Query psy14619
Match_columns 344
No_of_seqs 13 out of 15
Neff 1.7
Searched_HMMs 46136
Date Fri Aug 16 16:20:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14619hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5088 SOH1 Rad5p-binding pro 52.3 51 0.0011 28.6 6.2 89 6-115 22-110 (114)
2 TIGR00601 rad23 UV excision re 49.2 40 0.00086 33.2 5.7 14 26-39 248-261 (378)
3 COG5088 SOH1 Rad5p-binding pro 43.5 1.2E+02 0.0026 26.5 7.0 17 1-17 26-42 (114)
4 KOG4086|consensus 39.7 1.4E+02 0.0031 26.5 7.1 90 6-116 22-111 (130)
5 PF05669 Med31: SOH1; InterPr 36.6 13 0.00028 31.4 0.3 48 6-59 10-57 (101)
6 PF14624 Vwaint: VWA / Hh pro 36.0 1.1E+02 0.0024 24.3 5.3 43 87-129 14-56 (80)
7 TIGR00601 rad23 UV excision re 27.9 88 0.0019 30.8 4.4 14 17-30 248-261 (378)
8 smart00441 FF Contains two con 27.6 57 0.0012 22.4 2.2 38 5-42 5-43 (55)
9 PF09280 XPC-binding: XPC-bind 23.0 64 0.0014 24.4 1.9 9 30-38 5-13 (59)
10 PF01846 FF: FF domain; Inter 12.5 1E+02 0.0022 21.1 0.8 49 3-51 2-51 (51)
No 1
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=52.29 E-value=51 Score=28.62 Aligned_cols=89 Identities=13% Similarity=0.226 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhHHHHHHhhhHHHHHHhhhhHHHHHhhhhHHHHHhhhHHHHHHhhH
Q psy14619 6 LLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRN 85 (344)
Q Consensus 6 q~LqmL~nHqvLQmL~nHqvlqmL~nhqvlQML~NhqLfQmL~N~qLLQmL~NHllLQmL~NHllLQmL~NHllLQmL~N 85 (344)
-+.|||+|-++|..|..|+-|. ..--.++|+ ++-|-+|+-|-|.+-=..-|- .|--|.+
T Consensus 22 EFvQ~L~Np~Yl~~Ltq~~~fe---se~F~~YL~---YlEYWr~PeYs~fivYP~CL~---------------iL~lLn~ 80 (114)
T COG5088 22 EFVQSLANPQYLTLLTQQQIFE---SENFKNYLK---YLEYWRNPEYSQFIVYPNCLF---------------ILKLLNG 80 (114)
T ss_pred HHHHHhcCHHHHHHHHHhhhhc---CHHHHHHHH---HHHHhhCCcccceeechhHHH---------------HHHHhcc
Confidence 4667777777777776665442 111223332 344445554444332222221 2334555
Q ss_pred HHHHHHhhhhHHHHHhhhHHHHHHhhhhhh
Q psy14619 86 HLLIQMLRNHHLIRMLRNHLLIRMLRNHLQ 115 (344)
Q Consensus 86 hllLQmLsNHl~LQmLsNHLlLQmLsNHl~ 115 (344)
..+--+++++-++-+|-.-++++-|-.|.+
T Consensus 81 ~~~~~~vs~~~l~~~l~e~qy~~Wlnk~~e 110 (114)
T COG5088 81 FMESAIVSEDGLLEGLDELQYPQWLNKMVE 110 (114)
T ss_pred hhHhhhhhhhHHHHhhhHHHHHHHHHHHHH
Confidence 556666677777777777777777766654
No 2
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.17 E-value=40 Score=33.16 Aligned_cols=14 Identities=43% Similarity=0.650 Sum_probs=7.7
Q ss_pred HHHHHhHHHHHHhh
Q psy14619 26 IQMLRNHLLIQMLR 39 (344)
Q Consensus 26 lqmL~nhqvlQML~ 39 (344)
|..||+++-||.||
T Consensus 248 l~~Lr~~pqf~~lR 261 (378)
T TIGR00601 248 LEFLRNQPQFQQLR 261 (378)
T ss_pred HHHhhcCHHHHHHH
Confidence 45555555555555
No 3
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=43.52 E-value=1.2e+02 Score=26.46 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=11.9
Q ss_pred CcchhHHHHHHHHHHHH
Q psy14619 1 MLRNHLLIQMLRNHLLI 17 (344)
Q Consensus 1 ~l~nHq~LqmL~nHqvL 17 (344)
||+|-++|+.|..|+.+
T Consensus 26 ~L~Np~Yl~~Ltq~~~f 42 (114)
T COG5088 26 SLANPQYLTLLTQQQIF 42 (114)
T ss_pred HhcCHHHHHHHHHhhhh
Confidence 46777777777777654
No 4
>KOG4086|consensus
Probab=39.69 E-value=1.4e+02 Score=26.51 Aligned_cols=90 Identities=13% Similarity=0.263 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhHHHHHHhhhHHHHHHhhhhHHHHHhhhhHHHHHhhhHHHHHHhhH
Q psy14619 6 LLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRN 85 (344)
Q Consensus 6 q~LqmL~nHqvLQmL~nHqvlqmL~nhqvlQML~NhqLfQmL~N~qLLQmL~NHllLQmL~NHllLQmL~NHllLQmL~N 85 (344)
-+.|+|+|-.+|..|+.+.-| ++---..||+ +|.|-+|+.|-+.+.=.+-|-||. .|.+
T Consensus 22 EFVQ~LaNp~YLnfLaQ~g~f---k~e~F~nYLk---YLeYWk~PeYak~l~YP~CL~mLe---------------lL~~ 80 (130)
T KOG4086|consen 22 EFVQCLANPNYLNFLAQRGYF---KDEAFVNYLK---YLEYWKEPEYAKFLKYPQCLHMLE---------------LLQS 80 (130)
T ss_pred HHHHHhcChHHHHHHHHcccc---cCHHHHHHHH---HHHHhcCccHHHHHhhHhHHHHHH---------------Hhcc
Confidence 466777777777777666533 2222223332 455566666666655555554442 1222
Q ss_pred HHHHHHhhhhHHHHHhhhHHHHHHhhhhhhh
Q psy14619 86 HLLIQMLRNHHLIRMLRNHLLIRMLRNHLQI 116 (344)
Q Consensus 86 hllLQmLsNHl~LQmLsNHLlLQmLsNHl~~ 116 (344)
..+--+++|..++..|-.-++++-+..|.+-
T Consensus 81 ~~fr~~i~~~~~~k~ldeqq~~qW~~~~~kr 111 (130)
T KOG4086|consen 81 EQFRDEISNAQLAKFLDEQQYLQWQNYMRKR 111 (130)
T ss_pred HHHHHHHhhhHHHHHhhHHHHHHHHHHHHHH
Confidence 2333344555555555555555555544443
No 5
>PF05669 Med31: SOH1; InterPro: IPR008831 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=36.63 E-value=13 Score=31.38 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhHHHHHHhhhHHHHHHhhhh
Q psy14619 6 LLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQMLRNH 59 (344)
Q Consensus 6 q~LqmL~nHqvLQmL~nHqvlqmL~nhqvlQML~NhqLfQmL~N~qLLQmL~NH 59 (344)
-+.|.|+|..+|++|+.. .|+.+..-+.+|+ +|+|.+++.|.+++.=.
T Consensus 10 EFVQ~LaNp~Yl~~La~~---~y~~d~~F~nYLk---YL~YW~~P~Yakyl~YP 57 (101)
T PF05669_consen 10 EFVQCLANPQYLNYLAQQ---GYFEDPAFINYLK---YLQYWKRPEYAKYLVYP 57 (101)
T ss_dssp HHHHHTTSHHHHHHHH-S---GGGTSTHHHHHHH---HGGGGGSTTGGGG-SST
T ss_pred HHHHHhcCHHHHHHHHhc---CccCCHHHHHHHH---HHHHhCCCchhhhhcCh
Confidence 356777777777777644 3333333333332 23444555444444333
No 6
>PF14624 Vwaint: VWA / Hh protein intein-like
Probab=36.05 E-value=1.1e+02 Score=24.32 Aligned_cols=43 Identities=23% Similarity=0.392 Sum_probs=37.4
Q ss_pred HHHHHhhhhHHHHHhhhHHHHHHhhhhhhhhhcCCCCCCCcCc
Q psy14619 87 LLIQMLRNHHLIRMLRNHLLIRMLRNHLQIRTNAQKPPSPQNE 129 (344)
Q Consensus 87 llLQmLsNHl~LQmLsNHLlLQmLsNHl~~~~~~~~~~~~~~~ 129 (344)
+....+.+..++.-.--|+++-++.-|.+-|-|+-|.|.|+.-
T Consensus 14 qi~~a~~~~~~y~~~Gr~YllS~~ssH~~Qr~~s~~d~g~~~y 56 (80)
T PF14624_consen 14 QISEAMSSREYYERWGRHYLLSLLSSHSRQRCNSFKDPGPQQY 56 (80)
T ss_pred HHHHHHcCHHHHHHhhHHHHHHHHHHHHHHHhhhcCCCccccc
Confidence 4566778888899999999999999999999999999988754
No 7
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.88 E-value=88 Score=30.84 Aligned_cols=14 Identities=43% Similarity=0.650 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHH
Q psy14619 17 IQMLRNHLLIQMLR 30 (344)
Q Consensus 17 LQmL~nHqvlqmL~ 30 (344)
|..||+++.|+.||
T Consensus 248 l~~Lr~~pqf~~lR 261 (378)
T TIGR00601 248 LEFLRNQPQFQQLR 261 (378)
T ss_pred HHHhhcCHHHHHHH
Confidence 34444444444444
No 8
>smart00441 FF Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.
Probab=27.64 E-value=57 Score=22.37 Aligned_cols=38 Identities=16% Similarity=0.115 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHH-HHHHHHHHHHHHHhHHHHHHhhhHH
Q psy14619 5 HLLIQMLRNHLLI-QMLRNHLLIQMLRNHLLIQMLRNHL 42 (344)
Q Consensus 5 Hq~LqmL~nHqvL-QmL~nHqvlqmL~nhqvlQML~Nhq 42 (344)
..|..||+++.++ -+-.=..+...+.+|+.+.++.++-
T Consensus 5 ~~F~~LL~e~~~~~~~~~W~~~~~~~~~d~ry~~l~~~~ 43 (55)
T smart00441 5 EAFKELLKEHEVITPDTTWSEARKKLKNDPRYKALLSES 43 (55)
T ss_pred HHHHHHHHhCCCCCCCCcHHHHHHHHhcChHHHHhcChH
Confidence 4566677776554 2233334445555666555444443
No 9
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=22.95 E-value=64 Score=24.37 Aligned_cols=9 Identities=44% Similarity=0.464 Sum_probs=3.4
Q ss_pred HhHHHHHHh
Q psy14619 30 RNHLLIQML 38 (344)
Q Consensus 30 ~nhqvlQML 38 (344)
++++-|+.+
T Consensus 5 r~~Pqf~~l 13 (59)
T PF09280_consen 5 RNNPQFQQL 13 (59)
T ss_dssp TTSHHHHHH
T ss_pred HcChHHHHH
Confidence 333333333
No 10
>PF01846 FF: FF domain; InterPro: IPR002713 The FF domain may be involved in protein-protein interaction []. It often occurs as multiple copies and often accompanies WW domains IPR001202 from INTERPRO. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [].; PDB: 3HFH_B 2KIS_A 2DOD_A 2JUC_A 2LKS_A 1UZC_A 2KZG_A 2L9V_A 2DOF_A 2KFD_A ....
Probab=12.48 E-value=1e+02 Score=21.07 Aligned_cols=49 Identities=8% Similarity=0.042 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHh-hhHHHHHHhhhHH
Q psy14619 3 RNHLLIQMLRNHLLIQMLRNHLLIQMLRNHLLIQML-RNHLLIQMLRNHL 51 (344)
Q Consensus 3 ~nHq~LqmL~nHqvLQmL~nHqvlqmL~nhqvlQML-~NhqLfQmL~N~q 51 (344)
+...+.+||+++.+=-+..=..+...|.+|+.+.++ .+.--=.-+++.+
T Consensus 2 a~~~F~~lL~e~~i~~~s~W~~~~~~l~~dpry~~i~~~~~~R~~lF~ey 51 (51)
T PF01846_consen 2 AREAFKELLKEHKITPYSSWEEVKPKLSKDPRYKAIGDSESERESLFEEY 51 (51)
T ss_dssp HHHHHHHHHHHTTS-TTSSHHHHHHHHTTSCHHHHSTSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCCCcHHHHHHHHccCHHHHHhcCCHHHHHHHHHhC
Done!