Query 012967
Match_columns 452
No_of_seqs 205 out of 388
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:10:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012967hhsearch_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 5.9E-83 1.3E-87 617.7 22.8 227 216-445 1-229 (229)
2 PF14365 DUF4409: Domain of un 100.0 3E-38 6.5E-43 277.2 6.7 107 103-211 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 40.6 37 0.00081 25.3 3.4 36 311-351 16-51 (55)
4 PF07172 GRP: Glycine rich pro 29.8 40 0.00086 29.0 2.2 7 43-49 12-18 (95)
5 PF15102 TMEM154: TMEM154 prot 23.4 1.1E+02 0.0023 28.6 3.9 16 85-100 126-141 (146)
6 PF11239 DUF3040: Protein of u 23.0 63 0.0014 26.6 2.1 17 79-95 4-20 (82)
7 PF14604 SH3_9: Variant SH3 do 22.3 1E+02 0.0023 22.7 3.0 21 330-351 27-47 (49)
8 PF00018 SH3_1: SH3 domain; I 21.2 1.3E+02 0.0027 21.8 3.2 19 331-349 29-48 (48)
9 PF07438 DUF1514: Protein of u 21.1 57 0.0012 26.4 1.4 18 82-99 46-63 (66)
10 PRK09510 tolA cell envelope in 18.2 1.6E+02 0.0036 31.5 4.5 17 37-53 14-30 (387)
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=5.9e-83 Score=617.69 Aligned_cols=227 Identities=55% Similarity=1.086 Sum_probs=216.2
Q ss_pred EeeEEEEEeeecCcccCCCCccceehhhhcCcCCCCccEEEEeeeEcccccCCCccEEEEEEecCCccccceeccccCee
Q 012967 216 YYGAKASLNVWTPRVTDGYEFSLSQIWVISGSFSHDLNTIEAGWQVSPELYGDNYPRFFTYWTTDAYQATGCYNLLCSGF 295 (452)
Q Consensus 216 yyGa~a~inVw~P~V~~~~qfSlsqiwv~~G~~~~~~nsIeaGW~V~P~lYGD~~~rlF~yWT~D~y~~TGCyNl~CpGF 295 (452)
|||++|+||||+|+|+..+|||++||||.+|...+.+|+|||||+|+|+||||++||||+|||+|+|++||||||+||||
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 EEccCccccCcccccccccCCceeEEEEEEecCCCCCCeEEEeCCCeeeeeechhhhhhhhcCcceEEEccEEEcCCCCC
Q 012967 296 VQTNNKIAIGAAISPRSSYNGRQFDIGLMIWKDPKHGHWWLQFGSGLLVGYWPAFLFSHLRSHASMVQFGGEIVNSRSSG 375 (452)
Q Consensus 296 VQvs~~i~lG~~i~pvS~~~G~q~~i~i~I~kDp~tGnWWL~~g~~~~IGYWP~sLFt~L~~~A~~V~wGGeV~~~~~~~ 375 (452)
|||+++|+||++|+|+|+++|.|++|+|.|+||+++|||||.++ ++.|||||++||++|+++|+.|+|||||++++ +
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 CCCCCCCCCCCCCCCCCCceEEEeceEEEeCCCCccccC--cccccccCCCCeeeecCCCCceecEEEEcCC
Q 012967 376 FHTFTQMGSGHFAGEGFRRAAYFRNLQVVDWDNNLLPLT--NLHLLADHSNCYDIRQGRNNVWGTYFYYGGP 445 (452)
Q Consensus 376 ~~tsppMGSG~fp~~g~~kAAy~rni~vvd~~~~~~~~~--~l~~~~d~p~CY~v~~~~~~~~G~~f~yGGP 445 (452)
.|++|||||||||++|+++|||||||+++|.+++..++. .+++++|+|+||++....+.+||.+||||||
T Consensus 158 ~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~~~~g~~f~yGGP 229 (229)
T PF03080_consen 158 RHTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGDGDWGYYFFYGGP 229 (229)
T ss_pred CCCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccCCCcccEEEeeCC
Confidence 589999999999999999999999999999999988774 4678999999999998777889999999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=3e-38 Score=277.20 Aligned_cols=107 Identities=55% Similarity=0.942 Sum_probs=87.0
Q ss_pred EEeCCCCCEEeeeecCCCCCCCCCCCCCCCCCCCCCCCCCCCcc----cccccccceeccCCCCCCCCceeeeecChhhh
Q 012967 103 TIQSPDGDVIDCVLSHLQPAFDHPELRGQKPLDPPARPKGDERE----ETATESLQLWTDSGESCPEGTVPIRRTTEKDI 178 (452)
Q Consensus 103 tI~s~dGdiiDCVdi~kQPAfdHPlLKnH~iq~pP~~p~~~~~~----~~~~~~~q~w~~~g~~CP~GTVPIrR~t~~dl 178 (452)
||+|+||||||||||||||||||||||+|+ +.|+++|++.... .......|+|+.+| +||+|||||||+|+|||
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 699999999999999999999999999654 3344677765543 12334578999877 89999999999999999
Q ss_pred hhhhhhhhhccccccccc------ccCCCCCcceEEEEE
Q 012967 179 LRASSIKRFGRKLRRHVR------RDSTGGGHEHAVVFV 211 (452)
Q Consensus 179 lra~s~~~fg~k~~~~~~------~~~~~~gH~~Av~~~ 211 (452)
|||+|+.+||+|.+.... .+.+.+||||||+|+
T Consensus 79 lr~~s~~~~g~k~~~~~~~~~~~~~~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 79 LRAKSFKRFGRKPPSSISSPSSNKPDISSNGHEHAIAYV 117 (117)
T ss_pred hhhhhHHHcCCcCCCCcCCccccCCCCCCCCCceEEEeC
Confidence 999999999999754322 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=40.56 E-value=37 Score=25.32 Aligned_cols=36 Identities=19% Similarity=0.396 Sum_probs=22.1
Q ss_pred ccccCCceeEEEEEEecCCCCCCeEEEeCCCeeeeeechhh
Q 012967 311 RSSYNGRQFDIGLMIWKDPKHGHWWLQFGSGLLVGYWPAFL 351 (452)
Q Consensus 311 vS~~~G~q~~i~i~I~kDp~tGnWWL~~g~~~~IGYWP~sL 351 (452)
+|.-.|... .|.++...++||+-.. +.-.||.|++.
T Consensus 16 Ls~~~Gd~i----~v~~~~~~~~ww~~~~-~g~~G~~P~~~ 51 (55)
T PF07653_consen 16 LSFKKGDVI----EVLGEKDDDGWWLGEN-NGRRGWFPSSY 51 (55)
T ss_dssp -EB-TTEEE----EEEEEECSTSEEEEEE-TTEEEEEEGGG
T ss_pred eEEecCCEE----EEEEeecCCCEEEEEE-CCcEEEEcHHH
Confidence 444455543 3335556779998655 34679999975
No 4
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=29.85 E-value=40 Score=29.01 Aligned_cols=7 Identities=29% Similarity=0.591 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 012967 43 FVSFLLV 49 (452)
Q Consensus 43 ~~~~~~~ 49 (452)
|+++|||
T Consensus 12 ~LA~lLl 18 (95)
T PF07172_consen 12 LLAALLL 18 (95)
T ss_pred HHHHHHH
Confidence 3333333
No 5
>PF15102 TMEM154: TMEM154 protein family
Probab=23.40 E-value=1.1e+02 Score=28.58 Aligned_cols=16 Identities=13% Similarity=0.569 Sum_probs=12.3
Q ss_pred hHHHHHHHHHhhcCCC
Q 012967 85 KLKSVNAYLKKINKPA 100 (452)
Q Consensus 85 ~~~~i~~~L~~iNkp~ 100 (452)
+|+++.+=++.|||-+
T Consensus 126 Emeeldkwm~s~n~n~ 141 (146)
T PF15102_consen 126 EMEELDKWMNSMNRNA 141 (146)
T ss_pred hHHHHHhHHHhhccCc
Confidence 5778888888888765
No 6
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=23.04 E-value=63 Score=26.57 Aligned_cols=17 Identities=12% Similarity=0.358 Sum_probs=14.0
Q ss_pred ChhhhhhHHHHHHHHHh
Q 012967 79 PSKHMQKLKSVNAYLKK 95 (452)
Q Consensus 79 ~~~~~~~~~~i~~~L~~ 95 (452)
+.+|.+.++|||++|..
T Consensus 4 Se~E~r~L~eiEr~L~~ 20 (82)
T PF11239_consen 4 SEHEQRRLEEIERQLRA 20 (82)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 35777889999999975
No 7
>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=22.31 E-value=1e+02 Score=22.68 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=15.8
Q ss_pred CCCCeEEEeCCCeeeeeechhh
Q 012967 330 KHGHWWLQFGSGLLVGYWPAFL 351 (452)
Q Consensus 330 ~tGnWWL~~g~~~~IGYWP~sL 351 (452)
...+||+--. +...||.|++-
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 5788998654 45789999863
No 8
>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=21.23 E-value=1.3e+02 Score=21.75 Aligned_cols=19 Identities=26% Similarity=0.538 Sum_probs=13.2
Q ss_pred CCCeEEEeC-CCeeeeeech
Q 012967 331 HGHWWLQFG-SGLLVGYWPA 349 (452)
Q Consensus 331 tGnWWL~~g-~~~~IGYWP~ 349 (452)
+.+||+-.. ++...||.|+
T Consensus 29 ~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 29 DDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp SSSEEEEEETTTTEEEEEEG
T ss_pred CCCEEEEEECCCCcEEEeeC
Confidence 448998654 2357899996
No 9
>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=21.07 E-value=57 Score=26.38 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=13.0
Q ss_pred hhhhHHHHHHHHHhhcCC
Q 012967 82 HMQKLKSVNAYLKKINKP 99 (452)
Q Consensus 82 ~~~~~~~i~~~L~~iNkp 99 (452)
..+.+++.|..+++|||.
T Consensus 46 g~~gl~~~~~e~~r~~~~ 63 (66)
T PF07438_consen 46 GYEGLEEYEIEIERIKKD 63 (66)
T ss_pred CcchHHHHHHHHHHHHHH
Confidence 344567788888888875
No 10
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=18.22 E-value=1.6e+02 Score=31.47 Aligned_cols=17 Identities=12% Similarity=0.286 Sum_probs=12.5
Q ss_pred cchhHHHHHHHHHHHhh
Q 012967 37 VSVFPVFVSFLLVVSSL 53 (452)
Q Consensus 37 ~~~~~~~~~~~~~~~~~ 53 (452)
..+||++||+||+++++
T Consensus 14 aiiiSv~LHvlLi~lLi 30 (387)
T PRK09510 14 AIIISVVLHIILFALLI 30 (387)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35788899988766654
Done!