6	89	[                       ---------                 ]	Phage_cap_E	Phage major capsid protein E. Major capsid protein E is involved with the stabilisation of the condensed form of the DNA molecule in phage heads.
48	cd03060	71	14	20.9	58	[         ---                                     ]	GST_N_Omega_like	GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega GSTs. 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 TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Omega GSTs show little or no GSH-conjugating activity towards standard GST substrates. Instead, they catalyze the GSH dependent reduction of protein disulfides, dehydroascorbate and monomethylarsonate, activities which are more characteristic of glutaredoxins. Like Omega enzymes, proteins in this subfamily contain a conserved cysteine equivalent to the first cysteine in the CXXC motif of glutaredoxins, which is a redox active residue capable of reducing GSH mixed disulfides in a monothiol mechanism.
49	pfam10778	159	31	20.9	82	[                       ------                    ]	DehI	Halocarboxylic acid dehydrogenase DehI. Haloacid dehalogenases catalyse the removal of halides from organic haloacids. DehI can process both L- and D-substrates. A crucial aspartate residue is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of the configuration of either L- or D-substrates in contrast to D-only enzymes.