Query 013721
Match_columns 437
No_of_seqs 192 out of 377
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:43:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013721.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013721hhsearch_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 7.8E-73 1.7E-77 543.3 19.9 188 244-434 1-188 (229)
2 PF14365 DUF4409: Domain of un 100.0 8.9E-38 1.9E-42 273.2 6.0 107 131-239 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 52.4 14 0.0003 27.7 2.6 37 339-380 16-52 (55)
4 PF07438 DUF1514: Protein of u 32.9 46 0.001 27.1 2.8 15 69-83 3-17 (66)
5 PF14604 SH3_9: Variant SH3 do 28.4 75 0.0016 23.5 3.2 21 358-379 27-47 (49)
6 PF00018 SH3_1: SH3 domain; I 28.3 77 0.0017 22.9 3.2 33 340-377 15-48 (48)
7 COG1512 Beta-propeller domains 21.8 1.3E+02 0.0028 30.7 4.4 25 116-140 50-79 (271)
8 PRK09510 tolA cell envelope in 21.4 1.2E+02 0.0026 32.4 4.3 22 68-89 14-35 (387)
9 PF11853 DUF3373: Protein of u 19.1 85 0.0018 34.6 2.7 23 105-127 30-53 (489)
10 cd00174 SH3 Src homology 3 dom 17.1 1.7E+02 0.0036 20.2 3.1 22 358-379 30-51 (54)
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=7.8e-73 Score=543.34 Aligned_cols=188 Identities=55% Similarity=1.059 Sum_probs=180.5
Q ss_pred eeeeEEEEEeeccccccCCccceeeeeeccCcCCCCccEEEEeeeecccccCCCCcEEEEEEeeCCccccceeccCCCee
Q 013721 244 YYGAKASINVWAPRVVNQYEFSLSQMWVISGSFGDDLNTIEAGWQVSPELYGDNYPRFFTYWTTDAYQATGCYNLLCSGF 323 (437)
Q Consensus 244 yyGa~AtinVw~P~V~~~~qfSlsqIwv~sG~~~~~lnsIeaGW~V~P~lYGD~~~rlF~yWT~D~y~~tGCyNl~CpGF 323 (437)
|||++|+||||+|+|+..+|||++||||.+|...+.+|+|||||+|+|+||||++||||+|||+|+|++|||||++||||
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 79999999999999998779999999999997557799999999999999999999999999999999999999999999
Q ss_pred EEecCccccCcccccccccCCceeEEEEEEecCCCCcceEEEeCCceeeeeechhhcccccCCccEEEEceEEEcCCCCC
Q 013721 324 VQTNNRIAIGAAISPTSSYNGGQFDISLLIWKDPKHGNWWLEFGSGVLVGYWPSFLFTHLTDHASMVQFGGEIVNSRPSG 403 (437)
Q Consensus 324 VQvs~~i~lG~~i~pvS~~~G~Q~~i~l~I~KDp~tGnWWL~~g~~~~IGYWP~sLFt~L~~~A~~V~wGGeV~~~~~~~ 403 (437)
|||+++|+||++|+|+|+++|.|++|.|+|+||+++|||||+++ ++.|||||++||++|+++|+.|+|||||++.+ +
T Consensus 81 Vq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~-~~~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~--~ 157 (229)
T PF03080_consen 81 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYG-GEPIGYWPKSLFTSLADGATEVEWGGEVYSPP--G 157 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEe-cceeeeehHHhhhhhhcCceEEEEEEEEeCCC--C
Confidence 99999999999999999999999999999999999999999998 57999999999999999999999999999865 4
Q ss_pred CCCCCCCCCCccCCCCCCceEEEecceeeec
Q 013721 404 FHTSTQMGSGHFAAKDLGKHHISEIYKLLIG 434 (437)
Q Consensus 404 ~~tsppMGSG~fP~eG~~kAAY~r~i~v~~~ 434 (437)
.|++|||||||||++|+++|||||+|+|++.
T Consensus 158 ~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~ 188 (229)
T PF03080_consen 158 RHTSPPMGSGHFPSEGFGKAAYFRNIQVVDS 188 (229)
T ss_pred CCCCCCccCCcCCCCCCCccEEEEEEEEEcC
Confidence 5799999999999999999999999999875
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=8.9e-38 Score=273.22 Aligned_cols=107 Identities=56% Similarity=0.941 Sum_probs=87.5
Q ss_pred EEeCCCCCEEeeeecCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCcccceeeeccCCCCCCCCceeeeeCCchhh
Q 013721 131 TIQSPDGDIIDCVETHLQPAFDHPKLKGQRPLDPPARPNGHNPS----GMITEEFQLWSFSGESCPEGTIPIRRTTEQDV 206 (437)
Q Consensus 131 tI~s~dGdiiDCVdI~kQPAfdHPLLKnHkiq~pP~~p~~~~~~----~~~~~~~qlw~~~g~~CP~GTVPIrRtt~edl 206 (437)
||+|+|||+||||||||||||||||||+|+ +.|+++|++.... .......|+|+.+| +||+|||||||+|+|||
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK~~q-~~Ps~~p~~~~~~~~~~~~~~~~~q~w~~~g-~CP~GTVPIrRtt~~dl 78 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLKNIQ-MRPSSYPKGISSKESSSSSSKPISQLWHQNG-SCPEGTVPIRRTTKEDL 78 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhcCcc-cCcchhhhhcccccccccccccchhhhcccc-CCcCCceeeecCCHHHH
Confidence 699999999999999999999999999755 4455677766543 22334569999777 89999999999999999
Q ss_pred cccccccccccccccccc------ccCCCCCcceeEEEE
Q 013721 207 LRATSVGKFGRKKIRRVR------RDTNSNGHEHAVGYV 239 (437)
Q Consensus 207 lra~S~~~fg~k~~~~~~------~~~~~~gH~~Av~~~ 239 (437)
+||+|+.+||+|.+.... .+.+.+||||||+|+
T Consensus 79 lr~~s~~~~g~k~~~~~~~~~~~~~~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 79 LRAKSFKRFGRKPPSSISSPSSNKPDISSNGHEHAIAYV 117 (117)
T ss_pred hhhhhHHHcCCcCCCCcCCccccCCCCCCCCCceEEEeC
Confidence 999999999999764322 234677999999985
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=52.37 E-value=14 Score=27.69 Aligned_cols=37 Identities=22% Similarity=0.444 Sum_probs=22.8
Q ss_pred ccccCCceeEEEEEEecCCCCcceEEEeCCceeeeeechhhc
Q 013721 339 TSSYNGGQFDISLLIWKDPKHGNWWLEFGSGVLVGYWPSFLF 380 (437)
Q Consensus 339 vS~~~G~Q~~i~l~I~KDp~tGnWWL~~g~~~~IGYWP~sLF 380 (437)
+|.--|.. |.|.++...++||+-.. +.-.||.|++..
T Consensus 16 Ls~~~Gd~----i~v~~~~~~~~ww~~~~-~g~~G~~P~~~v 52 (55)
T PF07653_consen 16 LSFKKGDV----IEVLGEKDDDGWWLGEN-NGRRGWFPSSYV 52 (55)
T ss_dssp -EB-TTEE----EEEEEEECSTSEEEEEE-TTEEEEEEGGGE
T ss_pred eEEecCCE----EEEEEeecCCCEEEEEE-CCcEEEEcHHHE
Confidence 44445554 33445566779998655 346699999753
No 4
>PF07438 DUF1514: Protein of unknown function (DUF1514); InterPro: IPR009999 This entry is represented by Bacteriophage phi PVL, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown.
Probab=32.85 E-value=46 Score=27.06 Aligned_cols=15 Identities=33% Similarity=0.436 Sum_probs=11.5
Q ss_pred ChHHHHHHHHHHHhh
Q 013721 69 PIIPIFVSYLLVLSS 83 (437)
Q Consensus 69 ~~~~~~~~~~~~~~~ 83 (437)
+++++.++++||.++
T Consensus 3 IiiSIvLai~lLI~l 17 (66)
T PF07438_consen 3 IIISIVLAIALLISL 17 (66)
T ss_pred hhHHHHHHHHHHHHH
Confidence 577888888887776
No 5
>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=28.40 E-value=75 Score=23.49 Aligned_cols=21 Identities=19% Similarity=0.556 Sum_probs=15.9
Q ss_pred CCcceEEEeCCceeeeeechhh
Q 013721 358 KHGNWWLEFGSGVLVGYWPSFL 379 (437)
Q Consensus 358 ~tGnWWL~~g~~~~IGYWP~sL 379 (437)
...+||+--. +...||+|++-
T Consensus 27 ~~~~W~~g~~-~g~~G~~P~~y 47 (49)
T PF14604_consen 27 SDDGWWYGRN-TGRTGLFPANY 47 (49)
T ss_dssp SSTSEEEEEE-TTEEEEEEGGG
T ss_pred CCCCEEEEEE-CCEEEEECHHh
Confidence 4788998654 45789999874
No 6
>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=28.25 E-value=77 Score=22.90 Aligned_cols=33 Identities=24% Similarity=0.403 Sum_probs=18.7
Q ss_pred cccCCceeEEEEEEecCCCCcceEEEeC-Cceeeeeech
Q 013721 340 SSYNGGQFDISLLIWKDPKHGNWWLEFG-SGVLVGYWPS 377 (437)
Q Consensus 340 S~~~G~Q~~i~l~I~KDp~tGnWWL~~g-~~~~IGYWP~ 377 (437)
|...|..+ .|.++. +.+||+-.. ++...||.|+
T Consensus 15 s~~~Gd~i----~v~~~~-~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 15 SFKKGDII----EVLEKS-DDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp EB-TTEEE----EEEEES-SSSEEEEEETTTTEEEEEEG
T ss_pred eEECCCEE----EEEEec-CCCEEEEEECCCCcEEEeeC
Confidence 44445443 333433 348998654 3357899996
No 7
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=21.84 E-value=1.3e+02 Score=30.68 Aligned_cols=25 Identities=28% Similarity=0.472 Sum_probs=16.8
Q ss_pred HHHHHHHhhcCC-----CccEEeCCCCCEE
Q 013721 116 FIRAHLNKINKP-----AVKTIQSPDGDII 140 (437)
Q Consensus 116 ~i~~~Lk~iNKp-----~vKtI~s~dGdii 140 (437)
++|++|+.|-+. +|.+|.|-+|+.|
T Consensus 50 ~Leq~l~~L~~kt~~QiaVv~vpSt~g~~I 79 (271)
T COG1512 50 ALEQQLADLEQKTGAQIAVVTVPSTGGETI 79 (271)
T ss_pred HHHHHHHHHHhccCCeEEEEEecCCCCCCH
Confidence 478899998533 4677777666544
No 8
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=21.43 E-value=1.2e+02 Score=32.42 Aligned_cols=22 Identities=14% Similarity=0.114 Sum_probs=16.1
Q ss_pred CChHHHHHHHHHHHhhhccccc
Q 013721 68 SPIIPIFVSYLLVLSSSICLVH 89 (437)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~ 89 (437)
+.+||+++|+||++.|+++++.
T Consensus 14 aiiiSv~LHvlLi~lLi~gs~~ 35 (387)
T PRK09510 14 AIIISVVLHIILFALLIWSSFD 35 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4588999999988777655443
No 9
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=19.12 E-value=85 Score=34.56 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=13.9
Q ss_pred cCchHHHHH-HHHHHHHHHhhcCC
Q 013721 105 LRPEEELHK-LKFIRAHLNKINKP 127 (437)
Q Consensus 105 ~~~~~~~~~-~~~i~~~Lk~iNKp 127 (437)
++..++|++ +++|+++++.|++.
T Consensus 30 ~qkie~L~kql~~Lk~q~~~l~~~ 53 (489)
T PF11853_consen 30 LQKIEALKKQLEELKAQQDDLNDR 53 (489)
T ss_pred HHHHHHHHHHHHHHHHhhcccccc
Confidence 345566554 66677777666653
No 10
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=17.13 E-value=1.7e+02 Score=20.25 Aligned_cols=22 Identities=27% Similarity=0.489 Sum_probs=14.7
Q ss_pred CCcceEEEeCCceeeeeechhh
Q 013721 358 KHGNWWLEFGSGVLVGYWPSFL 379 (437)
Q Consensus 358 ~tGnWWL~~g~~~~IGYWP~sL 379 (437)
..++||.-...+...||.|++.
T Consensus 30 ~~~~w~~~~~~~~~~G~vP~~~ 51 (54)
T cd00174 30 SDDGWWEGRLLGGKRGLFPSNY 51 (54)
T ss_pred CCCCeEEEEECCCCEEEEcccc
Confidence 3567887654333789999865
Done!