Query 013658
Match_columns 438
No_of_seqs 201 out of 382
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:05:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013658hhsearch_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 4.1E-84 8.8E-89 623.4 24.0 227 201-431 1-229 (229)
2 PF14365 DUF4409: Domain of un 100.0 2.5E-40 5.4E-45 288.8 7.0 117 65-195 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 45.4 26 0.00056 26.0 3.1 37 296-337 15-51 (55)
4 COG1965 CyaY Protein implicate 26.8 51 0.0011 28.8 2.3 35 48-85 14-57 (106)
5 PF14604 SH3_9: Variant SH3 do 23.1 84 0.0018 23.0 2.6 21 316-337 27-47 (49)
6 PF00018 SH3_1: SH3 domain; I 22.9 94 0.002 22.2 2.8 34 297-335 14-48 (48)
7 PF11853 DUF3373: Protein of u 20.0 61 0.0013 35.4 1.8 24 37-60 27-52 (489)
8 PF13987 YedD: YedD-like prote 19.6 48 0.001 28.9 0.8 21 58-78 24-45 (111)
9 PHA02669 hypothetical protein; 17.4 1.4E+02 0.003 28.3 3.3 31 63-93 86-116 (210)
10 PF03607 DCX: Doublecortin; I 16.3 62 0.0013 24.9 0.6 37 39-78 7-43 (60)
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=4.1e-84 Score=623.38 Aligned_cols=227 Identities=59% Similarity=1.145 Sum_probs=216.3
Q ss_pred eeeeEEEEEeeCCcccccCccceeeeeeecCCCCCCCccEEEEeeEEcccccCCCCcEEEEEEeecCccccceecccCCe
Q 013658 201 VYGARATINVWDPSIQVVNEFSLSQIWVLSGSFDGSDLNSIEAGWQVSPELYGDSRPRLFTYWTSDSYQATGCYNLLCAG 280 (438)
Q Consensus 201 ~yGa~a~inVw~P~V~~~~qfS~sqiwi~~G~~~~~~~nsIeaGW~V~P~lYgD~~~rlf~yWT~D~y~~tGCyNl~CpG 280 (438)
|||++|+||||+|+|+.++|||++||||++|.. ...+|+|||||+|+|+||||++||||+|||+|+|++||||||+|||
T Consensus 1 y~G~~a~i~v~~p~v~~~~q~S~~~i~i~~g~~-~~~~~~i~~GW~V~P~lygd~~~~lf~~wt~d~~~~tgCyN~~CpG 79 (229)
T PF03080_consen 1 YYGARATISVWNPKVQQPDQFSLSQIWISNGSD-DDSLNSIEAGWQVYPSLYGDSRTRLFVYWTADGYQKTGCYNLDCPG 79 (229)
T ss_pred CeeeEEEEECcCCccCCccceeheeEEEEecCC-CCCCcEEEEeeeccccccCCCceEEEEEEEccCCCCcceeCCCCCc
Confidence 799999999999999987899999999999984 4679999999999999999999999999999999999999999999
Q ss_pred eEEecCccccCcccccccccCCceeEEEEeeecCCCCCCeeEEeCCCeeeeeechhhhhhhhcCccEEEEceEEeecCCC
Q 013658 281 FIQTNSRIAIGAAISPISTYAGNQFDITILIWKDPKLGNWWMGFGENLLVGYWPAELFTHLADHATMVEWGGEVVNSRAN 360 (438)
Q Consensus 281 FVQvs~~i~lG~~i~pvS~~~G~q~~i~i~I~kD~~tgnWWL~~g~~~~IGYWP~~LF~~l~~~A~~V~wGGeV~~~~~~ 360 (438)
|||||++|+||++|+|+|+++|+|++|+|.|+||+++|||||.+++ +.|||||++||++|+++|+.|+|||||++++
T Consensus 80 FVq~s~~i~~G~~~~~~S~~gG~q~~i~~~i~kD~~~gnWWL~~~~-~~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~-- 156 (229)
T PF03080_consen 80 FVQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGG-EPIGYWPKSLFTSLADGATEVEWGGEVYSPP-- 156 (229)
T ss_pred EEEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEec-ceeeeehHHhhhhhhcCceEEEEEEEEeCCC--
Confidence 9999999999999999999999999999999999999999999984 7999999999999999999999999999874
Q ss_pred CCCCCCCCCCCCCCCCCCCceeEEeccEEEcCCCCccccc--cceecccCCCceeeecCCCCccccEEEEeCC
Q 013658 361 GEHTSTQMGSGHFAEDGFGKASYFRNLEIVDSDNSLSSVR--DISILAENTNCYNIKNSYNNEWGTHFYYGGP 431 (438)
Q Consensus 361 g~~tsp~MGSG~fp~~g~~kAay~~ni~ivd~~~~~~~~~--~~~~~~d~p~CY~v~~~~~~~~G~~f~yGGP 431 (438)
+.|++|||||||||++|+++|||||||+++|.+++..++. .+++++|+|+||++......+||.+||||||
T Consensus 157 ~~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~~~~g~~f~yGGP 229 (229)
T PF03080_consen 157 GRHTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGDGDWGYYFFYGGP 229 (229)
T ss_pred CCCCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccCCCcccEEEeeCC
Confidence 4589999999999999999999999999999999988763 4678999999999999877889999999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=2.5e-40 Score=288.80 Aligned_cols=117 Identities=56% Similarity=0.899 Sum_probs=93.8
Q ss_pred EEeCCCCCeeeeeecCCCCCCCCCCCCCCCCCCCCCCCCcccccccccccccccccchhhhcccccccccCCCCCCCCce
Q 013658 65 TIESPDGDIIDCVHKRRQPALDHPLLKNHKIQRVPSQMPKMKKALKEDEASSERNNERVIIEGAWQMWHRNGTRCPKGTV 144 (438)
Q Consensus 65 tI~s~dGdiiDCVdi~kQPAfdHPlLKnHkiqm~Ps~~p~~~~~~~~~~s~~~~~~~~~~~~~~~q~w~~~g~~CP~GTV 144 (438)
||+|+|||||||||||||||||||||| +|||+|++.|++... . ++ .... ....+|+|++++ +||+|||
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK--~~q~~Ps~~p~~~~~-~--~~-----~~~~-~~~~~q~w~~~g-~CP~GTV 68 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLK--NIQMRPSSYPKGISS-K--ES-----SSSS-SKPISQLWHQNG-SCPEGTV 68 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhc--CcccCcchhhhhccc-c--cc-----cccc-cccchhhhcccc-CCcCCce
Confidence 799999999999999999999999999 477999999987662 1 01 0111 456789999987 9999999
Q ss_pred eeecCCchhhhccccccccccCcCCCCCCCccCCCCCccCCCCceeEEEEe
Q 013658 145 PIRRSTEHDVLRAKSLFDFGKKQHRRIPLHRRADAPDVVSGNGHEHAIAYT 195 (438)
Q Consensus 145 PIrR~t~~dllra~s~~~f~~k~~~~~~~~~~~~~~~~~~~~gH~~Ai~~~ 195 (438)
||||+|++|||||+|+.+||+|.+......... .+ ..+.+||||||+|+
T Consensus 69 PIrRtt~~dllr~~s~~~~g~k~~~~~~~~~~~-~~-~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 69 PIRRTTKEDLLRAKSFKRFGRKPPSSISSPSSN-KP-DISSNGHEHAIAYV 117 (117)
T ss_pred eeecCCHHHHhhhhhHHHcCCcCCCCcCCcccc-CC-CCCCCCCceEEEeC
Confidence 999999999999999999999987632211111 12 25788999999986
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=45.42 E-value=26 Score=26.02 Aligned_cols=37 Identities=22% Similarity=0.576 Sum_probs=23.4
Q ss_pred cccccCCceeEEEEeeecCCCCCCeeEEeCCCeeeeeechhh
Q 013658 296 PISTYAGNQFDITILIWKDPKLGNWWMGFGENLLVGYWPAEL 337 (438)
Q Consensus 296 pvS~~~G~q~~i~i~I~kD~~tgnWWL~~g~~~~IGYWP~~L 337 (438)
++|.-.|.... |.++...++||+-.. +.-.||.|++.
T Consensus 15 ~Ls~~~Gd~i~----v~~~~~~~~ww~~~~-~g~~G~~P~~~ 51 (55)
T PF07653_consen 15 ELSFKKGDVIE----VLGEKDDDGWWLGEN-NGRRGWFPSSY 51 (55)
T ss_dssp B-EB-TTEEEE----EEEEECSTSEEEEEE-TTEEEEEEGGG
T ss_pred ceEEecCCEEE----EEEeecCCCEEEEEE-CCcEEEEcHHH
Confidence 45666666433 335667779998755 35679999875
No 4
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism]
Probab=26.79 E-value=51 Score=28.82 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=25.3
Q ss_pred HHHHHHHHHHh---------CCCCceEEeCCCCCeeeeeecCCCCCC
Q 013658 48 LERIQKHLQKI---------NKPPVMTIESPDGDIIDCVHKRRQPAL 85 (438)
Q Consensus 48 ~~ei~~~L~~l---------nkp~vktI~s~dGdiiDCVdi~kQPAf 85 (438)
+..|+.+|... ...-|.||..++|-.| =|+|||++
T Consensus 14 ~~~Ied~le~~~~~~d~D~d~qg~VlTl~f~ngs~i---iINkQ~P~ 57 (106)
T COG1965 14 LLKIEDQLDEQDDEGDIDCEIQGGVLTLTFDNGSQI---IINKQEPL 57 (106)
T ss_pred HHHHHHHHHhhccCCCcceecCCCEEEEEECCCcEE---EEeCCChH
Confidence 45677776665 3568899999999543 38999975
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=23.12 E-value=84 Score=22.97 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=16.2
Q ss_pred CCCCeeEEeCCCeeeeeechhh
Q 013658 316 KLGNWWMGFGENLLVGYWPAEL 337 (438)
Q Consensus 316 ~tgnWWL~~g~~~~IGYWP~~L 337 (438)
...+||+--. +.-.||.|++-
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 5788998655 46889999863
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=22.94 E-value=94 Score=22.22 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=19.8
Q ss_pred ccccCCceeEEEEeeecCCCCCCeeEEeC-CCeeeeeech
Q 013658 297 ISTYAGNQFDITILIWKDPKLGNWWMGFG-ENLLVGYWPA 335 (438)
Q Consensus 297 vS~~~G~q~~i~i~I~kD~~tgnWWL~~g-~~~~IGYWP~ 335 (438)
+|..-|....| .++ .+.+||+-.. ++...||.|+
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 45555665443 232 3448998654 3357899996
No 7
>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=19.97 E-value=61 Score=35.41 Aligned_cols=24 Identities=17% Similarity=0.436 Sum_probs=15.9
Q ss_pred cccccccchhh--HHHHHHHHHHhCC
Q 013658 37 YTKYRQVSSLR--LERIQKHLQKINK 60 (438)
Q Consensus 37 ~~~~~~~~~l~--~~ei~~~L~~lnk 60 (438)
...+++-|+|. ++|||+|++.|++
T Consensus 27 ~~~~qkie~L~kql~~Lk~q~~~l~~ 52 (489)
T PF11853_consen 27 IDLLQKIEALKKQLEELKAQQDDLND 52 (489)
T ss_pred hHHHHHHHHHHHHHHHHHHhhccccc
Confidence 34455667776 7778888776654
No 8
>PF13987 YedD: YedD-like protein
Probab=19.65 E-value=48 Score=28.87 Aligned_cols=21 Identities=24% Similarity=0.662 Sum_probs=15.9
Q ss_pred hCCCCceE-EeCCCCCeeeeee
Q 013658 58 INKPPVMT-IESPDGDIIDCVH 78 (438)
Q Consensus 58 lnkp~vkt-I~s~dGdiiDCVd 78 (438)
+...|+.| |.|.+||..||--
T Consensus 24 vSpeAiASLivt~~GdTLDCRQ 45 (111)
T PF13987_consen 24 VSPEAIASLIVTKEGDTLDCRQ 45 (111)
T ss_pred cChhheeEEEEccCCCccchhh
Confidence 44556665 7899999999953
No 9
>PHA02669 hypothetical protein; Provisional
Probab=17.38 E-value=1.4e+02 Score=28.27 Aligned_cols=31 Identities=26% Similarity=0.457 Sum_probs=22.0
Q ss_pred ceEEeCCCCCeeeeeecCCCCCCCCCCCCCC
Q 013658 63 VMTIESPDGDIIDCVHKRRQPALDHPLLKNH 93 (438)
Q Consensus 63 vktI~s~dGdiiDCVdi~kQPAfdHPlLKnH 93 (438)
|.|--|.+|-..-=|-.-.||-|.||+..|-
T Consensus 86 vSTTSTS~gGTLtRv~~~~~p~~~~pmYENF 116 (210)
T PHA02669 86 VSTTSTSGGGTLSRVWVGGGPRFQHPMYENF 116 (210)
T ss_pred eeeeecCCCceEEeeeecCCCccCcchhhhh
Confidence 3444444555666777889999999998874
No 10
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=16.33 E-value=62 Score=24.86 Aligned_cols=37 Identities=22% Similarity=0.412 Sum_probs=22.0
Q ss_pred cccccchhhHHHHHHHHHHhCCCCceEEeCCCCCeeeeee
Q 013658 39 KYRQVSSLRLERIQKHLQKINKPPVMTIESPDGDIIDCVH 78 (438)
Q Consensus 39 ~~~~~~~l~~~ei~~~L~~lnkp~vktI~s~dGdiiDCVd 78 (438)
+++.-+.| +++|.++++.-+ .|+.+-|.||..|..++
T Consensus 7 ~~~s~e~l-L~~it~~v~l~~--gVr~lyt~~G~~V~~l~ 43 (60)
T PF03607_consen 7 RFRSFEQL-LDEITEKVQLPS--GVRKLYTLDGKRVKSLD 43 (60)
T ss_dssp THSSHHHH-HHHHHHSSSSTT--S-SEEEETTSSEESSGG
T ss_pred hhcCHHHH-HHHHHhhcCCCc--ccceEECCCCCEeCCHH
Confidence 33333334 556666554332 29999999998777665
Done!