Query 048524
Match_columns 313
No_of_seqs 135 out of 372
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:16:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048524.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048524hhsearch_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 1.4E-83 3.1E-88 588.8 24.2 222 83-306 1-229 (229)
2 PF14365 DUF4409: Domain of un 99.9 2E-28 4.4E-33 202.9 7.0 75 1-76 4-115 (117)
3 PF07653 SH3_2: Variant SH3 do 68.6 7.3 0.00016 27.3 3.4 37 173-213 16-52 (55)
4 PF14604 SH3_9: Variant SH3 do 46.4 24 0.00053 24.3 2.9 21 192-212 27-47 (49)
5 PF00018 SH3_1: SH3 domain; I 42.9 31 0.00067 23.3 3.0 33 173-210 14-48 (48)
6 cd00174 SH3 Src homology 3 dom 19.6 1.5E+02 0.0032 19.2 3.1 21 192-212 30-51 (54)
7 smart00326 SH3 Src homology 3 17.2 2E+02 0.0044 18.7 3.4 21 193-213 34-55 (58)
8 PF05687 DUF822: Plant protein 13.9 74 0.0016 27.6 0.5 11 120-130 56-67 (150)
9 KOG2096 WD40 repeat protein [G 13.2 2.2E+02 0.0048 28.2 3.5 32 13-44 68-116 (420)
10 PF08055 Trp_leader1: Tryptoph 13.2 98 0.0021 17.1 0.7 10 191-200 4-13 (18)
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=1.4e-83 Score=588.79 Aligned_cols=222 Identities=55% Similarity=1.104 Sum_probs=212.8
Q ss_pred eeeeEEEEEEeCCCCC-CCCcceeEeeeecCC-CCCCceEEEeEEEcC---CCCCcEEEEEEEecCcCCCcccccCCCcc
Q 048524 83 YYGARATINVWNPATY-QGEFSFAQIWVGSGE-GDEANTMEVGWLVNN---GENKTRLFTYWTRDDYRSTGCYNLVCPGF 157 (313)
Q Consensus 83 ~~G~~a~i~v~~p~v~-~~q~S~sqiwv~~g~-~~~~n~Ie~GW~V~P---gD~~~rlf~yWt~d~y~~tgCyN~~CpGF 157 (313)
|||++|+||||+|+|+ ++|||++||||+++. .+.+|+|||||+|+| +|++||||+|||+|+|++||||||+||||
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 7999999999999999 679999999999999 788999999999999 99999999999999999999999999999
Q ss_pred EEeccccccCcccccccccCCceEEEEEeEecCCCCCCeEEEECCeeeeeechhhcccccCCcceEEEeeEEeecCCCCC
Q 048524 158 VQTTTQISLGAAVEPVSRYGAEQFEIIITITKDKSSGNWWLLMQDQFIGYWPGSIFTSLADCSTEINWGGEITNSEFAGH 237 (313)
Q Consensus 158 Vqvs~~i~~G~~~~p~S~~~g~q~~i~~~i~kD~~~gnWWL~~~~~~IGYwP~sLF~~l~~~A~~V~wGGeV~~~~~~~~ 237 (313)
|||+++|+||++|+|+|+++|+|++|+|+|+||+.+|||||+++++.|||||++||+.|+++|+.|+|||||++++ +.
T Consensus 81 Vq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~~~~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~--~~ 158 (229)
T PF03080_consen 81 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGGEPIGYWPKSLFTSLADGATEVEWGGEVYSPP--GR 158 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEecceeeeehHHhhhhhhcCceEEEEEEEEeCCC--CC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999753 45
Q ss_pred CCCCCCCCCCCCCCCCCccEEEeccEEEcCCCCccCC--CCceeecCCCCceeeeccccCCcccEEEEcCC
Q 048524 238 HTSTQMGSGHFPEESFGKACFFRKIGYVDESGNMRDP--KDLQVYVTKPPCYDLRFAKYEGDGISFYFGGP 306 (313)
Q Consensus 238 ~~sp~MGSG~fp~~g~~~aay~~~i~~~d~~~~~~~~--~~~~~~~~~~~CY~v~~~~~~~~g~~f~yGGP 306 (313)
+++|||||||||++++++|||||+|+++|.+++.+++ ..+++++|+|+||+++.....+||.+|+||||
T Consensus 159 ~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~~~~g~~f~yGGP 229 (229)
T PF03080_consen 159 HTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGDGDWGYYFFYGGP 229 (229)
T ss_pred CCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccCCCcccEEEeeCC
Confidence 8999999999999999999999999999999988877 34678999999999998877889999999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=99.95 E-value=2e-28 Score=202.92 Aligned_cols=75 Identities=51% Similarity=0.845 Sum_probs=57.5
Q ss_pred CCCCCEEeeeecCCCCCCCCCCCCCCCCc---------------------------cCCCCCCceeeeecC---------
Q 048524 1 SEDGDVIDCVDINKQPAFNHPLLKSHTIQ---------------------------NGECPEGTIPILRTP--------- 44 (313)
Q Consensus 1 s~dGdi~DCVdi~kQpa~dHPlLKnH~iq---------------------------~g~CP~GTVPI~R~~--------- 44 (313)
|+||||||||||||||||||||||+|+.+ +++||+|||||||++
T Consensus 4 s~dGdi~DCVdi~kQPAfdHPlLK~~q~~Ps~~p~~~~~~~~~~~~~~~~~q~w~~~g~CP~GTVPIrRtt~~dllr~~s 83 (117)
T PF14365_consen 4 SPDGDIIDCVDIYKQPAFDHPLLKNIQMRPSSYPKGISSKESSSSSSKPISQLWHQNGSCPEGTVPIRRTTKEDLLRAKS 83 (117)
T ss_pred CCCCCeEeCEeccccccccCchhcCcccCcchhhhhcccccccccccccchhhhccccCCcCCceeeecCCHHHHhhhhh
Confidence 78999999999999999999999988766 459999999999999
Q ss_pred -CcCCCCCCCCcccccccCCCCCCCCCceEEEE
Q 048524 45 -HSNRRRRSYPTVSQKRRANDFSAPPGHEYALV 76 (313)
Q Consensus 45 -~~~~~k~~~~~~~~~~~~~~~~~~~gh~~A~~ 76 (313)
++|++|............++ ....||||||+
T Consensus 84 ~~~~g~k~~~~~~~~~~~~~~-~~~~gH~~Aia 115 (117)
T PF14365_consen 84 FKRFGRKPPSSISSPSSNKPD-ISSNGHEHAIA 115 (117)
T ss_pred HHHcCCcCCCCcCCccccCCC-CCCCCCceEEE
Confidence 36666653111111111112 57789999999
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=68.63 E-value=7.3 Score=27.27 Aligned_cols=37 Identities=24% Similarity=0.525 Sum_probs=24.3
Q ss_pred ccccCCceEEEEEeEecCCCCCCeEEEECCeeeeeechhhc
Q 048524 173 VSRYGAEQFEIIITITKDKSSGNWWLLMQDQFIGYWPGSIF 213 (313)
Q Consensus 173 ~S~~~g~q~~i~~~i~kD~~~gnWWL~~~~~~IGYwP~sLF 213 (313)
+|.-.|+...+ .++...++||+-..+...|++|++..
T Consensus 16 Ls~~~Gd~i~v----~~~~~~~~ww~~~~~g~~G~~P~~~v 52 (55)
T PF07653_consen 16 LSFKKGDVIEV----LGEKDDDGWWLGENNGRRGWFPSSYV 52 (55)
T ss_dssp -EB-TTEEEEE----EEEECSTSEEEEEETTEEEEEEGGGE
T ss_pred eEEecCCEEEE----EEeecCCCEEEEEECCcEEEEcHHHE
Confidence 45555655433 36667789998655667799999763
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=46.43 E-value=24 Score=24.26 Aligned_cols=21 Identities=24% Similarity=0.634 Sum_probs=16.8
Q ss_pred CCCCeEEEECCeeeeeechhh
Q 048524 192 SSGNWWLLMQDQFIGYWPGSI 212 (313)
Q Consensus 192 ~~gnWWL~~~~~~IGYwP~sL 212 (313)
...+||+--.+...||+|++-
T Consensus 27 ~~~~W~~g~~~g~~G~~P~~y 47 (49)
T PF14604_consen 27 SDDGWWYGRNTGRTGLFPANY 47 (49)
T ss_dssp SSTSEEEEEETTEEEEEEGGG
T ss_pred CCCCEEEEEECCEEEEECHHh
Confidence 678999865567899999864
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=42.92 E-value=31 Score=23.27 Aligned_cols=33 Identities=21% Similarity=0.475 Sum_probs=19.3
Q ss_pred ccccCCceEEEEEeEecCCCCCCeEEEEC-C-eeeeeech
Q 048524 173 VSRYGAEQFEIIITITKDKSSGNWWLLMQ-D-QFIGYWPG 210 (313)
Q Consensus 173 ~S~~~g~q~~i~~~i~kD~~~gnWWL~~~-~-~~IGYwP~ 210 (313)
+|..-|....| .++ .+.+||+-.. . ...||.|+
T Consensus 14 Ls~~~Gd~i~v----~~~-~~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 14 LSFKKGDIIEV----LEK-SDDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp SEB-TTEEEEE----EEE-SSSSEEEEEETTTTEEEEEEG
T ss_pred EeEECCCEEEE----EEe-cCCCEEEEEECCCCcEEEeeC
Confidence 34445555443 333 3349998654 3 58999996
No 6
>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=19.65 E-value=1.5e+02 Score=19.21 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=14.6
Q ss_pred CCCCeEEEEC-Ceeeeeechhh
Q 048524 192 SSGNWWLLMQ-DQFIGYWPGSI 212 (313)
Q Consensus 192 ~~gnWWL~~~-~~~IGYwP~sL 212 (313)
...+||.-.. +...|+.|++.
T Consensus 30 ~~~~w~~~~~~~~~~G~vP~~~ 51 (54)
T cd00174 30 SDDGWWEGRLLGGKRGLFPSNY 51 (54)
T ss_pred CCCCeEEEEECCCCEEEEcccc
Confidence 4667886554 33889999865
No 7
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=17.19 E-value=2e+02 Score=18.70 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=15.1
Q ss_pred CCCeEEEEC-Ceeeeeechhhc
Q 048524 193 SGNWWLLMQ-DQFIGYWPGSIF 213 (313)
Q Consensus 193 ~gnWWL~~~-~~~IGYwP~sLF 213 (313)
+..||.--. +...|+.|++..
T Consensus 34 ~~~w~~~~~~~~~~G~vP~~~v 55 (58)
T smart00326 34 DDGWWKGRLGRGKEGLFPSNYV 55 (58)
T ss_pred CCCeEEEEeCCCCEEEEchHHE
Confidence 778886543 367899998764
No 8
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=13.87 E-value=74 Score=27.63 Aligned_cols=11 Identities=45% Similarity=0.951 Sum_probs=8.9
Q ss_pred EEEeEEEcC-CC
Q 048524 120 MEVGWLVNN-GE 130 (313)
Q Consensus 120 Ie~GW~V~P-gD 130 (313)
-||||.|.| |.
T Consensus 56 ~eAGw~Ve~DGT 67 (150)
T PF05687_consen 56 REAGWTVEPDGT 67 (150)
T ss_pred HhCCEEEccCCC
Confidence 489999998 54
No 9
>KOG2096 consensus WD40 repeat protein [General function prediction only]
Probab=13.23 E-value=2.2e+02 Score=28.21 Aligned_cols=32 Identities=34% Similarity=0.566 Sum_probs=25.1
Q ss_pred CCCCCCCCCCC----CCCCCc--------cC-----CCCCCceeeeecC
Q 048524 13 NKQPAFNHPLL----KSHTIQ--------NG-----ECPEGTIPILRTP 44 (313)
Q Consensus 13 ~kQpa~dHPlL----KnH~iq--------~g-----~CP~GTVPI~R~~ 44 (313)
-|||-|.|||+ |.|+-. +| -|-+++|-|-.+.
T Consensus 68 ~~q~~f~Hpl~~~~LKgH~~~vt~~~FsSdGK~lat~~~Dr~Ir~w~~~ 116 (420)
T KOG2096|consen 68 AKQPTFVHPLNVSVLKGHKKEVTDVAFSSDGKKLATISGDRSIRLWDVR 116 (420)
T ss_pred ccCCCcccchhhhhhhccCCceeeeEEcCCCceeEEEeCCceEEEEecc
Confidence 48999999985 899887 33 5888888876554
No 10
>PF08055 Trp_leader1: Tryptophan leader peptide; InterPro: IPR012638 This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in down regulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa [].
Probab=13.22 E-value=98 Score=17.15 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=7.0
Q ss_pred CCCCCeEEEE
Q 048524 191 KSSGNWWLLM 200 (313)
Q Consensus 191 ~~~gnWWL~~ 200 (313)
+.+.|||-..
T Consensus 4 ~~~~nwwwta 13 (18)
T PF08055_consen 4 HQIQNWWWTA 13 (18)
T ss_pred ccccceeeec
Confidence 5678998653
Done!