Query 041780
Match_columns 422
No_of_seqs 163 out of 379
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 10:34:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041780.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041780hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03080 DUF239: Domain of unk 100.0 4.7E-83 1E-87 612.6 25.2 225 186-415 1-229 (229)
2 PF14365 DUF4409: Domain of un 100.0 1.2E-39 2.5E-44 282.6 7.1 117 48-181 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 67.2 9.1 0.0002 28.2 3.9 37 278-319 15-51 (55)
4 PF14604 SH3_9: Variant SH3 do 40.7 48 0.001 24.0 3.9 21 298-319 27-47 (49)
5 PF00018 SH3_1: SH3 domain; I 34.8 71 0.0015 22.6 3.9 24 293-317 24-48 (48)
6 PF13956 Ibs_toxin: Toxin Ibs, 31.3 28 0.0006 20.8 1.0 14 1-14 1-14 (19)
7 PHA03072 putative viral membra 27.8 84 0.0018 29.6 4.0 25 31-63 81-106 (190)
8 PF13987 YedD: YedD-like prote 22.9 35 0.00076 29.3 0.6 23 39-61 22-45 (111)
9 PF03356 Pox_LP_H2: Viral late 22.6 1.2E+02 0.0026 28.6 4.0 25 31-63 81-106 (189)
10 PHA02677 hypothetical protein; 20.0 93 0.002 26.9 2.5 16 5-20 2-17 (108)
No 1
>PF03080 DUF239: Domain of unknown function (DUF239); InterPro: IPR004314 This is a family of plant proteins, a small number of which are putative peptidases (see for example Q9XIN9 from SWISSPROT). However, the structure of the protein PDB3:3eu8 has an alpha-alpha toroid fold and is similar to a glucoamylase, PDB:1ayx. Such glucoamylases are involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity. Further structural comparisons also show relationships with other glycohydrolases.
Probab=100.00 E-value=4.7e-83 Score=612.56 Aligned_cols=225 Identities=46% Similarity=0.912 Sum_probs=214.4
Q ss_pred EeeeEEEEeeecCCcCCCCCceeEEEEeccCC-CCCcceEEEEEEEcccccCCCceEEEEEEeecCcccCcccCCCCCce
Q 041780 186 YIGAQGDINVWNPRVESPDDYTTAQIWLKGGP-GDNFESVEGGWVVNPKLYGDKLTRLFVYWTKDSYKSTGCFDAICSGF 264 (422)
Q Consensus 186 ~~Ga~a~inV~~p~v~~~~q~S~sqiwv~~g~-~~~~n~IeaGW~V~P~lYgD~~~rlf~yWt~d~y~~tGCyNl~CpGF 264 (422)
|||++|+||||+|+|+.++|||++||||++++ .+.+|+|||||+|+|+||||++||||+|||+|+|++||||||+||||
T Consensus 1 y~G~~a~i~v~~p~v~~~~q~S~~~i~i~~g~~~~~~~~i~~GW~V~P~lygd~~~~lf~~wt~d~~~~tgCyN~~CpGF 80 (229)
T PF03080_consen 1 YYGARATISVWNPKVQQPDQFSLSQIWISNGSDDDSLNSIEAGWQVYPSLYGDSRTRLFVYWTADGYQKTGCYNLDCPGF 80 (229)
T ss_pred CeeeEEEEECcCCccCCccceeheeEEEEecCCCCCCcEEEEeeeccccccCCCceEEEEEEEccCCCCcceeCCCCCcE
Confidence 79999999999999997779999999999999 78899999999999999999999999999999999999999999999
Q ss_pred EEecc-cccCccccccccCCCceeEEeEEEEEecCCCCeEEEecCceeeeeecchhchhcccCceEEEEeeEEecCCCCC
Q 041780 265 VQTGQ-VALGAAIGPWSISEGPQYYLPVGIYLDPNTKNWWLKVNGNIVVGYWPGSLFSYLSYSAILVEWGGQVYSPNVKK 343 (422)
Q Consensus 265 VQvs~-i~lG~~i~pvS~~~G~q~~i~i~I~kD~~tgnWWL~~~~~~~IGYwP~sLF~~l~~~A~~V~wGGeV~~~~~~~ 343 (422)
||+++ |+||++|+|+|+++|+|++|+|+|+||+.+|||||+++++ .|||||++||++|+++|+.|+|||||++++
T Consensus 81 Vq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~~~-~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~--- 156 (229)
T PF03080_consen 81 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGGE-PIGYWPKSLFTSLADGATEVEWGGEVYSPP--- 156 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEecc-eeeeehHHhhhhhhcCceEEEEEEEEeCCC---
Confidence 99999 9999999999999999999999999999999999999886 899999999999999999999999999985
Q ss_pred CCCCCCCCCCCcCCCCCCCccEEEeecEEEcCCCCccCCC--cceecccCCcceeEeecccCcCcCCeEEEeCC
Q 041780 344 TPHTKTAMGSGSFSHGLQGSACSIEHVRIIDFSLQLKYPQ--WVGTWADEYYCYDAYNYVKGYTTEPVFFFGGP 415 (422)
Q Consensus 344 ~~~~sp~MGSG~fp~~g~~~Aay~~ni~ivd~~~~~~~p~--~~~~~~d~~~CY~v~~~~~~~~~g~~f~yGGP 415 (422)
++|++|||||||||++++++|||||||+++|.++....+. .+++++|+|+||++..... .+||.+||||||
T Consensus 157 ~~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~-~~~g~~f~yGGP 229 (229)
T PF03080_consen 157 GRHTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGD-GDWGYYFFYGGP 229 (229)
T ss_pred CCCCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccC-CCcccEEEeeCC
Confidence 3589999999999999999999999999999999888774 4778999999999998733 679999999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=1.2e-39 Score=282.56 Aligned_cols=117 Identities=45% Similarity=0.716 Sum_probs=94.0
Q ss_pred eEEcCCCCeEeeeecCCCCCCCCCCCCCCCccCCCCCCCCcccccccccCCCCccceeecccCCCCCCCceeeeecChhh
Q 041780 48 SIKSEDGDIIDCVDIYKQPALDHPALKNHTIQLSPSFDIPAEKVDRRNESSRLPVTIQTWQKSGSCPNGTVPIRRIRRQD 127 (422)
Q Consensus 48 si~s~dGdiiDCVdi~kQPAfdHPlLKnH~iQ~~Ps~~p~~~~~~~~~~~~~~~~~~q~w~~~~~CP~GTVPIrR~t~~d 127 (422)
||+|+|||||||||||||||||||||| +|||+|++.|+..... ...+..+...+|+|+++++||+|||||||+++||
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK--~~q~~Ps~~p~~~~~~-~~~~~~~~~~~q~w~~~g~CP~GTVPIrRtt~~d 77 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLK--NIQMRPSSYPKGISSK-ESSSSSSKPISQLWHQNGSCPEGTVPIRRTTKED 77 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhc--CcccCcchhhhhcccc-cccccccccchhhhccccCCcCCceeeecCCHHH
Confidence 699999999999999999999999999 4779999999865432 1123345678999999999999999999999999
Q ss_pred hhhhhhhhhcCCCCCccccccccccccCCccccccccccccCCCCCceEEEEEE
Q 041780 128 LLRASSLQQFGRKVPEVSYAANRTDATHSKFESINNKTIHLGPLVDRSAAVLVT 181 (422)
Q Consensus 128 l~ra~s~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~A~~~~ 181 (422)
|+||+|+.+||+|.+..++ ......++ ....|||||++++
T Consensus 78 llr~~s~~~~g~k~~~~~~---~~~~~~~~-----------~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 78 LLRAKSFKRFGRKPPSSIS---SPSSNKPD-----------ISSNGHEHAIAYV 117 (117)
T ss_pred HhhhhhHHHcCCcCCCCcC---CccccCCC-----------CCCCCCceEEEeC
Confidence 9999999999999886543 11111111 1247999999984
No 3
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=67.16 E-value=9.1 Score=28.22 Aligned_cols=37 Identities=24% Similarity=0.617 Sum_probs=24.2
Q ss_pred ccccCCCceeEEeEEEEEecCCCCeEEEecCceeeeeecchh
Q 041780 278 PWSISEGPQYYLPVGIYLDPNTKNWWLKVNGNIVVGYWPGSL 319 (422)
Q Consensus 278 pvS~~~G~q~~i~i~I~kD~~tgnWWL~~~~~~~IGYwP~sL 319 (422)
++|.--|.. |.|.++...++||+-..++ ..||.|++.
T Consensus 15 ~Ls~~~Gd~----i~v~~~~~~~~ww~~~~~g-~~G~~P~~~ 51 (55)
T PF07653_consen 15 ELSFKKGDV----IEVLGEKDDDGWWLGENNG-RRGWFPSSY 51 (55)
T ss_dssp B-EB-TTEE----EEEEEEECSTSEEEEEETT-EEEEEEGGG
T ss_pred ceEEecCCE----EEEEEeecCCCEEEEEECC-cEEEEcHHH
Confidence 345555553 3344677788999876654 689999975
No 4
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=40.70 E-value=48 Score=24.01 Aligned_cols=21 Identities=24% Similarity=0.752 Sum_probs=16.2
Q ss_pred CCCCeEEEecCceeeeeecchh
Q 041780 298 NTKNWWLKVNGNIVVGYWPGSL 319 (422)
Q Consensus 298 ~tgnWWL~~~~~~~IGYwP~sL 319 (422)
...+||+--.+. ..||+|++-
T Consensus 27 ~~~~W~~g~~~g-~~G~~P~~y 47 (49)
T PF14604_consen 27 SDDGWWYGRNTG-RTGLFPANY 47 (49)
T ss_dssp SSTSEEEEEETT-EEEEEEGGG
T ss_pred CCCCEEEEEECC-EEEEECHHh
Confidence 588899876544 799999874
No 5
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=34.76 E-value=71 Score=22.63 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=15.5
Q ss_pred EEEecCCCCeEEEecCc-eeeeeecc
Q 041780 293 IYLDPNTKNWWLKVNGN-IVVGYWPG 317 (422)
Q Consensus 293 I~kD~~tgnWWL~~~~~-~~IGYwP~ 317 (422)
|.++ .+.+||+-.... ...||.|+
T Consensus 24 v~~~-~~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 24 VLEK-SDDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp EEEE-SSSSEEEEEETTTTEEEEEEG
T ss_pred EEEe-cCCCEEEEEECCCCcEEEeeC
Confidence 3444 344899876543 36999996
No 6
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=31.26 E-value=28 Score=20.78 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=8.9
Q ss_pred CcchhhHHHHHHHH
Q 041780 1 MEKTVYLFLLFGAI 14 (422)
Q Consensus 1 ~~~~~~~~~~~~~~ 14 (422)
|+|.+.++++|+++
T Consensus 1 MMk~vIIlvvLLli 14 (19)
T PF13956_consen 1 MMKLVIILVVLLLI 14 (19)
T ss_pred CceehHHHHHHHhc
Confidence 67777666665544
No 7
>PHA03072 putative viral membrane protein; Provisional
Probab=27.77 E-value=84 Score=29.62 Aligned_cols=25 Identities=32% Similarity=0.422 Sum_probs=15.9
Q ss_pred hHHHHH-HHHhcCCcccceEEcCCCCeEeeeecC
Q 041780 31 LPEIDR-KLKLLNRPAVKSIKSEDGDIIDCVDIY 63 (422)
Q Consensus 31 ~~ei~~-~L~~lNkp~vksi~s~dGdiiDCVdi~ 63 (422)
.+|.+| +++.++++.+-+ |-|||+=
T Consensus 81 ~iEsdrGr~~~~~r~d~f~--------F~CvDFG 106 (190)
T PHA03072 81 KLESDRGRLLAAGRDDLFE--------FNCVDFG 106 (190)
T ss_pred HHHhhhhhHhhcCCccceE--------EEeeecc
Confidence 335555 566667665544 7899984
No 8
>PF13987 YedD: YedD-like protein
Probab=22.93 E-value=35 Score=29.33 Aligned_cols=23 Identities=35% Similarity=0.703 Sum_probs=17.1
Q ss_pred HhcCCcccce-EEcCCCCeEeeee
Q 041780 39 KLLNRPAVKS-IKSEDGDIIDCVD 61 (422)
Q Consensus 39 ~~lNkp~vks-i~s~dGdiiDCVd 61 (422)
+++..-|+.| |-|.+||..||--
T Consensus 22 ~lvSpeAiASLivt~~GdTLDCRQ 45 (111)
T PF13987_consen 22 ALVSPEAIASLIVTKEGDTLDCRQ 45 (111)
T ss_pred cccChhheeEEEEccCCCccchhh
Confidence 3455566655 7899999999954
No 9
>PF03356 Pox_LP_H2: Viral late protein H2; InterPro: IPR005023 This entry represents the late protein H2 found in Vaccinia and other poxviruses. This protein is a highly conserved viral membrane protein found in all sequenced poxviruses, containing an N-terminal transmembrane domain and four conserved cysteines thought to be involved in the formation of intramolecular disulphide bonds []. H2 has been shown to be necessary for entry into the host cell and virus-induced cell-cell fusion, but is not required for virus morphogenesis or the attachment of virus particles to cells. It is part of an entry-fusion complex composed of eight viral membrane proteins [].
Probab=22.62 E-value=1.2e+02 Score=28.61 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=16.3
Q ss_pred hHHHHH-HHHhcCCcccceEEcCCCCeEeeeecC
Q 041780 31 LPEIDR-KLKLLNRPAVKSIKSEDGDIIDCVDIY 63 (422)
Q Consensus 31 ~~ei~~-~L~~lNkp~vksi~s~dGdiiDCVdi~ 63 (422)
.+|.+| +++.++++.+-+ |-|||+=
T Consensus 81 ~iEsdrGr~~~~~r~d~f~--------F~CvDFG 106 (189)
T PF03356_consen 81 KIESDRGRLLALGRDDLFE--------FNCVDFG 106 (189)
T ss_pred HHHhhhhhHhhcCcccceE--------EEeeecc
Confidence 336665 666667665554 7799974
No 10
>PHA02677 hypothetical protein; Provisional
Probab=19.96 E-value=93 Score=26.86 Aligned_cols=16 Identities=25% Similarity=0.330 Sum_probs=12.5
Q ss_pred hhHHHHHHHHHhhhcc
Q 041780 5 VYLFLLFGAISTLCNG 20 (422)
Q Consensus 5 ~~~~~~~~~~~~~~~~ 20 (422)
.++||+||.|+++++.
T Consensus 2 itLFLilCYFILIFNI 17 (108)
T PHA02677 2 ISLFLIICYFVLIFNI 17 (108)
T ss_pred eeeHHHHHHHHHHHHH
Confidence 3578899988888865
Done!