Query 036513
Match_columns 69
No_of_seqs 49 out of 51
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 02:48:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14631 FancD2: Fanconi anaem 99.9 1.2E-24 2.5E-29 186.6 -1.4 59 1-59 1366-1424(1426)
2 KOG4712 Uncharacterized conser 99.5 1.5E-15 3.3E-20 130.2 0.0 57 1-57 1266-1323(1335)
3 cd08684 C2A_Tac2-N C2 domain f 69.2 3.2 6.8E-05 28.4 1.5 42 1-43 51-93 (103)
4 PF09035 Tn916-Xis: Excisionas 56.9 11 0.00023 23.4 2.1 19 7-25 29-48 (67)
5 PF04697 Pinin_SDK_N: pinin/SD 48.2 15 0.00033 26.0 2.0 14 26-39 74-87 (134)
6 PF07683 CobW_C: Cobalamin syn 41.6 3.8 8.2E-05 24.2 -1.6 18 5-22 28-45 (94)
7 KOG0749 Mitochondrial ADP/ATP 37.2 20 0.00043 28.3 1.3 24 5-28 33-79 (298)
8 KOG3593 Predicted receptor-lik 37.1 16 0.00034 29.4 0.8 26 34-59 263-290 (355)
9 PF03974 Ecotin: Ecotin; Inte 30.2 22 0.00049 24.3 0.6 19 16-34 43-61 (128)
10 PF14112 DUF4284: Domain of un 29.8 36 0.00079 22.4 1.5 36 20-55 3-49 (122)
11 cd03589 CLECT_CEL-1_like C-typ 29.5 57 0.0012 19.8 2.3 17 16-33 64-80 (137)
12 smart00833 CobW_C Cobalamin sy 27.4 5.6 0.00012 23.2 -2.4 12 5-16 28-39 (92)
13 PF04871 Uso1_p115_C: Uso1 / p 24.8 43 0.00094 22.6 1.2 7 33-39 111-117 (136)
No 1
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=99.88 E-value=1.2e-24 Score=186.57 Aligned_cols=59 Identities=46% Similarity=0.749 Sum_probs=24.5
Q ss_pred CchhhhhhHHHHhhCCCcceeeecccccCCCCCcEeeeccccCCCCCcchhcccccCCC
Q 036513 1 MERFLFRVKALLHTKSSGCTFWMGNLKHKDLMGQVVSSQAYVDDLSNNVEEDLEGAVHE 59 (69)
Q Consensus 1 LE~fvfrVKalL~~n~c~~AFwmGNLKnkDL~G~~I~SQ~~~~d~~d~~eed~e~~~~~ 59 (69)
||+|||||||||++|+|++||||||||||||+|++|+||.+.++++|++|+|.+++..+
T Consensus 1366 lE~~v~~VKa~L~~n~c~~AFw~GnLKnrdL~G~eI~sq~~~~~~~d~~e~~~~~~~~~ 1424 (1426)
T PF14631_consen 1366 LETFVFRVKAMLVANNCSEAFWMGNLKNRDLDGEEILSQRSSEDDEDESEEDVESEVSE 1424 (1426)
T ss_dssp HHHHHHHHHHHH-SS--HHHHHHHHHTS-------------------------------
T ss_pred HHHHHHHHHHHHHHCCchhhhhhcccccCCCCCCeeeCCCCCccccccccccccchhcc
Confidence 69999999999999999999999999999999999999999888888777777666544
No 2
>KOG4712 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.52 E-value=1.5e-15 Score=130.24 Aligned_cols=57 Identities=33% Similarity=0.624 Sum_probs=52.4
Q ss_pred CchhhhhhHHHHhhCCCcceeeecccccCCCCCcEeeec-cccCCCCCcchhcccccC
Q 036513 1 MERFLFRVKALLHTKSSGCTFWMGNLKHKDLMGQVVSSQ-AYVDDLSNNVEEDLEGAV 57 (69)
Q Consensus 1 LE~fvfrVKalL~~n~c~~AFwmGNLKnkDL~G~~I~SQ-~~~~d~~d~~eed~e~~~ 57 (69)
+|..+.+||||++.|+|.+|||+||||||||+|+.|+|| +|.++++|+.++.+-++.
T Consensus 1266 ~E~~~~~~~a~~~~n~c~~aF~~G~lK~rdl~G~II~sQ~A~~d~s~dE~~~~~s~~~ 1323 (1335)
T KOG4712|consen 1266 LELLVCRVKAMLTLNNCREAFWLGNLKNRDLQGEIIKSQNATADESEDEMSSQASKSK 1323 (1335)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHhccccccccccchhhccccccccchhHHHHhhccCc
Confidence 478899999999999999999999999999999999999 889999999999984433
No 3
>cd08684 C2A_Tac2-N C2 domain first repeat found in Tac2-N (Tandem C2 protein in Nucleus). Tac2-N contains two C2 domains and a short C-terminus including a WHXL motif, which are key in stabilizing transport vesicles to the plasma membrane by binding to a plasma membrane. However unlike the usual carboxyl-terminal-type (C-type) tandem C2 proteins, it lacks a transmembrane domain, a Slp-homology domain, and a Munc13-1-interacting domain. Homology search analysis indicate that no known protein motifs are located in its N-terminus, making Tac2-N a novel class of Ca2+-independent, C-type tandem C2 proteins. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphos
Probab=69.19 E-value=3.2 Score=28.35 Aligned_cols=42 Identities=24% Similarity=0.358 Sum_probs=33.1
Q ss_pred CchhhhhhHHHHhhCCCcceeeecc-cccCCCCCcEeeeccccC
Q 036513 1 MERFLFRVKALLHTKSSGCTFWMGN-LKHKDLMGQVVSSQAYVD 43 (69)
Q Consensus 1 LE~fvfrVKalL~~n~c~~AFwmGN-LKnkDL~G~~I~SQ~~~~ 43 (69)
+|+|||+|| +.......=.|-+=| .|-|-.-|.-.+|+.+..
T Consensus 51 ~ETFVFqi~-l~qL~~V~L~fsv~~~~~RKe~iG~~sL~l~s~g 93 (103)
T cd08684 51 METFVFAIK-LQNLQTVRLVFKIQTQTPRKRTIGECSLSLRTLS 93 (103)
T ss_pred HHHHHHHHH-HhhccceEEEEEeeccCCccceeeEEEeecccCC
Confidence 599999996 677778877787665 567788899999998644
No 4
>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.
Probab=56.89 E-value=11 Score=23.39 Aligned_cols=19 Identities=21% Similarity=0.660 Sum_probs=13.7
Q ss_pred hhHHHH-hhCCCcceeeecc
Q 036513 7 RVKALL-HTKSSGCTFWMGN 25 (69)
Q Consensus 7 rVKalL-~~n~c~~AFwmGN 25 (69)
++..|+ ..++|.-.+|+||
T Consensus 29 klr~l~~~~~~~~f~~~~G~ 48 (67)
T PF09035_consen 29 KLRELAEENPDCPFVLWIGN 48 (67)
T ss_dssp HHHHHHHH-TT-SSEEEETT
T ss_pred HHHHHHHhCCCCCEEEEECC
Confidence 355677 6789999999998
No 5
>PF04697 Pinin_SDK_N: pinin/SDK conserved region; InterPro: IPR006787 This conserved region is found at the N-terminal of the member proteins. It is located adjacent and N-terminal to the pinin/SKD/memA domain IPR006786 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque [, ]. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=48.17 E-value=15 Score=26.03 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=11.6
Q ss_pred cccCCCCCcEeeec
Q 036513 26 LKHKDLMGQVVSSQ 39 (69)
Q Consensus 26 LKnkDL~G~~I~SQ 39 (69)
-|++|+.|..+..+
T Consensus 74 ~k~rd~~g~~~rl~ 87 (134)
T PF04697_consen 74 SKRRDISGAFSRLS 87 (134)
T ss_pred ccccCCCcceeEec
Confidence 47889999888877
No 6
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=41.64 E-value=3.8 Score=24.23 Aligned_cols=18 Identities=11% Similarity=0.224 Sum_probs=12.2
Q ss_pred hhhhHHHHhhCCCcceee
Q 036513 5 LFRVKALLHTKSSGCTFW 22 (69)
Q Consensus 5 vfrVKalL~~n~c~~AFw 22 (69)
|||+|+++..-++...+.
T Consensus 28 vlR~KG~v~~~~~~~~~~ 45 (94)
T PF07683_consen 28 VLRAKGIVWVADGPRRLV 45 (94)
T ss_dssp EEEEEEEE-BTT-SEEEE
T ss_pred EEEEEEEEEeCCcCeEEE
Confidence 799999999888744443
No 7
>KOG0749 consensus Mitochondrial ADP/ATP carrier proteins [Energy production and conversion]
Probab=37.24 E-value=20 Score=28.33 Aligned_cols=24 Identities=42% Similarity=0.692 Sum_probs=17.7
Q ss_pred hhhhHHHHhhCC--------------C---------cceeeeccccc
Q 036513 5 LFRVKALLHTKS--------------S---------GCTFWMGNLKH 28 (69)
Q Consensus 5 vfrVKalL~~n~--------------c---------~~AFwmGNLKn 28 (69)
|=|||-||+.-+ | --+||-||+-|
T Consensus 33 IERVKLlLQ~Q~~~~~~~~~YkGi~Dc~~r~~~eqG~~sfWRGN~an 79 (298)
T KOG0749|consen 33 IERVKLLLQVQDSEIAADKRYKGIVDCFVRIPKEQGFLSFWRGNLAN 79 (298)
T ss_pred HHHHHHHHHhccchhhhccCccchhheeeechhhhhhhheecccccc
Confidence 348888888755 1 24799999977
No 8
>KOG3593 consensus Predicted receptor-like serine/threonine kinase [Signal transduction mechanisms]
Probab=37.08 E-value=16 Score=29.45 Aligned_cols=26 Identities=23% Similarity=0.228 Sum_probs=13.3
Q ss_pred cEeeeccc--cCCCCCcchhcccccCCC
Q 036513 34 QVVSSQAY--VDDLSNNVEEDLEGAVHE 59 (69)
Q Consensus 34 ~~I~SQ~~--~~d~~d~~eed~e~~~~~ 59 (69)
+.|.||+. .+|+++++||..|++++|
T Consensus 263 ~~v~~~~~~v~ed~e~~eeea~Eee~~p 290 (355)
T KOG3593|consen 263 ETVLSSSTMVSEDSESDEEEAPEEETEP 290 (355)
T ss_pred hhhhccccccccccccccccchhhhcCC
Confidence 45666755 334444444444555555
No 9
>PF03974 Ecotin: Ecotin; InterPro: IPR023189 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This entry represents proteinase inhibitors that belong to MEROPS inhibitor family I11, clan IN. Ecotins are dimeric periplasmic proteins from Escherichia coli and related Gram-negative bacteria that have been shown to be potent inhibitors of many trypsin-fold serine proteases of widely varying substrate specificity, which belong to MEROPS peptidase family S1 (IPR001254 from INTERPRO) []. Phylogenetic analysis suggested that ecotin has an exogenous target, possibly neutrophil elastase. Ecotin from E. coli, Yersinia pestis, and Pseudomonas aeruginosa, all species that encounter the mammalian immune system inhibit neutrophil elastase strongly while ecotin from the plant pathogen Pantoea citrea inhibits neutrophil elastase 1000-fold less than the others []. They all potently inhibit pancreatic digestive peptidases trypsin and chymotrypsin, while showing more variable inhibition of the blood peptidases Factor Xa, thrombin, and urokinase-type plasminogen activator. This entry represents the structural domain of ecotin, consisting of 8 beta strands organised in 2 sheets.; PDB: 1P0S_E 1IFG_A 1FI8_E 1EZU_A 1N8O_E 1ECZ_A 1AZZ_C 1XX9_C 1SLW_A 1SLX_A ....
Probab=30.20 E-value=22 Score=24.27 Aligned_cols=19 Identities=32% Similarity=0.401 Sum_probs=15.6
Q ss_pred CCcceeeecccccCCCCCc
Q 036513 16 SSGCTFWMGNLKHKDLMGQ 34 (69)
Q Consensus 16 ~c~~AFwmGNLKnkDL~G~ 34 (69)
+|-..|..|+|..++|+|=
T Consensus 43 DCN~~~l~G~le~k~l~Gw 61 (128)
T PF03974_consen 43 DCNRYFLGGKLEEKTLQGW 61 (128)
T ss_dssp -SSBEEEEEEEEEEE-TTT
T ss_pred eeccceEccEEEEeeeCCC
Confidence 5888999999999999993
No 10
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=29.76 E-value=36 Score=22.38 Aligned_cols=36 Identities=31% Similarity=0.448 Sum_probs=23.3
Q ss_pred eeeecccccC-----------CCCCcEeeeccccCCCCCcchhcccc
Q 036513 20 TFWMGNLKHK-----------DLMGQVVSSQAYVDDLSNNVEEDLEG 55 (69)
Q Consensus 20 AFwmGNLKnk-----------DL~G~~I~SQ~~~~d~~d~~eed~e~ 55 (69)
.+|+||.+.. |-.|+.|.||-..+=.=+--+||--+
T Consensus 3 siWiG~f~s~~el~~Y~e~~Ydedgd~i~s~F~~df~i~~yDeDfie 49 (122)
T PF14112_consen 3 SIWIGNFKSEDELEEYFEIDYDEDGDSIPSQFCKDFGIDYYDEDFIE 49 (122)
T ss_pred EEEEecCCCHHHHHHHhCccccCCCCcccChHHHHcCCCccCchhcE
Confidence 5899998865 46888888886544433333455433
No 11
>cd03589 CLECT_CEL-1_like C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CEL-1 CTLD binds three calcium ions and has a high specificity for N-acteylgalactosamine (GalNAc). CEL-1 exhibits strong cytotoxicity which is inhibited by GalNAc. This protein may play a role as a toxin defending against predation. Echinoidin is found in the coelomic fluid of the sea urchin and is specific for GalBeta1-3GalNAc. Echinoidin has a cell adhesive activity towards human cancer cells which is not mediated through the CTLD. Both CEL-1 and Echinoidin are multimeric proteins comprised of multiple dimers linked by disulfide bonds.
Probab=29.54 E-value=57 Score=19.84 Aligned_cols=17 Identities=24% Similarity=0.673 Sum_probs=10.6
Q ss_pred CCcceeeecccccCCCCC
Q 036513 16 SSGCTFWMGNLKHKDLMG 33 (69)
Q Consensus 16 ~c~~AFwmGNLKnkDL~G 33 (69)
.-...|||| |..+.-.|
T Consensus 64 ~~~~~~WiG-l~~~~~~~ 80 (137)
T cd03589 64 DTPYGLWIG-LHDRTSEG 80 (137)
T ss_pred CCCCcEEEe-eecCCccC
Confidence 345789999 65444333
No 12
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=27.44 E-value=5.6 Score=23.22 Aligned_cols=12 Identities=25% Similarity=0.445 Sum_probs=9.8
Q ss_pred hhhhHHHHhhCC
Q 036513 5 LFRVKALLHTKS 16 (69)
Q Consensus 5 vfrVKalL~~n~ 16 (69)
|||+|+++...+
T Consensus 28 i~R~KG~v~~~~ 39 (92)
T smart00833 28 VLRAKGFFWLAS 39 (92)
T ss_pred eEEEEEEEEeCC
Confidence 899999997643
No 13
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=24.78 E-value=43 Score=22.63 Aligned_cols=7 Identities=43% Similarity=0.639 Sum_probs=3.7
Q ss_pred CcEeeec
Q 036513 33 GQVVSSQ 39 (69)
Q Consensus 33 G~~I~SQ 39 (69)
|+.|++=
T Consensus 111 G~eVSdd 117 (136)
T PF04871_consen 111 GEEVSDD 117 (136)
T ss_pred CCCccCC
Confidence 5555543
Done!