Query 045130
Match_columns 371
No_of_seqs 152 out of 375
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 10:08:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045130hhsearch_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 4.3E-84 9.4E-89 608.0 24.7 225 135-364 1-229 (229)
2 PF14365 DUF4409: Domain of un 100.0 1.3E-39 2.9E-44 276.8 7.3 108 21-130 1-117 (117)
3 PF07653 SH3_2: Variant SH3 do 69.1 7.6 0.00017 28.0 3.7 38 227-269 15-52 (55)
4 PF14604 SH3_9: Variant SH3 do 43.5 41 0.00088 23.8 3.8 21 247-268 27-47 (49)
5 PF00018 SH3_1: SH3 domain; I 35.0 68 0.0015 22.2 3.8 24 242-266 24-48 (48)
6 PF13987 YedD: YedD-like prote 22.9 35 0.00076 28.7 0.6 22 13-34 23-45 (111)
7 COG4913 Uncharacterized protei 17.2 84 0.0018 35.1 2.1 36 3-40 868-903 (1104)
8 cd00174 SH3 Src homology 3 dom 15.6 2.1E+02 0.0046 19.0 3.2 22 247-268 30-51 (54)
9 KOG2557 Uncharacterized conser 13.7 97 0.0021 31.8 1.4 20 175-194 279-298 (427)
10 PF15023 DUF4523: Protein of u 13.4 2.4E+02 0.0052 25.4 3.6 50 47-96 45-95 (166)
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=4.3e-84 Score=608.01 Aligned_cols=225 Identities=50% Similarity=0.962 Sum_probs=214.2
Q ss_pred eeeeEEEEeeeCCCCCCCCCceeEEEEeecCC-CCccceEEEeeEEcccccCCCceEEEEEEeecCccccccccCCCCee
Q 045130 135 YIGAQGDINVWNPKVDLPDDYTTAQIWLKGGP-GDNFESIEGGWVVNPKLYGDKLTRLFVYWTRDGYKSTGCFDAICSGF 213 (371)
Q Consensus 135 ~~G~~a~i~v~~p~v~~~~q~S~s~iwi~~g~-~~~~n~IeaGW~V~P~lYgD~~~rlf~yWt~d~y~~tgCyNl~CpGF 213 (371)
|||++|+||||+|+|+.++|||++||||++++ .+.+|+|||||+|+|+||||++||||+|||+|+|++||||||+||||
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 79999999999999997779999999999998 78899999999999999999999999999999999999999999999
Q ss_pred EEecc-cccCcccccccCCCCceeEEEEEEEeecCCCCeEEEeCCceeeeeecccccccccCCceEEEEeeEEecCCCCC
Q 045130 214 VQTGQ-IALGATISPISSSGGSQYYVTVGISLDPNSGNWWLKLNGNVVVGYWPGSLFGYLSHSATIVEWGGQVYSPNVKK 292 (371)
Q Consensus 214 VQvs~-i~lG~~i~pvS~~~G~q~~i~i~I~kD~~tgnWWL~~~~~~~IGYwP~sLF~~l~~~A~~v~wGGeV~~~~~~~ 292 (371)
|||++ |+||++|+|+|+++|+|++|+|+|+||+.+|||||+++++ .|||||++||+.|+++|+.|+|||||++++.
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 VQVSSSIALGAAISPVSTYGGKQYEITLSIFKDPKSGNWWLYYGGE-PIGYWPKSLFTSLADGATEVEWGGEVYSPPG-- 157 (229)
T ss_pred EEeCCccccceeeCCCccCCCceEEEEEEEEecCCCccEEEEEecc-eeeeehHHhhhhhhcCceEEEEEEEEeCCCC--
Confidence 99999 9999999999999999999999999999999999999886 8999999999999999999999999999853
Q ss_pred CCCCCCCCCCCccCCCCCCccEEEeecEEEcCCCCccCCC--cceeeccCCCceeeeecccCcccCCEEEEeCC
Q 045130 293 TPHTKTAMGSGEFSHSLQGSACSIEHVRIIDYSLQLKYPQ--WVGTWADEYYCYDAYNFVEGYTTEPVFFFGGP 364 (371)
Q Consensus 293 ~~~~sppMGSG~fp~~g~~~Aay~~ni~~vd~~~~~~~p~--~~~~~~d~~~CY~v~~~~~~~~~g~~f~yGGP 364 (371)
++++|||||||||++++++|||||||+++|+++..+.+. .+++++|+|+||++..... .+||.+||||||
T Consensus 158 -~~~sppMGSG~fp~~g~~~aAy~~~i~~~d~~~~~~~~~~~~~~~~~~~~~CY~~~~~~~-~~~g~~f~yGGP 229 (229)
T PF03080_consen 158 -RHTSPPMGSGHFPSEGFGKAAYFRNIQVVDSNGQFVDPNDDLLEVFADNPSCYDVSYIGD-GDWGYYFFYGGP 229 (229)
T ss_pred -CCCCCCccCCcCCCCCCCccEEEEEEEEEcCCCCCcCCcccceeEccCCCCceeEeeccC-CCcccEEEeeCC
Confidence 589999999999999999999999999999999888774 5778999999999998533 679999999999
No 2
>PF14365 DUF4409: Domain of unknown function (DUF4409)
Probab=100.00 E-value=1.3e-39 Score=276.82 Aligned_cols=108 Identities=51% Similarity=0.828 Sum_probs=93.0
Q ss_pred eEECCCCCeEeeeecCCCCCCCCCCCCCCCCCCCCCCCccchhcccCCCCCCcccccccccCCCCCCCceeeeecChhhh
Q 045130 21 SIKSEDGDIIDCVDIYKQSAFDHPALKNHKIQLKPSVDLLSEELDRRNESPRPVMMQTWQKSGSCPNGTVPIRRIQREDL 100 (371)
Q Consensus 21 si~s~dGdi~DCVdi~kQPafdHPlLKnH~iQ~~Ps~~~~~~~~~~~~~~~~~~~~q~~~~~~~CP~GTVPI~R~t~~dl 100 (371)
||+|+|||||||||||||||||||||| +|||+|++.|+........+.++...+|+|+++++||+|||||||+|+|||
T Consensus 1 tI~s~dGdi~DCVdi~kQPAfdHPlLK--~~q~~Ps~~p~~~~~~~~~~~~~~~~~q~w~~~g~CP~GTVPIrRtt~~dl 78 (117)
T PF14365_consen 1 TIQSPDGDIIDCVDIYKQPAFDHPLLK--NIQMRPSSYPKGISSKESSSSSSKPISQLWHQNGSCPEGTVPIRRTTKEDL 78 (117)
T ss_pred CccCCCCCeEeCEeccccccccCchhc--CcccCcchhhhhcccccccccccccchhhhccccCCcCCceeeecCCHHHH
Confidence 699999999999999999999999999 478999999987554423345567889999999999999999999999999
Q ss_pred hhhhchhccCCCCCCC---------CCCCCCcceEEEEE
Q 045130 101 LRAASLENFGRKAPEI---------PSSANKTNAALLVT 130 (371)
Q Consensus 101 ~ra~s~~~~~~k~~~~---------~~~~~~~~~A~~~~ 130 (371)
+||+|+.+|++|.+.. +...++|||||+++
T Consensus 79 lr~~s~~~~g~k~~~~~~~~~~~~~~~~~~gH~~Aia~~ 117 (117)
T PF14365_consen 79 LRAKSFKRFGRKPPSSISSPSSNKPDISSNGHEHAIAYV 117 (117)
T ss_pred hhhhhHHHcCCcCCCCcCCccccCCCCCCCCCceEEEeC
Confidence 9999999999997732 12345899999984
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=69.15 E-value=7.6 Score=27.99 Aligned_cols=38 Identities=24% Similarity=0.564 Sum_probs=24.6
Q ss_pred cccCCCCceeEEEEEEEeecCCCCeEEEeCCceeeeeeccccc
Q 045130 227 PISSSGGSQYYVTVGISLDPNSGNWWLKLNGNVVVGYWPGSLF 269 (371)
Q Consensus 227 pvS~~~G~q~~i~i~I~kD~~tgnWWL~~~~~~~IGYwP~sLF 269 (371)
++|.-.|.. |.|.++...++||+-..++ ..|+.|++..
T Consensus 15 ~Ls~~~Gd~----i~v~~~~~~~~ww~~~~~g-~~G~~P~~~v 52 (55)
T PF07653_consen 15 ELSFKKGDV----IEVLGEKDDDGWWLGENNG-RRGWFPSSYV 52 (55)
T ss_dssp B-EB-TTEE----EEEEEEECSTSEEEEEETT-EEEEEEGGGE
T ss_pred ceEEecCCE----EEEEEeecCCCEEEEEECC-cEEEEcHHHE
Confidence 345555553 3344677788999876654 5899999863
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=43.50 E-value=41 Score=23.83 Aligned_cols=21 Identities=24% Similarity=0.751 Sum_probs=16.0
Q ss_pred CCCCeEEEeCCceeeeeecccc
Q 045130 247 NSGNWWLKLNGNVVVGYWPGSL 268 (371)
Q Consensus 247 ~tgnWWL~~~~~~~IGYwP~sL 268 (371)
...+||+--.+. ..||+|++-
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 588899865544 699999874
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=34.99 E-value=68 Score=22.21 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=15.1
Q ss_pred EEeecCCCCeEEEeCCc-eeeeeecc
Q 045130 242 ISLDPNSGNWWLKLNGN-VVVGYWPG 266 (371)
Q Consensus 242 I~kD~~tgnWWL~~~~~-~~IGYwP~ 266 (371)
|.++. +..||+-.... ...||.|+
T Consensus 24 v~~~~-~~~Ww~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 24 VLEKS-DDGWWKVRNESTGKEGWVPS 48 (48)
T ss_dssp EEEES-SSSEEEEEETTTTEEEEEEG
T ss_pred EEEec-CCCEEEEEECCCCcEEEeeC
Confidence 34443 44899865432 36999996
No 6
>PF13987 YedD: YedD-like protein
Probab=22.87 E-value=35 Score=28.66 Aligned_cols=22 Identities=36% Similarity=0.745 Sum_probs=16.2
Q ss_pred hcCCcccee-EECCCCCeEeeee
Q 045130 13 LLNKPAVKS-IKSEDGDIIDCVD 34 (371)
Q Consensus 13 ~~nkp~vks-i~s~dGdi~DCVd 34 (371)
++...||.| |-|.+||++||--
T Consensus 23 lvSpeAiASLivt~~GdTLDCRQ 45 (111)
T PF13987_consen 23 LVSPEAIASLIVTKEGDTLDCRQ 45 (111)
T ss_pred ccChhheeEEEEccCCCccchhh
Confidence 445556655 7899999999953
No 7
>COG4913 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=17.17 E-value=84 Score=35.12 Aligned_cols=36 Identities=22% Similarity=0.441 Sum_probs=26.9
Q ss_pred chhHHHHHHHhcCCccceeEECCCCCeEeeeecCCCCC
Q 045130 3 TISEIDRRLKLLNKPAVKSIKSEDGDIIDCVDIYKQSA 40 (371)
Q Consensus 3 ~~~ei~~~l~~~nkp~vksi~s~dGdi~DCVdi~kQPa 40 (371)
|..+||..++.||-. +.-|.-..|..+ ||||-|||.
T Consensus 868 er~~IeERIe~IN~S-L~~vdfn~gRyl-hIdi~kQp~ 903 (1104)
T COG4913 868 ERALIEERIEAINDS-LRRVDFNSGRYL-HIDIAKQPV 903 (1104)
T ss_pred HHHHHHHHHHHHHHH-HhhccccCCceE-EeecccCCC
Confidence 677899999999964 344444555544 899999987
No 8
>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=15.59 E-value=2.1e+02 Score=18.98 Aligned_cols=22 Identities=18% Similarity=0.445 Sum_probs=14.3
Q ss_pred CCCCeEEEeCCceeeeeecccc
Q 045130 247 NSGNWWLKLNGNVVVGYWPGSL 268 (371)
Q Consensus 247 ~tgnWWL~~~~~~~IGYwP~sL 268 (371)
...+||.........|+.|++.
T Consensus 30 ~~~~w~~~~~~~~~~G~vP~~~ 51 (54)
T cd00174 30 SDDGWWEGRLLGGKRGLFPSNY 51 (54)
T ss_pred CCCCeEEEEECCCCEEEEcccc
Confidence 4667886654322589999875
No 9
>KOG2557 consensus Uncharacterized conserved protein, contains TLDc domain [Function unknown]
Probab=13.75 E-value=97 Score=31.84 Aligned_cols=20 Identities=35% Similarity=0.680 Sum_probs=17.4
Q ss_pred EeeEEcccccCCCceEEEEE
Q 045130 175 GGWVVNPKLYGDKLTRLFVY 194 (371)
Q Consensus 175 aGW~V~P~lYgD~~~rlf~y 194 (371)
-+|-|+|++|||++.-||.-
T Consensus 279 q~we~~pQF~Gd~~~fLfqL 298 (427)
T KOG2557|consen 279 QPWERYPQFYGDMKSFLFQL 298 (427)
T ss_pred CcccccCccCCccceeeeee
Confidence 57999999999999888753
No 10
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=13.36 E-value=2.4e+02 Score=25.43 Aligned_cols=50 Identities=24% Similarity=0.255 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCCccchhcccCCCCCCcccccccccCC-CCCCCceeeeecC
Q 045130 47 KNHKIQLKPSVDLLSEELDRRNESPRPVMMQTWQKSG-SCPNGTVPIRRIQ 96 (371)
Q Consensus 47 KnH~iQ~~Ps~~~~~~~~~~~~~~~~~~~~q~~~~~~-~CP~GTVPI~R~t 96 (371)
+.-.+-.+|+..|.......+..+.....-.+|+++. +=|.+||=+|-+.
T Consensus 45 ~EI~lTPkPs~mp~wKRk~~N~~~~gwKkc~lwkk~~kepPMsTIVVRWlk 95 (166)
T PF15023_consen 45 KEINLTPKPSRMPLWKRKAINNASEGWKKCHLWKKNTKEPPMSTIVVRWLK 95 (166)
T ss_pred hhhccCCCCcccchhhhhhhcccccceeeehhhcccCCCCCceeEEeehhh
Confidence 3333456777777532222112222223345787766 7999999998654
Done!