match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam09002	379	335	100.0	1E-33	[-------------------------------------------------]	DUF1887	Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.
2	pfam09670	379	103	97.9	5.1E-05	[   ---------------                               ]	Cas_Cas02710	CRISPR-associated protein (Cas_Cas02710). Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
3	cd09747	378	103	97.8	7.3E-05	[   ---------------                               ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as Cas02710 family
4	TIGR02710	380	96	97.6	0.00014	[   --------------                                ]	TIGR02710	CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
5	cd09702	378	86	96.7	0.0027	[   ------------                                  ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TIGR02710 family
6	cd09723	132	110	96.4	0.027	[---------------                                  ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as csx13 family
7	TIGR03642	124	88	95.6	0.13	[   ------------                                  ]	cas_csx14	CRISPR-associated protein, Csx14 family. This model describes a protein N-terminal protein sequence domain strictly associated with CRISPR and CRISPR-associated protein systems. This model and TIGR02584 identify two separate clades from a larger homology domain family, both CRISPR-associated, while other homologs are found that may not be. Members are found in bacteria that include Pelotomaculum thermopropionicum SI, Thermoanaerobacter tengcongensis MB4, and Roseiflexus sp. RS-1, and in archaea that include Thermoplasma volcanium, Picrophilus torridus, and Methanospirillum hungatei. The molecular function is unknown.
8	pfam09651	136	99	95.4	0.31	[   --------------                                ]	Cas_APE2256	CRISPR-associated protein (Cas_APE2256). This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.
9	cd09742	183	107	95.2	0.26	[   ---------------                               ]	Csm6_III-A	CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems; also known as APE2256 family
10	pfam09623	225	131	82.6	13	[-----------------                                ]	Cas_NE0113	CRISPR-associated protein NE0113 (Cas_NE0113). Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.
11	cd09655	198	88	81.8	18	[   ------------                                  ]	CasRa_I-A	CRISPR/Cas system-associated transcriptional regulator CasRa. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system
12	cd09741	219	43	77.8	15	[           ------                                ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family
13	pfam07788	70	54	77.8	5.1	[                                    -------      ]	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.
14	TIGR01884	203	86	74.4	32	[   ------------                                  ]	cas_HTH	CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
15	TIGR02619	149	107	73.5	34	[   --------------                                ]	TIGR02619	putative CRISPR-associated protein, APE2256 family. This model represents a conserved domain of about 150 amino acids found in at least five archaeal species and three bacterial species, exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In six of eight species, the member of this family is in the vicinity of a CRISPR/Cas locus.
16	PRK14677	107	60	71.0	8.1	[                                    -------      ]	PRK14677	hypothetical protein; Provisional
17	COG4006	278	51	64.6	49	[           -------                               ]	COG4006	CRISPR/Cas system-associated protein Csm6, COG1517 family
18	cd09732	221	93	63.7	65	[  -------------                                  ]	Csx1_III-U	CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TM1812 family
19	PRK14683	122	23	62.3	7.9	[                                    --           ]	PRK14683	hypothetical protein; Provisional
20	PRK12497	119	24	58.5	11	[                                   ---           ]	PRK12497	hypothetical protein; Reviewed
21	cd09694	181	104	58.5	91	[   ---------------                               ]	Csm6_III-A	CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems
22	pfam03008	95	23	55.3	13	[                                    --           ]	DUF234	Archaea bacterial proteins of unknown function.
23	pfam01870	89	33	52.7	18	[                                    ----         ]	Hjc	Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.
24	pfam13588	110	54	51.9	36	[                                   --------      ]	HSDR_N_2	Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
25	pfam08378	111	24	45.1	19	[                                   ---           ]	NERD	Nuclease-related domain. The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.
26	cd00523	123	39	44.8	22	[                                   -----         ]	archeal_HJR	Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
27	COG0792	114	24	39.7	30	[                                   ---           ]	YraN	Predicted endonuclease distantly related to archaeal Holliday junction resolvase
28	pfam09455	372	98	37.9	98	[  -------------                                  ]	Cas_DxTHG	CRISPR-associated (Cas) DxTHG family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. The family describes Cas proteins of about 400 residues that include the motif
29	PRK14686	119	24	37.7	35	[                                   ---           ]	PRK14686	hypothetical protein; Provisional
30	COG1591	137	23	37.6	32	[                                    --           ]	COG1591	Holliday junction resolvase, archaeal type
31	COG3340	224	120	36.4	2.4E+02	[------------------                               ]	PepE	Peptidase E
32	pfam13635	154	25	35.0	48	[                                   ---           ]	DUF4143	Domain of unknown function (DUF4143). This domain is almost always found C-terminal to an ATPase core family.
33	cd08549	332	110	34.3	2.9E+02	[-----------------                                ]	G1PDH_related	Glycerol-1-phosphate_dehydrogenase and related proteins. Bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. The proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids.
34	PRK14681	158	21	33.8	55	[                                    --           ]	PRK14681	hypothetical protein; Provisional
35	PRK14678	120	23	33.2	68	[                                    --           ]	PRK14678	hypothetical protein; Provisional
36	pfam04313	142	38	33.1	97	[                                   -----         ]	HSDR_N	Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
37	pfam06956	183	91	32.8	86	[  -------------                                  ]	RtcR	Regulator of RNA terminal phosphate cyclase. RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain pfam00158 in the central region of the protein sequence.
38	cd01719	70	45	28.4	1.4E+02	[                               -------           ]	Sm_G	Sm protein G. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure.
39	PRK14689	124	20	27.0	57	[                                    --           ]	PRK14689	hypothetical protein; Provisional
40	PRK14682	117	23	26.1	76	[                                    --           ]	PRK14682	hypothetical protein; Provisional
41	cd06356	334	96	25.4	59	[--------------                                   ]	PBP1_Amide_Urea_BP_like	Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
42	PRK14680	134	25	22.8	94	[                                   ---           ]	PRK14680	hypothetical protein; Provisional
43	cd04895	72	13	21.9	55	[                               --                ]	ACT_ACR_1	ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
44	pfam09572	251	25	21.1	1.3E+02	[                                   ---           ]	RE_XamI	XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
45	COG5493	231	56	20.7	1.3E+02	[                                   --------      ]	COG5493	Uncharacterized protein
46	PRK14675	125	22	20.6	1E+02	[                                    --           ]	PRK14675	hypothetical protein; Provisional