match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd00175	129	123	99.9	1.5E-22	[        ---------------------                    ]	SNc	Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
2	pfam00565	106	105	99.8	7.3E-22	[          -------------------                    ]	SNase	Staphylococcal nuclease homologue. Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87)
3	COG1525	192	128	99.8	6.5E-21	[       ----------------------                    ]	YncB	Endonuclease YncB, thermonuclease family
4	pfam00932	111	95	99.2	1.1E-10	[                                --------------   ]	LTD	Lamin Tail Domain. The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies.
5	cd11844	56	31	88.5	0.52	[                                  -----          ]	SH3_CAS	Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
6	cd12003	62	21	88.2	0.33	[                                    ---          ]	SH3_EFS	Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member, Embryonal Fyn-associated Substrate. EFS is also called HEFS, CASS3 (Cas scaffolding protein family member 3) or SIN (Src-interacting protein). It was identified based on interactions with the Src kinases, Fyn and Yes. It plays a role in thymocyte development and acts as a negative regulator of T cell proliferation. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
7	cd12001	68	26	87.1	0.36	[                                   ----          ]	SH3_BCAR1	Src homology 3 domain of the CAS (Crk-Associated Substrate) scaffolding protein family member, Breast Cancer Anti-estrogen Resistance 1. BCAR1, also called p130cas or CASS1, is the founding member of the CAS family of scaffolding proteins and was originally identified through its ability to associate with Crk. The name BCAR1 was designated because the human gene was identified in a screen for genes that promote resistance to tamoxifen. It is widely expressed and its deletion is lethal in mice. It plays a role in regulating cell motility, survival, proliferation, transformation, cancer progression, and bacterial pathogenesis. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
8	pfam08206	58	43	86.2	0.25	[   -------                                       ]	OB_RNB	Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
9	cd12002	57	23	83.0	1.5	[                                    ---          ]	SH3_NEDD9	Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member, Neural precursor cell Expressed, Developmentally Down-regulated 9. NEDD9 is also called human enhancer of filamentation 1 (HEF1) or CAS-L (Crk-associated substrate in lymphocyte). It was first described as a gene predominantly expressed in early embryonic brain, and was also isolated from a screen of human proteins that regulate filamentous budding in yeast, and as a tyrosine phosphorylated protein in lymphocytes. It promotes metastasis in different solid tumors. NEDD9 localizes in focal adhesions and associates with FAK and Abl kinase. It also interacts with SMAD3 and the proteasomal machinery which allows its rapid turnover; these interactions are not shared by other CAS proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
10	TIGR03096	135	61	78.0	3.4	[                                -----------      ]	nitroso_cyanin	nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
11	PRK06518	177	34	74.2	2.3	[                       ------                    ]	PRK06518	hypothetical protein; Provisional
12	pfam06586	231	95	74.0	11	[                       -----------------         ]	TraK	TraK protein. This family consists of several TraK proteins from Escherichia coli, Salmonella typhi and Salmonella typhimurium. TraK is known to be essential for pilus assembly but its exact role in this process is unknown.
13	COG2967	126	47	68.9	6.9	[                                  -------        ]	ApaG	Uncharacterized protein affecting Mg2+/Co2+ transport
14	pfam13157	92	37	67.3	13	[                                --------         ]	DUF3992	Protein of unknown function (DUF3992). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 122 amino acids in length. There is a single completely conserved residue T that may be functionally important.
15	pfam04379	90	46	64.0	11	[                                  -------        ]	DUF525	Protein of unknown function (DUF525). Members of this family include the bacterial protein ApaG and the C termini of some F-box proteins (pfam00646). F-box proteins contain a carboxyl-terminal domain that interacts with protein substrates, so this family may be involved in protein-protein interaction. The function of ApaG proteins is unknown, but mutations in the Salmonella typhimurium ApaG homologue corD gives a phenotype of low-level cobalt resistance and decreased magnesium efflux by effects on the CorA magnesium transport system.
16	cd12048	56	25	62.4	3.6	[                                    ----         ]	SH3_DOCK3_B	Src Homology 3 domain of Class B Dedicator of Cytokinesis 3. Dock3, also called modifier of cell adhesion (MOCA), and presenilin binding protein (PBP), is a class B DOCK and is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. It regulates N-cadherin dependent cell-cell adhesion, cell polarity, and neuronal morphology. It promotes axonal growth by stimulating actin polymerization and microtubule assembly. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus; Dock3 is a specific GEFs for Rac. The SH3 domain of Dock3 binds to DHR-2 in an autoinhibitory manner; binding of the scaffold protein Elmo to the SH3 domain of Dock3 exposes the DHR-2 domain and promotes GEF activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
17	PRK05461	127	47	60.4	14	[                                  -------        ]	apaG	CO2+/MG2+ efflux protein ApaG; Reviewed
18	TIGR03035	206	24	59.7	6.6	[          ----                                   ]	trp_arylform	arylformamidase. One of several pathways of tryptophan degradation is as follows: tryptophan 2,3-dioxygenase (1.13.11.11) uses 02 to convert Trp to L-formylkynurenine. Arylformamidase (3.5.1.9) hydrolyzes the product to L-kynurenine and formate. Kynureninase (3.7.1.3) hydrolyzes L-kynurenine to anthranilate plus alanine. Members of the seed alignment for this model are bacterial predicted metal-dependent hydrolases. All are supported as arylformamidase (3.5.1.9) by an operon structure in which kynureninase and/or tryptophan 2,3-dioxygenase genes are adjacent. The members from Bacillus cereus, Pseudomonas aeruginosa and Ralstonia metallidurans were characterized. An example from Pseudomonas fluorescens is given the gene symbol qbsH instead of kynB because of its role in quinolobactin biosynthesis, which begins with tryptophan. All members of this family should be arylformamidase (3.5.1.9).
19	pfam11191	104	33	56.4	42	[      -----                                      ]	DUF2782	Protein of unknown function (DUF2782). This is a bacterial family of proteins whose function is unknown.
20	pfam04314	108	58	51.9	27	[                               ----------        ]	DUF461	Protein of unknown function (DUF461). Putative membrane or periplasmic protein.
21	pfam04744	381	87	50.8	42	[                                 ----------------]	Monooxygenase_B	Monooxygenase subunit B protein. Family of membrane associated monooxygenases (EC 1.13.12.-) which utilize O(2) to oxidize their substrate. Family members include both ammonia and methane monooxygenases involved in the oxidation of their respective substrates. These enzymes are multi-subunit complexes. This family represents the B subunit of the enzyme; the A subunit is thought to contain the active site..
22	PRK13612	113	47	50.2	14	[                     -------                     ]	PRK13612	photosystem II reaction center protein Psb28; Provisional
23	pfam14016	130	44	49.8	25	[                                  ------         ]	DUF4232	Protein of unknown function (DUF4232). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 177 and 242 amino acids in length. Many members of this family are lipoproteins.
24	cd10029	233	81	49.7	5.7	[           -----------------                     ]	UDG_F3_SMUG	SMUG: single-strand-selective monofunctional uracil-DNA glycosylase. SMUG (single-strand-selective monofunctional uracil-DNA glycosylase) is classified as Family 3 of Uracil-DNA glycosylase (UDG) enzymes. SMUG is a DNA repair enzyme that catalyzes the removal of mismatched uracil and its derivatives from DNA to initiate DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, DNA repair enzymes are essential for maintaining the integrity of genetic information. A Family 3 UDG from human was first characterized to remove Uracil from ssDNA, hence the name hSMUG (single-strand-selective monofunctional uracil-DNA glycosylase). However, subsequent research has shown that hSMUG1 and its rat ortholog can remove Uracil and its oxidized pyrimidine derivatives from both, ssDNA and dsDNA. The SMUG targeted mismatched uracil derivatives include 5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU). SMUGs are found in Eubacteria and Eukarya.
25	PRK13559	361	27	47.8	5.9	[                                         ------  ]	PRK13559	hypothetical protein; Provisional
26	TIGR01713	259	20	45.6	25	[                                ---              ]	typeII_sec_gspC	type II secretion system protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
27	COG1188	100	26	43.6	30	[        ----                                     ]	HslR	Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain
28	cd06188	283	20	43.0	12	[                                      ---        ]	NADH_quinone_reductase	Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain.
29	pfam02563	83	34	43.0	30	[                                      --------   ]	Poly_export	Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.
30	cd04223	95	47	42.9	55	[                                 --------        ]	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.
31	pfam08737	401	30	42.9	11	[                                    -----        ]	Rgp1	Rgp1. Rgp1 forms heterodimer with Ric1 (pfam07064) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor.
32	cd05468	141	46	41.3	57	[                                  --------       ]	pVHL	von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronectin and collagen IV within the extracellular matrix. It works to stabilize microtubules and foster the maintenance of primary cilium. It also has been reported to promote the stabilization and activation of p53 in a HIF-independent manner and, in neuronal cells, promote apoptosis by down-regulation of Jun-B.
33	pfam09478	80	42	39.9	53	[                                  ------         ]	CBM49	Carbohydrate binding domain CBM49. This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose.
34	PRK10691	219	51	39.4	54	[ ----------                                      ]	PRK10691	hypothetical protein; Provisional
35	PRK08582	139	45	39.3	61	[        -------                                  ]	PRK08582	hypothetical protein; Provisional
36	pfam14263	124	43	37.1	39	[                                  ------         ]	DUF4354	Domain of unknown function (DUF4354). Several members of this family are annotated as being ATP/GTP-binding site motif A (P-loop) proteins, but this could not be confirmed. The one PDB:3NRF structure solved for this family exhibits an immunoglobin-like beta-sandwich fold. Crystal packing suggests that a tetramer is a significant oligomerization state, and a disulfide bridge is formed between Cys 125 at the C-terminal end of the monomer, and Cys 69.
37	cd12673	81	27	36.9	27	[                       ----                      ]	RRM_BOULE	RNA recognition motif in protein BOULE. This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.
38	cd02788	96	26	35.8	18	[       ---                                       ]	MopB_CT_NDH-1_NuoG2-N7	MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a
39	pfam02170	115	42	35.6	52	[       -------                                   ]	PAZ	PAZ domain. This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
40	cd06186	210	90	34.9	19	[       -----------------                         ]	NOX_Duox_like_FAD_NADP	NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation.
41	cd09218	219	26	33.8	30	[                                      ----       ]	TLP-PA	allergenic/antifungal thaumatin-like proteins: plant and animal homologs. This subfamily is represented by the thaumatin-like proteins (TLPs), Cherry Allergen Pru Av 2 TLP, Peach PpAZ44 TLP (a propylene-induced TLP in abscission), the Caenorhabditis elegans thaumatin family member (thn-6), and other plant and animal homologs. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Due to their inducible expression by environmental stresses such as pathogen/pest attack, drought and cold, plant TLPs are classified as the pathogenesis-related (PR) protein family 5 (PR5). Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun a 3; Arizona cypress, Cup a3; Japanese cedar, Cry j3). TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. It has been proposed that the antifungal activity of plant PR5 proteins relies on the strong electronegative character of this cleft. Some TLPs hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. TLPs within this subfamily contain 16 conserved Cys residues.
42	cd03277	213	74	32.3	24	[ --------------                                  ]	ABC_SMC5_euk	ATP-binding cassette domain of eukaryotic SMC5 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
43	PRK04452	319	76	32.0	41	[            --------------                       ]	PRK04452	acetyl-CoA decarbonylase/synthase complex subunit delta; Provisional
44	COG3111	128	64	31.3	79	[----------                                       ]	YdeI	Predicted periplasmic protein YdeI with OB-fold, BOF family
45	cd12072	57	16	30.8	25	[                    --                           ]	SH3_FNBP1L	Src Homology 3 domain of Formin Binding Protein 1-Like. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. The SH3 domain of the related protein, CIP4, associates with Gapex-5, a Rab31 GEF. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
46	PRK07045	388	63	30.0	18	[                                      -----------]	PRK07045	putative monooxygenase; Reviewed
47	pfam07661	22	13	29.7	24	[                                            --   ]	MORN_2	MORN repeat variant. This family represents an apparent variant of the pfam02493 repeat (personal obs:C Yeats).
48	pfam13473	104	42	28.5	95	[                                  --------       ]	Cupredoxin_1	Cupredoxin-like domain. The cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel.
49	cd11318	391	104	27.4	2.7E+02	[                         ---------------------   ]	AmyAc_bac_fung_AmyA	Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes bacterial and fungal proteins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase.
50	pfam14646	424	56	27.1	1.8E+02	[                                 ---------       ]	MYCBPAP	MYCBP-associated protein family. This family of eukaryotic proteins includes the mammalian MYCBP-associated proteins. These proteins may be synaptic processes and may have a role in spermatogenesis.
51	PRK13254	148	29	26.3	1.1E+02	[       ----                                      ]	PRK13254	cytochrome c-type biogenesis protein CcmE; Reviewed
52	COG2847	151	71	26.2	1.7E+02	[                              ------------       ]	COG2847	Copper(I)-binding protein
53	COG3836	255	23	25.4	29	[                          ---                    ]	HpcH	2-keto-3-deoxy-L-rhamnonate aldolase RhmA
54	cd02775	101	32	24.7	1.3E+02	[       -----                                     ]	MopB_CT	Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site. This hierarchy is of the conserved MopB_CT domain present in many, but not all, MopB homologs.
55	cd05910	455	46	24.7	42	[                                       -------   ]	FACL_like_1	Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions.
56	TIGR03779	410	55	24.2	70	[      ------------                               ]	Bac_Flav_CT_M	Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
57	pfam12988	137	61	24.1	1E+02	[ ----------                                      ]	DUF3872	Domain of unknown function, B. Theta Gene description (DUF3872). Based on Bacteroides thetaiotaomicron gene BT_2593, a conserved protein found in a conjugate transposon. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture.
58	pfam12508	200	29	24.0	90	[      -----                                      ]	DUF3714	Protein of unknown function (DUF3714). This domain family is found in bacteria, and is approximately 200 amino acids in length.
59	pfam13550	164	34	24.0	75	[      -----                                      ]	Phage-tail_3	Putative phage tail protein. This putative domain is found in the large gene transfer agent protein. These produce defective phage like particles. This domain is similar to other phage-tail protein families.
60	pfam00314	212	25	23.8	57	[                                       ---       ]	Thaumatin	Thaumatin family.
61	pfam12272	157	24	23.3	67	[                                -----            ]	DUF3610	Protein of unknown function (DUF3610). This domain family is found in eukaryotes, and is typically between 146 and 160 amino acids in length. There are two conserved sequence motifs: FNN and IDS.
62	COG1990	122	26	22.4	35	[                            ---                  ]	Pth2	Peptidyl-tRNA hydrolase
63	cd11576	378	29	22.1	35	[                                      -----      ]	GH99_GH71_like_2	Uncharacterized glycoside hydrolase family 99-like domain. This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism. The domain may co-occur with other domains involved in the binding/processing of glycans.
64	pfam04797	374	50	22.1	1.2E+02	[                                --------         ]	Herpes_ORF11	Herpesvirus dUTPase protein. This family of proteins are found in Herpesvirus proteins. This family includes proteins called ORF10 and ORF11 amongst others. However, these proteins seem to be related to other dUTPases pfam00692 suggesting that these proteins are also dUTPases (Bateman A pers. obs.).
65	pfam13377	157	38	21.8	1.4E+02	[          ------                                 ]	Peripla_BP_3	Periplasmic binding protein-like domain. Thi domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain likely acts to bind a small molecule ligand that the DNA-binding domain responds to.
66	PRK00249	222	78	21.5	1.3E+02	[      ------------                               ]	flgH	flagellar basal body L-ring protein; Reviewed
67	pfam15161	65	21	21.3	61	[                        ---                      ]	Neuropep_like	Neuropeptide-like. This family contains putative neuropeptides.
68	pfam13349	166	21	20.9	2.9E+02	[---                                              ]	DUF4097	Domain of unknown function (DUF4097).
69	pfam08980	95	18	20.8	71	[        ---                                      ]	DUF1883	Domain of unknown function (DUF1883). This domain is found in a set of hypothetical bacterial proteins.
70	pfam01246	71	15	20.7	53	[                                    ---          ]	Ribosomal_L24e	Ribosomal protein L24e.
71	pfam10636	38	18	20.7	1.3E+02	[        ---                                      ]	hemP	Hemin uptake protein hemP. This is a bacterial family of proteins that are involved in the uptake of the iron source hemin.
72	PRK13848	98	10	20.5	81	[                         --                      ]	PRK13848	conjugal transfer protein TraC; Provisional
73	pfam02560	73	14	20.4	66	[        --                                       ]	Cyanate_lyase	Cyanate lyase C-terminal domain. Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
74	cd09137	186	84	20.1	3.1E+02	[              --------------                     ]	PLDc_PGS1_euk_2	Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases. Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer.
75	pfam13489	157	59	20.1	1.4E+02	[               ---------                         ]	Methyltransf_23	Methyltransferase domain. This family appears to be a methyltransferase domain.