Query 045556
Match_columns 96
No_of_seqs 121 out of 1089
Neff 5.1
Searched_HMMs 29240
Date Mon Mar 25 05:09:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045556.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/045556hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4ayb_B DNA-directed RNA polyme 100.0 2.1E-35 7.1E-40 257.7 4.4 90 1-96 890-987 (1131)
2 1twf_B DNA-directed RNA polyme 100.0 2.1E-35 7.1E-40 260.2 4.2 89 2-96 990-1086(1224)
3 2a6h_C DNA-directed RNA polyme 100.0 3.1E-33 1.1E-37 245.1 3.8 90 1-96 848-988 (1119)
4 3h0g_B DNA-directed RNA polyme 100.0 7.6E-33 2.6E-37 243.9 5.0 89 2-96 979-1075(1210)
5 3lu0_C DNA-directed RNA polyme 100.0 1.3E-32 4.3E-37 243.3 1.7 90 1-96 1075-1226(1342)
6 2g7j_A Putative cytoplasmic pr 29.3 12 0.00043 25.3 0.2 35 14-50 77-111 (124)
7 1h4r_A Merlin; FERM, neurofibr 22.2 19 0.00064 26.4 0.0 10 32-41 3-12 (314)
8 2d8c_A Phosphatidylcholine:cer 21.2 19 0.00066 22.9 -0.1 29 60-90 20-48 (97)
9 2wyq_A HHR23A, UV excision rep 20.0 71 0.0024 18.3 2.3 27 59-85 25-55 (85)
10 2f3n_A SH3 and multiple ankyri 20.0 17 0.00058 21.6 -0.5 30 61-90 6-35 (76)
No 1
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Probab=100.00 E-value=2.1e-35 Score=257.72 Aligned_cols=90 Identities=22% Similarity=0.284 Sum_probs=85.5
Q ss_pred CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHh
Q 045556 1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKA 72 (96)
Q Consensus 1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~ 72 (96)
.||+|+|+|| |||++||+ +|||||||||||||||||||+|+++| ..|+++|.+...+++.+.|.++
T Consensus 890 vvs~i~p~eD----MPf~~dG~--~~DiilNP~gvPSRMniGqilE~~~gk~~~~~g~~~~atpf~~~~~e~~~~~l~~~ 963 (1131)
T 4ayb_B 890 VIGMLIPQVD----MPYTVKGV--VPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKY 963 (1131)
T ss_dssp EEEEEECTTT----SEEETTSC--CCSEECCTTSSTTTTCHHHHHHHHHHHHHHHHCCCCBCCTTSSCCTHHHHHHHHHT
T ss_pred eeeeeccccc----CCcCCCCC--CccEEECCCCCcccCcHHHHHHHHHHHHHHhCCCceecCccCCCcHHHHHHHHHHc
Confidence 3799999999 99999999 99999999999999999999999999 5678888888889999999999
Q ss_pred ccCCCCCceeecCCCCccCCCCCC
Q 045556 73 CKQTANPCKTLDGQMGNPFKEHVL 96 (96)
Q Consensus 73 g~~~~g~e~lydG~TGe~~~~~I~ 96 (96)
||+++|+++||||+|||+|+++|+
T Consensus 964 g~~~~g~~~lydG~TGe~~~~~i~ 987 (1131)
T 4ayb_B 964 GYLPDATEVTYDGRTGQKIKSRIY 987 (1131)
T ss_dssp TSCTTSEECEEETTTCCBCSSCEE
T ss_pred CCCCCCCEEEeCCCCCCEecCcEE
Confidence 999999999999999999999985
No 2
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Probab=100.00 E-value=2.1e-35 Score=260.21 Aligned_cols=89 Identities=22% Similarity=0.287 Sum_probs=86.0
Q ss_pred cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556 2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC 73 (96)
Q Consensus 2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g 73 (96)
||.|+|+|| |||++||+ +|||||||||||||||||||+||++| ..|+++|.+.+++++.+.|+++|
T Consensus 990 is~i~p~eD----MPf~~dG~--~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~~~L~~~g 1063 (1224)
T 1twf_B 990 IGITYRRED----MPFTAEGI--VPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHG 1063 (1224)
T ss_dssp EEEEECTTT----SCEETTSC--CCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTT
T ss_pred eeeeccccc----CCcCCCCC--CccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHHHHHHHcC
Confidence 799999999 99999999 99999999999999999999999999 56888999999999999999999
Q ss_pred cCCCCCceeecCCCCccCCCCCC
Q 045556 74 KQTANPCKTLDGQMGNPFKEHVL 96 (96)
Q Consensus 74 ~~~~g~e~lydG~TGe~~~~~I~ 96 (96)
|+++|+++||||+||++|+++|+
T Consensus 1064 ~~~~G~e~ly~G~TG~~~~~~i~ 1086 (1224)
T 1twf_B 1064 YQSRGFEVMYNGHTGKKLMAQIF 1086 (1224)
T ss_dssp SCTTSEECEECTTTCCBCSSCEE
T ss_pred CCCCCCEEeecCCCCCCccceEE
Confidence 99999999999999999999985
No 3
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Probab=99.97 E-value=3.1e-33 Score=245.06 Aligned_cols=90 Identities=27% Similarity=0.399 Sum_probs=83.2
Q ss_pred CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc-------cccccc-cCCCcHHHHHHHHHHh
Q 045556 1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR-------HFDERY-KQKGSRKLVLSKLYKA 72 (96)
Q Consensus 1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG-------~~dg~~-~~~~~~~~i~~~L~~~ 72 (96)
.||+|+|+|| |||++||+ +|||||||||||||||||||+||++| ...+++ |++.+.+++.+.|+++
T Consensus 848 Vis~i~p~eD----MPf~~dG~--~pDiIlNPhgvPSRMtiGqllE~~lG~a~~~~g~~~atp~F~~~~~~~i~~~L~~~ 921 (1119)
T 2a6h_C 848 VVAKILPVED----MPHLPDGT--PVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQA 921 (1119)
T ss_dssp EEEEEECTTT----SCBCSSSC--BCSEECCSTTTTTTTBTHHHHHHHHHHHHHHTTEEEECCTTTSCCHHHHHHHHHHH
T ss_pred eEEeeeccCC----CccccCCC--CccEEeCCCcCccccchhhhhHHHhhhHHhhcCCceEecccCCCCHHHHHHHHHHh
Confidence 3799999999 99999999 99999999999999999999999999 223566 7778999999999999
Q ss_pred -----------------------------cc--------------CCCCCceeecCCCCccCCCCCC
Q 045556 73 -----------------------------CK--------------QTANPCKTLDGQMGNPFKEHVL 96 (96)
Q Consensus 73 -----------------------------g~--------------~~~g~e~lydG~TGe~~~~~I~ 96 (96)
|| +++|+++||||+|||+|+++|+
T Consensus 922 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~Gk~~lydG~TGe~~~~~I~ 988 (1119)
T 2a6h_C 922 FEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIV 988 (1119)
T ss_dssp HHHHHHHHHHHTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTTEECCBCSSSCCBCSSCEE
T ss_pred hhhccccccccccccchhhhhhhhhhhcCCcccccccchhhhcccCCCCceEeecCCCCCCccceEE
Confidence 99 9999999999999999999985
No 4
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.97 E-value=7.6e-33 Score=243.92 Aligned_cols=89 Identities=26% Similarity=0.312 Sum_probs=85.4
Q ss_pred cceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc--------cccccccCCCcHHHHHHHHHHhc
Q 045556 2 LLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR--------HFDERYKQKGSRKLVLSKLYKAC 73 (96)
Q Consensus 2 ~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG--------~~dg~~~~~~~~~~i~~~L~~~g 73 (96)
||+|+|+|| |||++||+ +||||||||||||||||||++|+++| ..|+++|.+.+.+++.+.|+++|
T Consensus 979 i~~i~~~ed----mPf~~~G~--~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g 1052 (1210)
T 3h0g_B 979 IGMTYRHED----MPFSAQGI--VPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHG 1052 (1210)
T ss_dssp EEEEECTTT----SCCBTTTB--CCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSCCHHHHHHHHHTTT
T ss_pred eeEEecccc----CCcCCCCC--CCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCCcHHHHHHHHHHcC
Confidence 789999999 99999999 99999999999999999999999999 35788899999999999999999
Q ss_pred cCCCCCceeecCCCCccCCCCCC
Q 045556 74 KQTANPCKTLDGQMGNPFKEHVL 96 (96)
Q Consensus 74 ~~~~g~e~lydG~TGe~~~~~I~ 96 (96)
|+++|+++||||+||++|+++|+
T Consensus 1053 ~~~~G~~~l~~g~tg~~~~~~i~ 1075 (1210)
T 3h0g_B 1053 FQSRGFEVMYHGHTGRKLVAQVF 1075 (1210)
T ss_dssp SCTTSCBCCBCSSSCCBCSSCBE
T ss_pred cCCCCCEEEEcCCCCCCccccEE
Confidence 99999999999999999999985
No 5
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C*
Probab=99.97 E-value=1.3e-32 Score=243.30 Aligned_cols=90 Identities=29% Similarity=0.413 Sum_probs=82.0
Q ss_pred CcceeccCCCccCCCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccccc---c------------------------
Q 045556 1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHF---D------------------------ 53 (96)
Q Consensus 1 ~~~~i~~~ed~~eDMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG~~---d------------------------ 53 (96)
.||+|+|+|| |||++||+ +|||||||||||||||||||+|||+|.. -
T Consensus 1075 Vis~I~p~ED----MPf~~dG~--~pDIIlNP~gvPSRMnIGqilE~~lG~aa~~~G~~i~~~~~~~~~~~~~r~~~~~~ 1148 (1342)
T 3lu0_C 1075 VISKINPIED----MPYDENGT--PVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRA 1148 (1342)
T ss_dssp EECCCCCTTT----SCEETTEE--ECSEECCGGGTTSSCBTHHHHHHHHHHGGGTSSTHHHHTTTHHHHCTTTHHHHHHH
T ss_pred eEEEEecccC----CCCCCCCC--CCcEEeCCCCCCCccchhhhhHHhhhHHHHhcCchHHHHHHhhhhhHHHHHHHHHH
Confidence 3799999999 99999999 9999999999999999999999999910 0
Q ss_pred ----------------------------------ccc-cCCCcHHHHHHHHHHhccCCCCCceeecCCCCccCCCCCC
Q 045556 54 ----------------------------------ERY-KQKGSRKLVLSKLYKACKQTANPCKTLDGQMGNPFKEHVL 96 (96)
Q Consensus 54 ----------------------------------g~~-~~~~~~~~i~~~L~~~g~~~~g~e~lydG~TGe~~~~~I~ 96 (96)
+++ |.+++.+++.+.|.++||+++|+++||||+|||+|+++|+
T Consensus 1149 y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTPvFdga~~~~i~~~L~~aG~~~~Gk~~LydGrTGe~f~~~V~ 1226 (1342)
T 3lu0_C 1149 YDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226 (1342)
T ss_dssp TTTTCCCSSSCCTTTSCHHHHHHTTTTTSSCTTCBCCSSSSCCHHHHHHHTSSSSSCSSSCBCCBCSSSCSBCSSCBC
T ss_pred hhcccccchhhhhcccchHHHHHHhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCCCEEEEcCCCCCCccccee
Confidence 222 6778899999999999999999999999999999999996
No 6
>2g7j_A Putative cytoplasmic protein; STR72, autostructure, structural genomics, PSI, protein STRU initiative; NMR {Salmonella typhimurium} SCOP: d.198.5.1
Probab=29.30 E-value=12 Score=25.31 Aligned_cols=35 Identities=9% Similarity=0.155 Sum_probs=28.1
Q ss_pred CCCCcCCCCCCCCcEEeCCCCCCCCcccccccccccc
Q 045556 14 LWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLR 50 (96)
Q Consensus 14 DMPf~~dG~~~~pDiIiNPhgvPSRMtIGqllE~~lG 50 (96)
..|---.|- .++..=-||||-|||.+-+.++.+.|
T Consensus 77 ~FPlyl~g~--~~~~yGIpHGFSSR~~L~r~l~~~F~ 111 (124)
T 2g7j_A 77 NFPLYLGGE--THEHYGIPHGFSSRIALERYLNGLFG 111 (124)
T ss_dssp CSCCCCSSS--SCCEEECEECCSCHHHHHHHHHHHHT
T ss_pred cCCcccccC--cccccCCCcCcchHHHHHHHHHHhhc
Confidence 356555788 88899999999999998887777665
No 7
>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A
Probab=22.24 E-value=19 Score=26.36 Aligned_cols=10 Identities=20% Similarity=0.355 Sum_probs=0.0
Q ss_pred CCCCCCCccc
Q 045556 32 PLEVPPRMNI 41 (96)
Q Consensus 32 PhgvPSRMtI 41 (96)
|+|+||||.+
T Consensus 3 ~~~~~~~~~~ 12 (314)
T 1h4r_A 3 AGAIASRMSF 12 (314)
T ss_dssp ----------
T ss_pred CCCCCccccc
Confidence 7899999996
No 8
>2d8c_A Phosphatidylcholine:ceramide cholinephosphotransferase 1; cell-free protein synthesis, protein regulation, lipid metabolism, structural genomics; NMR {Mus musculus} SCOP: a.60.1.2
Probab=21.22 E-value=19 Score=22.89 Aligned_cols=29 Identities=17% Similarity=-0.082 Sum_probs=20.6
Q ss_pred CcHHHHHHHHHHhccCCCCCceeecCCCCcc
Q 045556 60 GSRKLVLSKLYKACKQTANPCKTLDGQMGNP 90 (96)
Q Consensus 60 ~~~~~i~~~L~~~g~~~~g~e~lydG~TGe~ 90 (96)
=+.+++.++|++.||..+.... -+ .+|+.
T Consensus 20 Ws~edV~~WL~~~Gl~~Y~~~F-~~-IdG~~ 48 (97)
T 2d8c_A 20 WSPKKVADWLLENAMPEYCEPL-EH-FTGQD 48 (97)
T ss_dssp CCTTHHHHHHHHTTCTTTTTTT-TT-CCHHH
T ss_pred CCHHHHHHHHHHcCCHHHHHHH-Hc-CCCHH
Confidence 3678999999999998766433 34 55543
No 9
>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A
Probab=20.00 E-value=71 Score=18.28 Aligned_cols=27 Identities=15% Similarity=0.090 Sum_probs=16.7
Q ss_pred CCcHHHHHHHHHH----hccCCCCCceeecC
Q 045556 59 KGSRKLVLSKLYK----ACKQTANPCKTLDG 85 (96)
Q Consensus 59 ~~~~~~i~~~L~~----~g~~~~g~e~lydG 85 (96)
..++.++.+++.+ .|....--..+|+|
T Consensus 25 ~~TV~~lK~~i~~~~~~~gip~~~qrLi~~G 55 (85)
T 2wyq_A 25 DETVKVLKEKIEAEKGRDAFPVAGQKLIYAG 55 (85)
T ss_dssp TSBHHHHHHHHHHHHCTTTCCGGGEEEEETT
T ss_pred CCCHHHHHHHHHhhccccCCCHHHeEEEECC
Confidence 3578888888888 45554333345543
No 10
>2f3n_A SH3 and multiple ankyrin repeat domains 3; postsynaptic density, SAM domain, shank, scaffolding protein, structural protein; 2.10A {Rattus norvegicus} SCOP: a.60.1.2 PDB: 2f44_A
Probab=20.00 E-value=17 Score=21.61 Aligned_cols=30 Identities=13% Similarity=-0.221 Sum_probs=20.1
Q ss_pred cHHHHHHHHHHhccCCCCCceeecCCCCcc
Q 045556 61 SRKLVLSKLYKACKQTANPCKTLDGQMGNP 90 (96)
Q Consensus 61 ~~~~i~~~L~~~g~~~~g~e~lydG~TGe~ 90 (96)
+.+++.++|...|+..+.....-++.+|+.
T Consensus 6 s~~~V~~WL~~lgl~~Y~~~F~~~~idg~~ 35 (76)
T 2f3n_A 6 SKFDVGDWLESIHLGEHRDRFEDHEIEGAH 35 (76)
T ss_dssp CHHHHHHHHHHTTCGGGHHHHHHTTCCGGG
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHcCCCHHH
Confidence 577888888888887655544445555543
Done!