Query 037116
Match_columns 69
No_of_seqs 100 out of 164
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:49:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037116hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3609 Predicted transcriptio 73.5 6.7 0.00014 24.0 3.6 30 3-32 19-50 (89)
2 PF05456 eIF_4EBP: Eukaryotic 55.3 5.9 0.00013 26.0 0.8 16 42-57 48-64 (116)
3 PF11420 Subtilosin_A: Bacteri 36.6 9.5 0.00021 20.1 -0.3 12 5-16 14-25 (35)
4 cd08876 START_1 Uncharacterize 28.7 1.1E+02 0.0023 19.9 3.7 25 7-31 167-191 (195)
5 PF03364 Polyketide_cyc: Polyk 28.6 89 0.0019 18.6 3.0 24 7-30 106-129 (130)
6 COG5251 TAF40 Transcription in 27.5 72 0.0016 22.7 2.7 28 3-30 162-189 (199)
7 PF04564 U-box: U-box domain; 25.3 70 0.0015 18.3 2.0 21 5-25 50-70 (73)
8 PF06786 UPF0253: Uncharacteri 24.2 37 0.00081 20.3 0.7 14 2-15 15-28 (66)
9 PRK04964 hypothetical protein; 24.2 37 0.00081 20.3 0.7 14 2-15 15-28 (66)
10 PF10604 Polyketide_cyc2: Poly 21.0 1.6E+02 0.0035 17.1 3.1 25 8-32 112-136 (139)
No 1
>COG3609 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]
Probab=73.48 E-value=6.7 Score=23.97 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=23.7
Q ss_pred hhhhccCCChH--HHHHHHHHHHHHHHHhHHH
Q 037116 3 ASLERNLLPDA--VIRRLCRKILADRLHSVII 32 (69)
Q Consensus 3 ~~~E~g~lPD~--~iR~gIR~Ll~~RL~~~~~ 32 (69)
.++++|..+.. +||.|+|.++.++......
T Consensus 19 ~lV~~G~y~s~SeviR~alr~l~~~~~~~~~~ 50 (89)
T COG3609 19 ELVESGRYKSRSEVIRAALRLLLEKRVDEEAR 50 (89)
T ss_pred HHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788888865 9999999999987665443
No 2
>PF05456 eIF_4EBP: Eukaryotic translation initiation factor 4E binding protein (EIF4EBP); InterPro: IPR008606 This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1, -2 and -3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F [].; GO: 0008190 eukaryotic initiation factor 4E binding, 0045947 negative regulation of translational initiation; PDB: 2JGB_B 2V8Y_F 1WKW_B 3HXG_C 3U7X_D 3M94_C 3M93_C 2V8X_B 3HXI_C 2V8W_B ....
Probab=55.33 E-value=5.9 Score=25.95 Aligned_cols=16 Identities=19% Similarity=0.584 Sum_probs=7.9
Q ss_pred HHHhHHHH-ccccCccc
Q 037116 42 LAVNLNFV-DMREMPIA 57 (69)
Q Consensus 42 ~~~~~~fi-~Lr~~PIA 57 (69)
--|.++|+ ++|.+|+|
T Consensus 48 IIYdR~FLL~~RnSPlS 64 (116)
T PF05456_consen 48 IIYDRKFLLECRNSPLS 64 (116)
T ss_dssp ----HHHHHCTCG----
T ss_pred EEEeHHHHHHhcCCCcc
Confidence 45789999 99999998
No 3
>PF11420 Subtilosin_A: Bacteriocin subtilosin A; InterPro: IPR021539 Subtilosin A is a bacteriocin from Bacillus subtilis.The protein has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31 []. ; PDB: 1PXQ_A.
Probab=36.61 E-value=9.5 Score=20.07 Aligned_cols=12 Identities=33% Similarity=0.396 Sum_probs=4.3
Q ss_pred hhccCCChHHHH
Q 037116 5 LERNLLPDAVIR 16 (69)
Q Consensus 5 ~E~g~lPD~~iR 16 (69)
+-.|++||+.+-
T Consensus 14 l~dgpipdfeia 25 (35)
T PF11420_consen 14 LVDGPIPDFEIA 25 (35)
T ss_dssp -TTTT---S--S
T ss_pred hccCCCCcchhh
Confidence 346999999773
No 4
>cd08876 START_1 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family. Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the START family (STARDs), it is known which lipids bind in this pocket; these include cholesterol (STARD1, -3, -4, and -5), 25-hydroxycholesterol (STARD5), phosphatidylcholine (STARD2, -7, and -10), phosphatidylethanolamine (STARD10) and ceramides (STARD11). Mammalian STARDs participate in the control of various cellular processes, including lipid trafficking between intracellular compartments, lipid metabolism, and modulation of signaling events. Mutation or altered expression of STARDs is linked to diseases such as cancer, genetic disorders, a
Probab=28.75 E-value=1.1e+02 Score=19.89 Aligned_cols=25 Identities=8% Similarity=0.162 Sum_probs=20.4
Q ss_pred ccCCChHHHHHHHHHHHHHHHHhHH
Q 037116 7 RNLLPDAVIRRLCRKILADRLHSVI 31 (69)
Q Consensus 7 ~g~lPD~~iR~gIR~Ll~~RL~~~~ 31 (69)
+|++|.++++...+....+-+..+.
T Consensus 167 ~g~iP~~lv~~~~~~~~~~~l~~l~ 191 (195)
T cd08876 167 GGSIPGWLANAFAKDAPYNTLENLR 191 (195)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999888777666543
No 5
>PF03364 Polyketide_cyc: Polyketide cyclase / dehydrase and lipid transport; InterPro: IPR005031 Members of this family of enzymes from Streptomyces spp. are involved in polyketide (linear poly-beta-ketones) synthesis.; PDB: 1T17_A 3GGN_B 2KCZ_A 2D4R_B 2REZ_A 2RES_A 3TVQ_A 2RER_A 2KF2_A 3TL1_A ....
Probab=28.63 E-value=89 Score=18.55 Aligned_cols=24 Identities=25% Similarity=0.373 Sum_probs=20.4
Q ss_pred ccCCChHHHHHHHHHHHHHHHHhH
Q 037116 7 RNLLPDAVIRRLCRKILADRLHSV 30 (69)
Q Consensus 7 ~g~lPD~~iR~gIR~Ll~~RL~~~ 30 (69)
.+++|..+++..++..+.+.++..
T Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~~~ 129 (130)
T PF03364_consen 106 PGPLPGFLARQFFRRDLRQMLEAF 129 (130)
T ss_dssp SSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHhHHHHHHHHHHHHHHHHHHhh
Confidence 477899999999999999887653
No 6
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=27.47 E-value=72 Score=22.72 Aligned_cols=28 Identities=21% Similarity=0.063 Sum_probs=24.6
Q ss_pred hhhhccCCChHHHHHHHHHHHHHHHHhH
Q 037116 3 ASLERNLLPDAVIRRLCRKILADRLHSV 30 (69)
Q Consensus 3 ~~~E~g~lPD~~iR~gIR~Ll~~RL~~~ 30 (69)
.|.+.|++-.+=+|-++|+++.+++...
T Consensus 162 ~w~~sgpl~p~h~reayr~~~k~~~~~~ 189 (199)
T COG5251 162 KWLTSGPLIPFHKREAYRYKLKKYLKKL 189 (199)
T ss_pred HhcccCCCChHHHHHHHHHHHHhhhccc
Confidence 4788999999999999999999988754
No 7
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=25.30 E-value=70 Score=18.33 Aligned_cols=21 Identities=19% Similarity=0.414 Sum_probs=16.5
Q ss_pred hhccCCChHHHHHHHHHHHHH
Q 037116 5 LERNLLPDAVIRRLCRKILAD 25 (69)
Q Consensus 5 ~E~g~lPD~~iR~gIR~Ll~~ 25 (69)
-+..++|+..+|..|...+.+
T Consensus 50 ~~~~l~pn~~Lk~~I~~~~~~ 70 (73)
T PF04564_consen 50 SESDLIPNRALKSAIEEWCAE 70 (73)
T ss_dssp SGGGSEE-HHHHHHHHHHHHH
T ss_pred CcccceECHHHHHHHHHHHHH
Confidence 356789999999999988765
No 8
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=24.21 E-value=37 Score=20.31 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=10.9
Q ss_pred hhhhhccCCChHHH
Q 037116 2 LASLERNLLPDAVI 15 (69)
Q Consensus 2 i~~~E~g~lPD~~i 15 (69)
|+.-+.|++||++-
T Consensus 15 IgSGd~gYiP~Ai~ 28 (66)
T PF06786_consen 15 IGSGDQGYIPDAIG 28 (66)
T ss_pred hcCCccccCcHHHH
Confidence 55678999999853
No 9
>PRK04964 hypothetical protein; Provisional
Probab=24.18 E-value=37 Score=20.32 Aligned_cols=14 Identities=29% Similarity=0.377 Sum_probs=10.9
Q ss_pred hhhhhccCCChHHH
Q 037116 2 LASLERNLLPDAVI 15 (69)
Q Consensus 2 i~~~E~g~lPD~~i 15 (69)
|+.-+.|++|+++-
T Consensus 15 IgSGd~gYiP~Ai~ 28 (66)
T PRK04964 15 IGSGDLGYVPDALG 28 (66)
T ss_pred hcCCccccCcHHHH
Confidence 55678999999863
No 10
>PF10604 Polyketide_cyc2: Polyketide cyclase / dehydrase and lipid transport; InterPro: IPR019587 This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily []. ; PDB: 3QRZ_C 3CNW_A 3P9V_A 3OQU_B 3NEF_B 3JRQ_B 3KAY_A 3JRS_A 3KDJ_A 3NMN_C ....
Probab=20.97 E-value=1.6e+02 Score=17.13 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=20.1
Q ss_pred cCCChHHHHHHHHHHHHHHHHhHHH
Q 037116 8 NLLPDAVIRRLCRKILADRLHSVII 32 (69)
Q Consensus 8 g~lPD~~iR~gIR~Ll~~RL~~~~~ 32 (69)
|++++.+++..++..+++.|+.+..
T Consensus 112 ~~~~~~~~~~~~~~~~~~~l~~l~~ 136 (139)
T PF10604_consen 112 GWLAGPLLRPAVKRIVREALENLKR 136 (139)
T ss_dssp TSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhhHHHHHHHHHHHHHHHHHHHhc
Confidence 5677888999999998888887654
Done!