match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd09732	221	216	100.0	6.6E-61	[ --------------------------------                ]	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
2	pfam09455	372	316	100.0	7.2E-54	[ ----------------------------------              ]	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
3	TIGR02221	218	188	100.0	4.5E-45	[ --------------------                            ]	cas_TM1812	CRISPR-associated protein, TM1812 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. This family, represented by TM1812 of Thermotoga maritima, is found also in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, a large plasmid of Synechocystis sp. PCC 6803, and Fibrobacter succinogenes S85.
4	cd09668	214	186	100.0	7.4E-42	[ --------------------                            ]	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
5	cd09671	346	270	99.9	7.9E-21	[ -------------------------------                 ]	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 DxTHG family
6	TIGR02549	21	20	98.7	1.1E-09	[             --                                  ]	CRISPR_DxTHG	CRISPR-associated DxTHG motif protein. This model describes a short region highly conserved between two otherwise substantially different CRISPR-associated (cas) proteins, TIGR02221 and TIGR01987. This region includes the motif
7	TIGR01897	410	184	98.5	2E-06	[ -------------------                             ]	cas_MJ1666	CRISPR-associated protein, MJ1666 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. This model describes a Cas protein about 400 residues in length, found mostly in the Archaea but also in Aquifex.
8	cd09660	394	150	98.5	1.5E-06	[ ----------------                                ]	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 MJ1666 family
9	cd09728	400	153	98.5	3.1E-06	[ ----------------                                ]	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 DxTHG family
10	pfam09670	379	255	97.8	0.027	[    ------------------------------               ]	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).
11	COG1517	406	133	97.5	0.00072	[----------------                                 ]	Csx1	CRISPR/Cas system-associated protein Csx1, contains CARF domain
12	cd09747	378	255	97.4	0.035	[    ------------------------------               ]	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
13	pfam09002	379	121	96.8	0.025	[     ---------------                             ]	DUF1887	Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins.
14	TIGR02710	380	142	95.7	0.34	[    -----------------                            ]	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).
15	cd09702	378	150	95.4	0.11	[    ------------------                           ]	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
16	TIGR01884	203	112	90.6	2.4	[   --------------                                ]	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.
17	pfam09651	136	87	90.5	2.5	[     ----------                                  ]	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.
18	cd09655	198	77	88.5	3.3	[        ---------                                ]	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
19	cd09742	183	101	87.5	4.1	[    -----------                                  ]	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
20	pfam09623	225	122	85.4	11	[    -------------                                ]	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.
21	TIGR03642	124	105	84.6	4.3	[   ------------                                  ]	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.
22	cd04223	95	16	74.1	1.6	[             -                                   ]	N2OR_C	The C-terminal cupredoxin domain of Nitrous-oxide reductase. Nitrous-oxide reductase participates in nitrogen metabolism and catalyzes the last step in dissimilatory nitrate reduction, the two-electron reduction of N2O to N2. It contains copper ions as cofactors in the form of a binuclear CuA center at the site of electron entry and a tetranuclear CuZ centre at the active site. The C-terminus of Nitrous-oxide reductase is a cupredoxin domain.
23	cd09723	132	106	73.3	16	[   ------------                                  ]	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
24	cd09741	219	118	61.4	1E+02	[    -------------                                ]	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
25	TIGR01357	344	139	60.6	70	[    ----------------                             ]	aroB	3-dehydroquinate synthase. This model represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids.
26	TIGR03504	44	27	45.6	33	[                              --                 ]	FimV_Cterm	FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
27	COG0788	287	120	43.0	20	[     -------------                               ]	PurU	Formyltetrahydrofolate hydrolase
28	pfam13041	50	22	41.4	33	[                              --                 ]	PPR_2	PPR repeat family. This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR.
29	PRK06027	286	118	38.6	59	[     -------------                               ]	purU	formyltetrahydrofolate deformylase; Reviewed
30	TIGR02619	149	93	38.6	1.9E+02	[     -----------                                 ]	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.
31	TIGR03706	300	71	36.0	1.5E+02	[     ---------                                   ]	exo_poly_only	exopolyphosphatase. It appears that a single enzyme may act as both exopolyphosphatase (Ppx) and guanosine pentaphosphate phosphohydrolase (GppA) in a number of species. Members of the seed alignment use to define this exception-level model are encoded adjacent to a polyphosphate kinase 1 gene, and the trusted cutoff is set high enough (425) that no genome has a second hit. Therefore all members may be presumed to at least share exopolyphospatase activity, and may lack GppA activity. GppA acts in the stringent response.
32	cd00006	122	55	34.7	1.5E+02	[        ------                                   ]	PTS_IIA_man	PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
33	cd07941	273	115	33.4	38	[  --------------                                 ]	DRE_TIM_LeuA3	Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown. Members of this family have an N-terminal TIM barrel domain that belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM"td>
34	TIGR00246	153	95	33.1	2.5E+02	[      -----------                                ]	tRNA_RlmH_YbeA	rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
35	pfam10243	506	59	32.6	88	[                         -------                 ]	MIP-T3	Microtubule-binding protein MIP-T3. This protein, which interacts with both microtubules and TRAF3 (tumor necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.
36	TIGR04246	578	17	31.5	23	[             -                                   ]	nitrous_NosZ_Gp	nitrous-oxide reductase, Sec-dependent. This model represents the nitrous-oxide reductase protein NosZ as characterized in Geobacillus thermodenitrificans. In contrast to the related form in Pseudomonas stutzeri, this version lacks a recognizable twin-arginine translocation (TAT) signal at the N-terminus. Consequently, its accessory protein may differ. Some members of this family have an additional cytochrome c-like domain at the C-terminus.
37	COG0248	492	72	31.4	1.8E+02	[     ---------                                   ]	GppA	Exopolyphosphatase/pppGpp-phosphohydrolase
38	pfam13374	42	29	30.8	1.3E+02	[                              --                 ]	TPR_10	Tetratricopeptide repeat.
39	pfam08588	56	41	29.2	50	[             ----                                ]	DUF1769	Protein of unknown function (DUF1769). Family of fungal protein with unknown function.
40	TIGR03302	235	31	28.5	2.8E+02	[                             ---                 ]	OM_YfiO	outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
41	TIGR00756	35	23	27.4	97	[                              --                 ]	PPR	pentatricopeptide repeat domain (PPR motif). This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
42	PRK14953	486	124	26.3	7.4E+02	[    ------------------                           ]	PRK14953	DNA polymerase III subunits gamma and tau; Provisional
43	pfam07719	34	26	25.7	1.5E+02	[                              --                 ]	TPR_2	Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515.
44	PRK12544	206	50	25.6	55	[       ------                                    ]	PRK12544	RNA polymerase sigma factor; Provisional
45	pfam04100	375	111	25.3	4.6E+02	[                  -------------                  ]	Vps53_N	Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events.
46	pfam01535	31	23	25.0	1.1E+02	[                              --                 ]	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.
47	COG2893	143	53	24.7	1.7E+02	[        ------                                   ]	ManX	Phosphotransferase system, mannose/fructose-specific component IIA
48	COG4105	254	30	24.3	3E+02	[                              --                 ]	BamD	Outer membrane protein assembly factor BamD, BamD/ComL family
49	pfam12854	34	25	24.3	84	[                              --                 ]	PPR_1	PPR repeat. This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known.
50	cd12831	287	72	23.6	5.3E+02	[                       --------                  ]	TmCorA-like_u2	Uncharacterized bacterial subfamily of the Thermotoga maritima CorA-like family. This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the TmCorA-like family are found in all three kingdoms of life. It is a functionally diverse family which includes the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and three Saccharomyces cerevisiae proteins: two located in the plasma membrane: the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport.
51	cd15474	352	73	23.3	8.3E+02	[                         -------                 ]	Myo5p-like_CBD_fungal	cargo binding domain of fungal myosin V -like proteins. Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. In case of Myo4 it has been shown to bind to the adapter protein She3p (Swi5p-dependent HO expression 3), which in turn anchors myosin 4 to its cargos, zip-coded mRNP (messenger ribonucleoprotein particles) and tER (tubular endoplasmic reticulum). Myo 2 binds to Vac17, vacuole-specific cargo adaptor, and Mmr1, mitochondria-specific cargo adaptor. Both adaptors bind competitivly at the same site.
52	pfam01418	77	49	22.1	3E+02	[                            ------               ]	HTH_6	Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is Escherichia coli rpiR, a regulator of the expression of rpiB gene.
53	pfam13428	44	26	21.9	1.8E+02	[                              --                 ]	TPR_14	Tetratricopeptide repeat.
54	pfam15463	139	71	21.9	4.9E+02	[                   --------                      ]	ECM11	Extracellular mutant protein 11. ECM11 is a family of largely fungal proteins. ECM11 interacts with Cdc6, an essential protein involved in the initiation of DNA replication, and is a nuclear protein involved in maintaining chromatin structure. It was previously identified as a protein involved in yeast cell wall biogenesis and organisation, but is also found to be required in meiosis where its function is related to DNA replication and crossing-over.
55	TIGR02386	1140	119	21.7	2.7E+02	[             --------------                      ]	rpoC_TIGR	DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
56	COG4006	278	87	21.5	3.9E+02	[     ----------                                  ]	COG4006	CRISPR/Cas system-associated protein Csm6, COG1517 family
57	pfam15112	307	127	20.6	8.6E+02	[                   -------------                 ]	DUF4559	Domain of unknown function (DUF4559). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. This family includes human protein CXorf38.
58	pfam01934	120	45	20.4	94	[                                            -----]	DUF86	Protein of unknown function DUF86. The function of members of this family is unknown.