match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG1624	247	225	99.7	1.2E-18	[       ----------------------------------------- ]	DisA_N	Diadenylate cyclase (c-di-AMP synthetase), DisA_N domain
2	COG5493	231	151	99.2	1.3E-09	[                    -----------------------------]	COG5493	Uncharacterized protein
3	pfam02457	122	115	99.1	9.1E-12	[                           --------------------  ]	DisA_N	DisA bacterial checkpoint controller nucleotide-binding. The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, pfam10635, that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, pfam00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis.
4	pfam07788	70	55	97.9	2.1E-05	[                                      ---------  ]	DUF1626	Protein of unknown function (DUF1626). This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaebacteria. One member is thought to be similar to tropomyosin.
5	PRK13482	352	102	93.0	0.059	[                             ------------------  ]	PRK13482	DNA integrity scanning protein DisA; Provisional
6	COG1623	349	97	91.5	0.17	[                              -----------------  ]	DisA	Diadenylate cyclase (c-di-AMP synthetase), DNA integrity scanning protein DisA
7	PRK05802	320	76	78.5	1.2	[             --------------                      ]	PRK05802	hypothetical protein; Provisional
8	pfam12729	181	95	67.6	69	[      ---------------------                      ]	4HB_MCP_1	Four helix bundle sensory module for signal transduction. This family is a four helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterized in E coli chemoreceptors.
9	cd11297	133	52	65.4	6.6	[             ---------                           ]	LabA_like_N_1	Uncharacterized subfamily of N-terminal LabA-like domains. This N-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of this subfamily may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). The function of the N-terminal domain is unknown. LabA_like domains exhibit some similarity to the NYN domain, a distant relative of the PIN-domain nucleases.
10	pfam13292	272	121	58.7	58	[                ----------------------           ]	DXP_synthase_N	1-deoxy-D-xylulose-5-phosphate synthase. This family contains 1-deoxyxylulose-5-phosphate synthase (DXP synthase), an enzyme which catalyses the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate, to yield 1-deoxy-D- xylulose-5-phosphate, a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6).
11	pfam04977	80	32	44.9	1.2E+02	[                       -----                     ]	DivIC	Septum formation initiator. DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil.
12	pfam12644	61	33	44.3	90	[                        ------                   ]	DUF3782	Protein of unknown function (DUF3782). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
13	PRK10628	246	43	42.8	9.3	[              --------                           ]	PRK10628	LigB family dioxygenase; Provisional
14	cd00090	78	41	40.4	64	[  -------                                        ]	HTH_ARSR	Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
15	pfam02887	117	102	36.1	0.49	[ -------------------                             ]	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.
16	PRK03846	198	35	35.1	25	[                                   ------        ]	PRK03846	adenylylsulfate kinase; Provisional
17	pfam06825	54	34	32.3	1.2E+02	[                       ------                    ]	HSBP1	Heat shock factor binding protein 1. Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response.
18	PRK06286	91	25	32.0	8.7	[                               ---               ]	PRK06286	putative monovalent cation/H+ antiporter subunit G; Reviewed
19	pfam13863	126	106	31.9	2.5E+02	[       ----------------------                    ]	DUF4200	Domain of unknown function (DUF4200). This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.
20	pfam06005	72	31	31.7	1E+02	[                       -----                     ]	DUF904	Protein of unknown function (DUF904). This family consists of several bacterial and archaeal hypothetical proteins of unknown function.
21	TIGR00159	211	122	30.1	6.5	[                        -----------------------  ]	TIGR00159	TIGR00159 family protein. These proteins have no detectable global or local homology to any protein of known function. Members are restricted to the bacteria and found broadly in lineages other than the Proteobacteria.
22	COG5420	71	31	29.9	1E+02	[                    -----                        ]	COG5420	Uncharacterized protein
23	COG1422	201	19	29.0	1.7E+02	[                         ---                     ]	COG1422	Uncharacterized archaeal membrane protein, DUF106 family, distantly related to YidC/Oxa1
24	pfam03008	95	46	28.6	32	[                                --------         ]	DUF234	Archaea bacterial proteins of unknown function.
25	cd01475	224	55	28.3	36	[                                         --------]	vWA_Matrilin	VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
26	COG1154	627	125	27.9	1.7E+02	[                ----------------------           ]	Dxs	Deoxyxylulose-5-phosphate synthase
27	cd11529	116	51	26.3	1.2E+02	[     --------                                    ]	NTP-PPase_MazG_Cterm	Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'. MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related domains in tandem, this family corresponding to the C-terminal MazG-like domain. EcMazG functions as a regulator of cellular response to starvation by lowering the cellular concentration of guanosine 3',5'-bispyrophosphate (ppGpp). EcMazG exists as a dimer. Each monomer contains two tandem MazG-like domains with similarly folded globular structures. However, only the C-terminal domain has well-ordered active sites and exhibits an NTPase activity responsible for the regulation of bacterial cell survival under nutritional stress. Divalent ions, such as Mg2+ or Mn2+, are required for activity, along with structural features such as EEXX(E/D) motifs and key basic catalytic residues. It has been shown that the C-terminus NTPase activity is responsible for regulation of bacterial cell survival under nutritional stress.
28	TIGR01255	744	126	23.7	1.2E+02	[                   -----------------------       ]	pyr_form_ly_1	formate acetyltransferase 1. Alternate names: pyruvate formate-lyase; formate C-acetyltransferase This enzyme converts formate + acetyl-CoA into pyruvate + CoA. This model describes formate acetyltransferase 1. More distantly related putative formate acetyltransferases have also been identified, including formate acetyltransferase 2 from E. coli, which is excluded from this model.
29	PRK08444	353	106	23.7	2.1E+02	[             -----------------------             ]	PRK08444	hypothetical protein; Provisional
30	pfam05384	159	119	23.0	5.3E+02	[ --------------------------                      ]	DegS	Sensor protein DegS. This is small family of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterize the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon. The family also contains one sequence from Thermoanaerobacter tengcongensis, which is described as sensory transduction histidine kinases.
31	COG0466	782	39	22.9	9.9E+02	[        ------                                   ]	Lon	ATP-dependent Lon protease, bacterial type
32	pfam01963	261	28	22.7	4.8E+02	[                -----                            ]	TraB	TraB family. pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus.
33	PRK13951	488	20	22.5	77	[                    -----                        ]	PRK13951	bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
34	pfam07362	72	26	22.4	91	[                ------                           ]	CcdA	Post-segregation antitoxin CcdA. This family consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein.
35	COG2919	117	32	21.9	3.4E+02	[                       -----                     ]	FtsB	Cell division protein FtsB
36	pfam11166	97	18	21.4	2.7E+02	[                        ---                      ]	DUF2951	Protein of unknown function (DUF2951). This family of proteins has no known function. It has a highly conserved sequence.
37	cd05248	317	22	20.5	28	[                              ------             ]	ADP_GME_SDR_e	ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs. This subgroup contains ADP-L-glycero-D-mannoheptose 6-epimerase, an extended SDR, which catalyzes the NAD-dependent interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose. This subgroup has the canonical active site tetrad and NAD(P)-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX
38	pfam03904	229	66	20.3	6.8E+02	[                    -----------                  ]	DUF334	Domain of unknown function (DUF334). Staphylococcus aureus plasmid proteins with no characterized function.
39	pfam07926	132	42	20.3	2.4E+02	[       ------                                    ]	TPR_MLP1_2	TPR/MLP1/MLP2-like protein. The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.
40	PRK06851	367	18	20.2	3.8E+02	[                   --                            ]	PRK06851	hypothetical protein; Provisional