Query psy1131
Match_columns 353
No_of_seqs 349 out of 1629
Neff 6.0
Searched_HMMs 29240
Date Fri Aug 16 23:38:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1131.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/1131hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4ayb_A DNA-directed RNA polyme 100.0 2.8E-60 9.7E-65 513.1 10.6 222 41-266 290-544 (880)
2 3h0g_A DNA-directed RNA polyme 100.0 7.6E-59 2.6E-63 524.5 9.3 221 39-265 321-575 (1752)
3 1twf_A B220, DNA-directed RNA 100.0 9.5E-58 3.3E-62 515.8 11.6 223 39-265 315-569 (1733)
4 1hqm_D DNA-directed RNA polyme 100.0 5.5E-52 1.9E-56 456.8 -7.5 199 31-246 324-553 (1265)
5 2a6h_D DNA-directed RNA polyme 100.0 4.2E-51 1.4E-55 450.9 -0.5 201 28-245 581-812 (1524)
6 3lu0_D DNA-directed RNA polyme 100.0 8.3E-48 2.8E-52 419.9 -1.3 193 30-243 308-523 (1407)
7 4ayb_A DNA-directed RNA polyme 100.0 2.1E-38 7.3E-43 342.6 2.8 112 242-353 406-517 (880)
8 3h0g_A DNA-directed RNA polyme 100.0 7.6E-37 2.6E-41 345.8 3.6 197 142-353 334-548 (1752)
9 2a6h_D DNA-directed RNA polyme 100.0 5.6E-37 1.9E-41 338.9 -0.4 110 240-349 687-796 (1524)
10 1hqm_D DNA-directed RNA polyme 100.0 4.2E-37 1.4E-41 338.9 -4.8 110 240-349 427-536 (1265)
11 1twf_A B220, DNA-directed RNA 100.0 4.3E-36 1.5E-40 339.8 3.3 113 241-353 430-542 (1733)
12 3lu0_D DNA-directed RNA polyme 100.0 1E-35 3.5E-40 325.2 -0.3 189 142-351 330-519 (1407)
13 3qqc_A DNA-directed RNA polyme 95.1 0.0022 7.6E-08 64.4 -1.5 36 42-81 358-394 (436)
14 2j7n_A RNA-dependent RNA polym 70.5 10 0.00035 41.8 8.2 54 134-189 571-636 (1022)
15 1wid_A DNA-binding protein RAV 52.3 9.9 0.00034 31.3 3.2 62 13-74 50-117 (130)
16 1yel_A AT1G16640; CESG, protei 50.4 6.4 0.00022 30.9 1.7 45 16-60 41-89 (104)
17 4i1k_A B3 domain-containing tr 34.0 17 0.00057 30.7 1.8 55 15-69 80-140 (146)
18 2k8f_B Cellular tumor antigen 28.4 24 0.00082 23.0 1.4 29 297-326 7-35 (39)
No 1
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=100.00 E-value=2.8e-60 Score=513.08 Aligned_cols=222 Identities=39% Similarity=0.631 Sum_probs=197.1
Q ss_pred CCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHHHH
Q psy1131 41 CGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFELV 91 (353)
Q Consensus 41 ~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~lV 91 (353)
.+.+..+.|. |.|++|+|+||+|||||||++++|+|+ ++|. +|+++|
T Consensus 290 ~~~rp~ksl~----~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~~l~~~v 365 (880)
T 4ayb_A 290 RSGRPLRTLA----QRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFV 365 (880)
T ss_dssp TTSCCCCCHH----HHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHHHHHHHH
T ss_pred CCCCcccchh----hhhcccchhhhhcccceeecccCceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHHHHHHHH
Confidence 3445556664 599999999999999999999988872 3454 899999
Q ss_pred HhCCCCCCCceEEEeCCCceEEeecCCCCCc--cccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeee
Q psy1131 92 RRGNSQYPGAKYIVRDNGERIDLRFHPKPSD--LHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 169 (353)
Q Consensus 92 ~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~--~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~ 169 (353)
.|||+.||||+++++++|.++.+++...... ..|++||+|+||+.|||+|||||||||||+|||||++++++|+||||
T Consensus 366 ~ng~~~~pga~~~i~~~~~~~~l~~~~~~~~~~~~l~~g~~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktirl 445 (880)
T 4ayb_A 366 INGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRL 445 (880)
T ss_dssp HHTTSSSSCEEEEECSSCCEEEGGGCSSCTTHHHHCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEEE
T ss_pred HcCCccccchhhhhhccceEEEeecchhhhHHHHhccccceEeeeeecCcEEEecCCCcccccceeeeeeecccCceeee
Confidence 9999999999999999999999987654433 25899999999999999999999999999999999999999999999
Q ss_pred ecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccc--
Q psy1131 170 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHI-- 247 (353)
Q Consensus 170 ~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l-- 247 (353)
||+||+||||||||||||+|||||++||+||++||++++|++||++|+|+++++||+++|+|+||.++.|+++++++.
T Consensus 446 hp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~~~~~~~~~ 525 (880)
T 4ayb_A 446 NLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQIL 525 (880)
T ss_dssp CGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHSBSGGGCBCSSSSSBCSCCCSHHHHHHHHHTSSSCEECHHHHHHHH
T ss_pred ccccccccccCcccceeEEeccCCHHHHHHHHHHHhChhccccCCCCCccccccccHHHHhHHhhcCcccCCHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999987652
Q ss_pred cCcceeeecCCcccccccc
Q psy1131 248 RDGDLVIFNRQPTLHKMSM 266 (353)
Q Consensus 248 ~d~d~vI~nrqPtIhk~s~ 266 (353)
...+..+...+|++.++..
T Consensus 526 ~~~~~~~~~~~p~i~~~~~ 544 (880)
T 4ayb_A 526 GVADVKIDLGEPAILAPRE 544 (880)
T ss_dssp TTSCCCCCCCSCSEESSSE
T ss_pred cccceecccCccceeccee
Confidence 2334445567788887654
No 2
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=7.6e-59 Score=524.51 Aligned_cols=221 Identities=54% Similarity=0.864 Sum_probs=198.1
Q ss_pred ccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHH
Q psy1131 39 LQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFE 89 (353)
Q Consensus 39 l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~ 89 (353)
++.+.+..+.| .|.|++|+|+||.|||||||++++|+|+ .+|. +||+
T Consensus 321 ~~~~~rp~k~~----~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~ 396 (1752)
T 3h0g_A 321 LQKSGRPLKSI----RARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQE 396 (1752)
T ss_dssp CSSSSCCCCCH----HHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTHHHHHH
T ss_pred cccCCCCCcch----HhhhhcccccccccccccccCCccceeecCCCCcccceeeChHHHHHhcCCCccccHHHHHHHHH
Confidence 34444555555 5699999999999999999999988862 3454 8999
Q ss_pred HHHhCCCCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeee
Q psy1131 90 LVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 169 (353)
Q Consensus 90 lV~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~ 169 (353)
+|.|||+.||||+||++++|.+++|++.++.....|++||+|+|||.+||+|||||||||||+|||||++++++|+||||
T Consensus 397 lv~nG~~~~pga~~v~~~~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~gktirl 476 (1752)
T 3h0g_A 397 LVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRL 476 (1752)
T ss_dssp HHHHCTTSSSCEEEEECTTCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSSSSEEE
T ss_pred HHHcCCccccCceeeecCCCcEeechhhchhhhhhcCcCcEEEeeeccCCeEEEecCcccchhhcccccceeecCceeee
Confidence 99999999999999999999999999887766678999999999999999999999999999999999999999999999
Q ss_pred ecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeecccccccc-
Q psy1131 170 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIR- 248 (353)
Q Consensus 170 ~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~- 248 (353)
||+||+||||||||||||+|+||+++||+||++||++.+|+++|++|+|+++++||+++|+|+||.++.|+++++++..
T Consensus 477 h~~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~~~e~~~l~ 556 (1752)
T 3h0g_A 477 NLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIM 556 (1752)
T ss_dssp EGGGSGGGTCCSSSCEEEEECCCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEETHHHHGGG
T ss_pred chhhCCCccCccccceeeeeccCCHHHHHHHHHHhcCccceecCCCCCceeeecchhhhheeeeccccccCCHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999887531
Q ss_pred ----CcceeeecCCccccccc
Q psy1131 249 ----DGDLVIFNRQPTLHKMS 265 (353)
Q Consensus 249 ----d~d~vI~nrqPtIhk~s 265 (353)
+.+. ..++|+|.|+.
T Consensus 557 ~~~~~~~~--~~~~pai~kp~ 575 (1752)
T 3h0g_A 557 LWVPDWDG--ILPPPVILKPK 575 (1752)
T ss_dssp GCSSSCCS--SCCCCSBCSSS
T ss_pred HhhcccCC--ccCccceecCc
Confidence 1222 24678888864
No 3
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=100.00 E-value=9.5e-58 Score=515.83 Aligned_cols=223 Identities=50% Similarity=0.782 Sum_probs=197.5
Q ss_pred ccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc----------------------------ccch-HHHH
Q psy1131 39 LQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF----------------------------RMNL-RMFE 89 (353)
Q Consensus 39 l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf----------------------------~~N~-~Lr~ 89 (353)
.+.+.+..+-| .|.|++|+|+||+|||||||++++|+|+ .+|. +|++
T Consensus 315 ~~~~~rp~k~i----~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ni~~l~~ 390 (1733)
T 1twf_A 315 LQKSGRPVKSI----RARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQ 390 (1733)
T ss_dssp SSCTTCCCCCS----TTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHH
T ss_pred ccCCCccchhH----HHHhccccchhhhcccccccCcccceEEeCCCCcccccccCcHHHHHhCCCCccccHHHHHHHHH
Confidence 34444555555 4599999999999999999999988872 3454 7999
Q ss_pred HHHhCCCCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCceeee
Q psy1131 90 LVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 169 (353)
Q Consensus 90 lV~nGp~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~r~ 169 (353)
+|.|||+.||||+++++++|.+++|++..+.....|++||+|+|||.+||+|||||||||||+|||||++++++|+||||
T Consensus 391 lv~~g~~~~~ga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~~tirl 470 (1733)
T 1twf_A 391 LVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRL 470 (1733)
T ss_dssp HHHHTTTSSSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEE
T ss_pred HHHcCCccCCCceeEEcCCCcEEeccccchhhhhhcccCCEEEeeeccCCEEEEeCCCccccccceeEEEEEccCCeEEe
Confidence 99999999999999999999999999877666677999999999999999999999999999999999999999999999
Q ss_pred ecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccccccccC
Q psy1131 170 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVERHIRD 249 (353)
Q Consensus 170 ~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~kee~~l~d 249 (353)
||+||+||||||||||||+|+|||++||+||++||++.+|+++|++|+|+++++||+++|+|+||.++.|+++++++..-
T Consensus 471 np~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~~~e~~~~~ 550 (1733)
T 1twf_A 471 NLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNML 550 (1733)
T ss_dssp CGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHH
T ss_pred ChhhcCCCCccchhhhhhhhcCCCHHHHHHHHHHhcCcccEEecCCCCeeEeeeccccccceeeecCcccCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998875211
Q ss_pred ---cceeeecCCccccccc
Q psy1131 250 ---GDLVIFNRQPTLHKMS 265 (353)
Q Consensus 250 ---~d~vI~nrqPtIhk~s 265 (353)
.+..-..++|+|.|+.
T Consensus 551 ~~~~~~~~~~~~pai~kp~ 569 (1733)
T 1twf_A 551 YWVPDWDGVIPTPAIIKPK 569 (1733)
T ss_dssp HHSTTCCSCCCCCSBCSSS
T ss_pred HhhhhhcCccCCccccCcc
Confidence 1111134678988864
No 4
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=100.00 E-value=5.5e-52 Score=456.82 Aligned_cols=199 Identities=18% Similarity=0.301 Sum_probs=170.2
Q ss_pred CCCCCCccccCCcEE-eeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHH
Q psy1131 31 HPKPSDLHLQCGYKV-ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMF 88 (353)
Q Consensus 31 ~~~~~~~~l~~g~~v-erhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr 88 (353)
+.+++.+..+.+.+. .+.|. |.|++|+|+||.|||||||++++|+|+ .+++.++
T Consensus 324 n~~~g~~~~~~~~rp~lksl~----~~LkGK~GrfR~NLmGKRVdfSaRSVI~pdP~L~i~evGvP~~~A~~L~~P~~~~ 399 (1265)
T 1hqm_D 324 NGRRGSPVTNPGSERPLRSLT----DILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLK 399 (1265)
T ss_dssp CCSSCCCSSCSSCCCCCCCST----TTSSSTTCTTTTTTSCCEETTCCCCBEEECCSSSSSBCCCBHHHHHHHHHHHHHH
T ss_pred CCCCCCCccCCCCCccccchh----hhcccchhhhhhhhcccccCcccceeEecCCCcccccccChHHHHHHhCcHHHHH
Confidence 434443444556665 66664 499999999999999999999999983 2335789
Q ss_pred HHHHhCC-CCCCCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCcee
Q psy1131 89 ELVRRGN-SQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF 167 (353)
Q Consensus 89 ~lV~nGp-~~~pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t~ 167 (353)
+||.||+ ..+++|++++++.+. . -..+|.|+||+.+||+|||||||||||+|||||++++++++||
T Consensus 400 ~lv~~g~~~~i~~ak~~i~~~~~--------~-----~~~~~~v~~~v~~gd~VLlNRqPTLHr~sIma~~~~l~~~kti 466 (1265)
T 1hqm_D 400 KMEEKAFAPNVKAARRMLERQRD--------I-----KDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSI 466 (1265)
T ss_dssp HHHHTTCSSCSHHHHHHHCSSSC--------C-----CHHHHTTTTTTTTTCCEECCCSSCCSGGGSCEEBCCCBSSSSE
T ss_pred HHHHcCCcchhhhhhhhhhhccc--------c-----CCccceeEEEeccCcEEEEecCcccccccccceeEEecCCCeE
Confidence 9999997 467888876643110 0 1124778999999999999999999999999999999999999
Q ss_pred eeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccc--------ee
Q psy1131 168 RMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD--------VF 239 (353)
Q Consensus 168 r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD--------~F 239 (353)
||||+||+||||||||||||+|+|||++||+|++.||++++|++||++|+|+++++||+++|+|+||.++ .|
T Consensus 467 rlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~~~~~~~~~~F 546 (1265)
T 1hqm_D 467 QLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAF 546 (1265)
T ss_dssp EECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTSSSSBSSSSSSSCSSSSCSSCCCTTHHHHHHHTTCCCCCCCCCCCCS
T ss_pred EechhhcCCcCCCcccceEEEecCCCHHHHHHHHHHhCccccEecCCCCCeeEeeeccccceeEEeccccCCccCCCccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999988 57
Q ss_pred ecccccc
Q psy1131 240 LDKVERH 246 (353)
Q Consensus 240 ~~kee~~ 246 (353)
+++++++
T Consensus 547 ~~~~e~~ 553 (1265)
T 1hqm_D 547 ATPEEAL 553 (1265)
T ss_dssp SCCTHHH
T ss_pred CCHHHHH
Confidence 7777765
No 5
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=100.00 E-value=4.2e-51 Score=450.87 Aligned_cols=201 Identities=19% Similarity=0.313 Sum_probs=170.3
Q ss_pred eccCCCCCCccccCCcEE-eeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccch
Q psy1131 28 LRFHPKPSDLHLQCGYKV-ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNL 85 (353)
Q Consensus 28 l~~~~~~~~~~l~~g~~v-erhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~ 85 (353)
|-.+.+++.+..+.|.+. .+.|.| .|++|+|+||+|||||||+++.|+|+ .+.+
T Consensus 581 liDN~~~g~p~~~~~~Rp~lKslsq----~LkGKeGRFRqNLlGKRVDySgRSVI~pdP~L~l~evGvP~~mA~eLt~Pf 656 (1524)
T 2a6h_D 581 LLDNGRRGAPVTNPGSDRPLRSLTD----ILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPF 656 (1524)
T ss_dssp HHCSSSSSCCBCSSSCCCBCCCHHH----HHSTTTCHHHHHHHCEEESSEEEEEEEECTTSCTTEEEEEHHHHHHHTHHH
T ss_pred HhcCCCCCCCccCCCCCCcCcchhh----hccccccccccccccccccccCcceEecCCCccccccCCcHHHHHHhccHH
Confidence 344555555555667666 677754 99999999999999999999999883 2345
Q ss_pred HHHHHHHhCCCCC-CCceEEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecC
Q psy1131 86 RMFELVRRGNSQY-PGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPW 164 (353)
Q Consensus 86 ~Lr~lV~nGp~~~-pGA~~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~ 164 (353)
.|++||.||+..+ ++|++++++.+. . -..+|.|+||+.+||+|||||||||||+|||||+++++++
T Consensus 657 ~~r~Lv~nG~a~nik~AK~li~~~~~--------~-----~~~v~dVlr~vidgd~VLlNRqPTLHRlSIqAf~~kl~~g 723 (1524)
T 2a6h_D 657 LLKKMEEKGIAPNVKAARRMLERQRD--------I-----KDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEG 723 (1524)
T ss_dssp HHHHHHHSTTCSSHHHHHHHHSSGGG--------C-----CHHHHHHHHHHSTTCCEEEECSSCCSGGGEEEEEEEEESS
T ss_pred HHHHHHHcCCccchhhhhHHHhhhcc--------c-----cccchhhheeeccCceEEEccCCcccccccceeEEEEcCC
Confidence 8999999998654 788876532100 0 1124789999999999999999999999999999999999
Q ss_pred ceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccc-------
Q psy1131 165 STFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRD------- 237 (353)
Q Consensus 165 ~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD------- 237 (353)
+||||||+||+||||||||||||+|+|||++||+||+.||++++|++||++|+|+++++||+++|+|+||.++
T Consensus 724 kTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~~LM~~~~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~~~~~~~g 803 (1524)
T 2a6h_D 724 QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAG 803 (1524)
T ss_dssp SCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHHHHSBTTTCCBCSSSSSBSSCCCHHHHHHHHHHHCCCCCCCCSC
T ss_pred ccceeChhhcCCccCCcccceeeEecCCCHHHHHHHHHHhCCccceecCCCCCeeeeecccchhhheecccccccccCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999974
Q ss_pred -eeeccccc
Q psy1131 238 -VFLDKVER 245 (353)
Q Consensus 238 -~F~~kee~ 245 (353)
.|+++++.
T Consensus 804 ~~F~~~~e~ 812 (1524)
T 2a6h_D 804 LEFATPEEA 812 (1524)
T ss_dssp CCTTSCHHH
T ss_pred ceeCCHHHH
Confidence 45555544
No 6
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=100.00 E-value=8.3e-48 Score=419.93 Aligned_cols=193 Identities=21% Similarity=0.324 Sum_probs=160.5
Q ss_pred cCCCCCCccccCCcEEeeeccccceeEeecCCCccccceeeeeeeeeccccc---------------------ccchHHH
Q psy1131 30 FHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTF---------------------RMNLRMF 88 (353)
Q Consensus 30 ~~~~~~~~~l~~g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~~vf---------------------~~N~~Lr 88 (353)
.+.+++......+.+..+.|. |.|++|+|+||.|+|||||++++|+|+ ..++.++
T Consensus 308 Dn~~~g~~~~~~~~rplksl~----qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L~i~evGvP~~~A~~L~~Pf~i~ 383 (1407)
T 3lu0_D 308 DNGRRGRAITGSNKRPLKSLA----DMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYG 383 (1407)
T ss_dssp CSSSSCCCCBTTBCCCCCCTT----HHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSCCTTEEEEESHHHHHHTCHHHHH
T ss_pred CCCCCCCcccCCCCCcccchH----HHhccccchhhcccccCCCCCcCceEEeCCCCccceeeeCCHHHHHHhcchHHHH
Confidence 344444333445566667775 499999999999999999999999883 2234677
Q ss_pred HHHHhCCC-CCCCce-EEEeCCCceEEeecCCCCCccccccccEEeeeeccCCeeeEecCCCccccceeeeeEEEecCce
Q psy1131 89 ELVRRGNS-QYPGAK-YIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWST 166 (353)
Q Consensus 89 ~lV~nGp~-~~pGA~-~v~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~~t 166 (353)
+|..+|+. .++.|+ ++.+.+ ...|.|+||+.+||+|||||||||||+|||||++++++++|
T Consensus 384 ~L~~~g~~~~i~~ak~~v~~~~-----------------~~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~kt 446 (1407)
T 3lu0_D 384 KLELRGLATTIKAAKKMVEREE-----------------AVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKA 446 (1407)
T ss_dssp HHTTSSSCSSTTTTTTTTTSSC-----------------SSHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSS
T ss_pred HHHHcCccccHHHHHHHHHhcC-----------------CchhhHHHHHhhceeeeecCCcccccccceeeeEEecCCce
Confidence 88888864 334443 221111 12366889999999999999999999999999999999999
Q ss_pred eeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceeeeeeeeeeeeeeccccceeeccc
Q psy1131 167 FRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKV 243 (353)
Q Consensus 167 ~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~gliQD~i~g~~~LT~rD~F~~ke 243 (353)
|||||++|+||||||||||||+|+|||++||+|++.||++++|++||++|+|+++++||+++|+|+||.++.|...+
T Consensus 447 irlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~~~~~~~ 523 (1407)
T 3lu0_D 447 IQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGE 523 (1407)
T ss_dssp EEECTGGGGTTTCCSSSCEEEEECCCSSHHHHTTTTSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCCCCSCCS
T ss_pred EEeChhhcccccCCcccceeeeecCCCHHHHHHHHHHHhCccccccCCCCCceeeecccchheeEEeecccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998765443
No 7
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Probab=100.00 E-value=2.1e-38 Score=342.55 Aligned_cols=112 Identities=54% Similarity=0.880 Sum_probs=108.9
Q ss_pred cccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCe
Q psy1131 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQ 321 (353)
Q Consensus 242 kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~ 321 (353)
..++++.++|+|++||||||||+|||||++++++++|||+||++|+||||||||||||+|+|||++|++||++||++++|
T Consensus 406 ~V~rhl~dgd~VLlNRqPTLHr~si~a~~~~l~~gktirlhp~vC~~yNADFDGDeMnvHvPqS~eA~aEa~~Lm~~~~n 485 (880)
T 4ayb_A 406 VVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKN 485 (880)
T ss_dssp EEEEECCTTCEEEEECSSCCSGGGEEEEEEEECSSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHSBSGGG
T ss_pred eEeeeeecCcEEEecCCCcccccceeeeeeecccCceeeeccccccccccCcccceeEEeccCCHHHHHHHHHHHhChhc
Confidence 45678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 322 IITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 322 ~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
++||++|+|+++++||+++|+|+||.+|+|++
T Consensus 486 ilsP~~G~Pii~~~QD~vlg~y~lT~~~~~~~ 517 (880)
T 4ayb_A 486 IITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517 (880)
T ss_dssp CBCSSSSSBCSCCCSHHHHHHHHHTSSSCEEC
T ss_pred cccCCCCCccccccccHHHHhHHhhcCcccCC
Confidence 99999999999999999999999999999975
No 8
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=7.6e-37 Score=345.79 Aligned_cols=197 Identities=48% Similarity=0.749 Sum_probs=145.9
Q ss_pred eEecCCCccccceeeeeEE------EecCceeeeecccCCCCCCCCCCCce--eeeccCC--HhhHHHHHHHhcCCceee
Q psy1131 142 IFNRQPTLHKMSMMGHRVR------VLPWSTFRMNLSCTSPYNADFDGDEM--NLHVPQS--METRAEVENIHVTPRQII 211 (353)
Q Consensus 142 l~nRqPtLhr~s~ma~~~~------~~~~~t~r~~~~~c~~~NADFDGDem--nlh~Pqs--~~a~aE~~~l~~~~~~~l 211 (353)
.+...-...|.++||.||. |.++..|++|.+- -| .+| +|++|+. .....+++++.....
T Consensus 334 ~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evG-vP-------~~~A~~Lt~Pe~vt~~ni~~l~~lv~nG~--- 402 (1752)
T 3h0g_A 334 RLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELG-VP-------RSIAKTLTYPETVTPYNIYQLQELVRNGP--- 402 (1752)
T ss_dssp HHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCB-CC-------HHHHTSCCCCCBCCTTTHHHHHHHHHHCT---
T ss_pred hhhcccccccccccccccCCccceeecCCCCcccceee-Ch-------HHHHHhcCCCccccHHHHHHHHHHHHcCC---
Confidence 3444567788888877665 5566667776633 34 344 5556633 233445555542211
Q ss_pred ecCCCCceeeeeeeeeeeee----eccc----cceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccc
Q psy1131 212 TPQNNRPVMGIVQDTLTAVR----KMTK----RDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNL 283 (353)
Q Consensus 212 sP~~g~Pi~gliQD~i~g~~----~LT~----rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~ 283 (353)
+..|....+... .+.+ .... .-...++.++++.++|.||+||||||||+|||||++++++|+|||+|+
T Consensus 403 ---~~~pga~~v~~~-~~~~~~l~~~~~~~~~~l~~g~~v~r~l~~gd~Vl~NRqPtLHr~sima~~~~v~~gktirlh~ 478 (1752)
T 3h0g_A 403 ---DEHPGAKYIIRD-TGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNL 478 (1752)
T ss_dssp ---TSSSCEEEEECT-TCCBCCTTTTCSCCCCCCCSSCEEEECCCSCCEEEEECSSCCSGGGEEEEECCCCSSSSEEEEG
T ss_pred ---ccccCceeeecC-CCcEeechhhchhhhhhcCcCcEEEeeeccCCeEEEecCcccchhhcccccceeecCceeeech
Confidence 111222222110 0000 0000 011345667889999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 284 SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 284 ~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
++|+||||||||||||+|+|||++|||||++||++++|++||++|+|+++++||+|+|+|+||.+|+|++
T Consensus 479 ~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~vlg~y~lT~~~~f~~ 548 (1752)
T 3h0g_A 479 SVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLT 548 (1752)
T ss_dssp GGSGGGTCCSSSCEEEEECCCSTTHHHHHHHTCCTTTTSEETTTTEESCCCCTHHHHHHHHHHSTTCEEE
T ss_pred hhCCCccCccccceeeeeccCCHHHHHHHHHHhcCccceecCCCCCceeeecchhhhheeeeccccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999985
No 9
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=100.00 E-value=5.6e-37 Score=338.89 Aligned_cols=110 Identities=24% Similarity=0.445 Sum_probs=105.0
Q ss_pred eccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCC
Q psy1131 240 LDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTP 319 (353)
Q Consensus 240 ~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~ 319 (353)
.+....++.++|+|++||||||||+|||||++++++|+||++||++|+||||||||||||+|+|||++|++|++.||+++
T Consensus 687 v~dVlr~vidgd~VLlNRqPTLHRlSIqAf~~kl~~gkTiRLhplVC~pyNADFDGDEMnvHvPqS~eAraEA~~LM~~~ 766 (1524)
T 2a6h_D 687 VWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSA 766 (1524)
T ss_dssp HHHHHHHHSTTCCEEEECSSCCSGGGEEEEEEEEESSSCEEECSGGGTTTTCCTTTCEEEEECCCSHHHHHHHHHHSBTT
T ss_pred chhhheeeccCceEEEccCCcccccccceeEEEEcCCccceeChhhcCCccCCcccceeeEecCCCHHHHHHHHHHhCCc
Confidence 34445567899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeecCCCCCceEEeehheeeeeeeecccc
Q psy1131 320 RQIITPQNNRPVMGIVQDTLTAVRKMTKRD 349 (353)
Q Consensus 320 ~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d 349 (353)
+|++||++|+|+++++||+++|+|+||.+|
T Consensus 767 ~nilsP~~G~Pi~~~~QD~vlG~y~LT~~~ 796 (1524)
T 2a6h_D 767 HNLLSPASGEPLAKPSRDIILGLYYITQVR 796 (1524)
T ss_dssp TCCBCSSSSSBSSCCCHHHHHHHHHHHCCC
T ss_pred cceecCCCCCeeeeecccchhhheeccccc
Confidence 999999999999999999999999999985
No 10
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=100.00 E-value=4.2e-37 Score=338.88 Aligned_cols=110 Identities=24% Similarity=0.445 Sum_probs=106.0
Q ss_pred eccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCC
Q psy1131 240 LDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTP 319 (353)
Q Consensus 240 ~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~ 319 (353)
.+....++.++|+|++||||||||+|||||++++++|+||++||++|+||||||||||||+|+|||++|+||+++||+++
T Consensus 427 ~~~v~~~v~~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlhp~vC~~yNADFDGDeMnvHvPqs~eA~aEa~~Lm~~~ 506 (1265)
T 1hqm_D 427 VWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSA 506 (1265)
T ss_dssp HHTTTTTTTTTCCEECCCSSCCSGGGSCEEBCCCBSSSSEEECGGGHHHHCCCSSSCBCCCCCCCSTHHHHTTSSSSBSS
T ss_pred cceeEEEeccCcEEEEecCcccccccccceeEEecCCCeEEechhhcCCcCCCcccceEEEecCCCHHHHHHHHHHhCcc
Confidence 34455678899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeecCCCCCceEEeehheeeeeeeecccc
Q psy1131 320 RQIITPQNNRPVMGIVQDTLTAVRKMTKRD 349 (353)
Q Consensus 320 ~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d 349 (353)
+|++||++|+|+++++||+++|+|+||.+|
T Consensus 507 ~nilsP~~G~Pi~~~~QD~vlg~y~LT~~~ 536 (1265)
T 1hqm_D 507 HNLLSPASGEPLAKPSRDIILGLYYITQVR 536 (1265)
T ss_dssp SSSSSCSSSSCSSCCCTTHHHHHHHTTCCC
T ss_pred ccEecCCCCCeeEeeeccccceeEEecccc
Confidence 999999999999999999999999999999
No 11
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=100.00 E-value=4.3e-36 Score=339.77 Aligned_cols=113 Identities=70% Similarity=1.098 Sum_probs=109.7
Q ss_pred ccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEEeecCChhHHHHHHHHhcCCC
Q psy1131 241 DKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPR 320 (353)
Q Consensus 241 ~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~~~p~s~~a~~E~~~l~~~~~ 320 (353)
++.++++.++|.|++||||||||+|||||++++++|+|||+|+++|+||||||||||||+|+|||++|||||++||++++
T Consensus 430 ~~v~r~l~~gd~VllNRqPTLHr~si~a~~~~v~~~~tirlnp~vC~~yNADFDGDeMnvHvPqs~eAraEa~~Lm~~~~ 509 (1733)
T 1twf_A 430 WKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL 509 (1733)
T ss_dssp CEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECGGGHHHHTCCSSSCEEEEECCCSHHHHHHHHHHTBGGG
T ss_pred CEEEeeeccCCEEEEeCCCccccccceeEEEEEccCCeEEeChhhcCCCCccchhhhhhhhcCCCHHHHHHHHHHhcCcc
Confidence 45577889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCCCceEEeehheeeeeeeecccccccC
Q psy1131 321 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353 (353)
Q Consensus 321 ~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f~~ 353 (353)
|++||++|+|+++++||+|+|+|+||.+|+|++
T Consensus 510 nilsP~~G~Pi~~~~QD~v~g~y~lT~~~~f~~ 542 (1733)
T 1twf_A 510 QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542 (1733)
T ss_dssp GSEETTTTEESCCCCHHHHHHHHHHHSTTCEEE
T ss_pred cEEecCCCCeeEeeeccccccceeeecCcccCC
Confidence 999999999999999999999999999999975
No 12
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=100.00 E-value=1e-35 Score=325.17 Aligned_cols=189 Identities=20% Similarity=0.366 Sum_probs=137.8
Q ss_pred eEecCCCccccceeeeeEEEecCceeeeecccCCCCCCCCCCCceeeeccCCHhhHHHHHHHhcCCceeeecCCCCceee
Q psy1131 142 IFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMG 221 (353)
Q Consensus 142 l~nRqPtLhr~s~ma~~~~~~~~~t~r~~~~~c~~~NADFDGDemnlh~Pqs~~a~aE~~~l~~~~~~~lsP~~g~Pi~g 221 (353)
.+.-.....|.++||.||.+.....|--.| ...=||+. +|.... .|+.....+.+.. ..|
T Consensus 330 rLkGKeGrfR~NLmGKRVDfSaRSVIspdP--------~L~i~evG--vP~~~A--~~L~~Pf~i~~L~---~~g----- 389 (1407)
T 3lu0_D 330 MIKGKQGRFRQNLLGKRVDYSGRSVITVGP--------YLRLHQCG--LPKKMA--LELFKPFIYGKLE---LRG----- 389 (1407)
T ss_dssp HHHTSSSTHHHHTTCCCCSSBCEEEEEECS--------SCCTTEEE--EESHHH--HHHTCHHHHHHHT---TSS-----
T ss_pred HhccccchhhcccccCCCCCcCceEEeCCC--------Cccceeee--CCHHHH--HHhcchHHHHHHH---HcC-----
Confidence 344456788889998887765543332222 22335544 565553 2332211111100 011
Q ss_pred eeeeeeeeee-eccccceeeccccccccCcceeeecCCcccccccccceeeEEecCceeeccccccCCCCCCCCCCeeEE
Q psy1131 222 IVQDTLTAVR-KMTKRDVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNL 300 (353)
Q Consensus 222 liQD~i~g~~-~LT~rD~F~~kee~~l~d~d~vI~nrqPtIhk~s~~~~~~~i~~~~ti~~~~~~~~~~naDFDGDem~~ 300 (353)
.... +.+++ ++...+...+....++.++|.+++|||||||++|+|||++++++|+||++||++|+||||||||||||+
T Consensus 390 ~~~~-i~~ak~~v~~~~~~v~~vl~~vi~gd~VLlNRqPTLHr~sIma~~~~l~~~ktirlnp~vC~~yNADFDGDeMnv 468 (1407)
T 3lu0_D 390 LATT-IKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAV 468 (1407)
T ss_dssp SCSS-TTTTTTTTTSSCSSHHHHHHTTTTSCCEEEEESSCCSGGGEEEEEEEEESSSSEEECTGGGGTTTCCSSSCEEEE
T ss_pred cccc-HHHHHHHHHhcCCchhhHHHHHhhceeeeecCCcccccccceeeeEEecCCceEEeChhhcccccCCcccceeee
Confidence 1111 12222 222223333444456788999999999999999999999999999999999999999999999999999
Q ss_pred eecCChhHHHHHHHHhcCCCeeecCCCCCceEEeehheeeeeeeecccccc
Q psy1131 301 HVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVF 351 (353)
Q Consensus 301 ~~p~s~~a~~E~~~l~~~~~~~~s~~~g~p~~~~~QD~~~g~~~lt~~d~f 351 (353)
|+|||++|++|+++||++++|++||++|+|+++++||+++|+|+||.+|.|
T Consensus 469 HvPqs~eAraEa~~Lm~~~~nilsP~~G~Pi~~~~QD~llG~y~lT~~~~~ 519 (1407)
T 3lu0_D 469 HVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVN 519 (1407)
T ss_dssp ECCCSSHHHHTTTTSSBTTTCCSCSSSSSCSSCCCSHHHHHHHHHSCCCCC
T ss_pred ecCCCHHHHHHHHHHHhCccccccCCCCCceeeecccchheeEEeeccccc
Confidence 999999999999999999999999999999999999999999999999975
No 13
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus}
Probab=95.13 E-value=0.0022 Score=64.41 Aligned_cols=36 Identities=6% Similarity=-0.077 Sum_probs=9.2
Q ss_pred CcEEeeeccccceeEeecCCCccccceeeeeeeeecc-ccc
Q psy1131 42 GYKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPW-STF 81 (353)
Q Consensus 42 g~~verhl~d~~~~~~~~~~~l~r~~~mGkRv~v~p~-~vf 81 (353)
+.+..+.| .|.|++|+|+||.|+|||||+++.+ +|+
T Consensus 358 ~~rp~ksi----~~rLkGKeGRfR~NL~GKRVdy~~~~s~~ 394 (436)
T 3qqc_A 358 SGRPLKTL----AQRLKGKEGRFRGNLSGGAGSGAGSGSVL 394 (436)
T ss_dssp TSCBCCCH----HHHHCC-----------------------
T ss_pred CCCCccch----HhhhccccceecCcCCCCCCCcccchhHH
Confidence 44555555 5699999999999999999999999 775
No 14
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A
Probab=70.46 E-value=10 Score=41.83 Aligned_cols=54 Identities=19% Similarity=0.107 Sum_probs=37.5
Q ss_pred eeccCCeeeEecCCCccccceeeeeEEEecC------------ceeeeecccCCCCCCCCCCCceeee
Q psy1131 134 HIRDGDLVIFNRQPTLHKMSMMGHRVRVLPW------------STFRMNLSCTSPYNADFDGDEMNLH 189 (353)
Q Consensus 134 ~l~~gd~vl~nRqPtLhr~s~ma~~~~~~~~------------~t~r~~~~~c~~~NADFDGDemnlh 189 (353)
.+..|..||+-|.|+||..=++=.++.-.|. +-=|=+++.|+ +.|+|||+-++-
T Consensus 571 ~~l~gg~VlVtRnP~lhPGDIrvv~AV~~PeL~hL~DvIVFp~kG~Rplps~lS--GGDLDGD~Y~Vi 636 (1022)
T 2j7n_A 571 TLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVIIFSTKGDVPLAKKLS--GGDYDGDMAWVC 636 (1022)
T ss_dssp EEECSEEEEEECSSCCSGGGEEEEEECCCGGGTTCCSEEEECSCSSSCHHHHTT--TCCSSSCEEEEE
T ss_pred eeecCceEEEEeCCCcCcCceeEEEeccChhhhccCCeEEccCCCCCCChhHhc--CCCCCCCeEEEE
Confidence 3566778999999999999998766665543 11122333444 489999998764
No 15
>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2
Probab=52.33 E-value=9.9 Score=31.29 Aligned_cols=62 Identities=24% Similarity=0.411 Sum_probs=41.1
Q ss_pred CCceEEEe-ccCeEEeeccCC--CCCCccccCCcE---EeeeccccceeEeecCCCccccceeeeeee
Q psy1131 13 PGAKYIVR-DNGERIDLRFHP--KPSDLHLQCGYK---VERHIRDGDLVIFNRQPTLHKMSMMGHRVR 74 (353)
Q Consensus 13 pga~~vi~-~~g~r~~l~~~~--~~~~~~l~~g~~---verhl~d~~~~~~~~~~~l~r~~~mGkRv~ 74 (353)
+|...+.. .+|+.-.+++.. ......|.-||. -+..|+.||+++|.+..+--+.=.++.|-.
T Consensus 50 ~~~~l~l~D~~Gk~W~fr~~~~~~~~~~~Lt~GW~~FV~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~ 117 (130)
T 1wid_A 50 KGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSR 117 (130)
T ss_dssp CCEEEEEEETTTEEEEEEEEEETTTTEEEEESSHHHHHHHTTCCTTCEEEEEECCSSSCCEEEEEECC
T ss_pred CcEEEEEEeCCCCEEEEEEEEECCCCceEEcCChHHHHHHcCCCCCCEEEEEEecCCCcEEEEEEEEC
Confidence 45555544 478877776542 233457889987 688999999999999874333334554443
No 16
>1yel_A AT1G16640; CESG, protein structure initiative, structural genomics, center for eukaryotic structural genomics, unknown function; NMR {Arabidopsis thaliana} SCOP: b.142.1.2
Probab=50.42 E-value=6.4 Score=30.92 Aligned_cols=45 Identities=16% Similarity=0.343 Sum_probs=35.5
Q ss_pred eEEEe-ccCeEEeeccCCCCCCccccCCcE---EeeeccccceeEeecC
Q psy1131 16 KYIVR-DNGERIDLRFHPKPSDLHLQCGYK---VERHIRDGDLVIFNRQ 60 (353)
Q Consensus 16 ~~vi~-~~g~r~~l~~~~~~~~~~l~~g~~---verhl~d~~~~~~~~~ 60 (353)
..+.+ .+|+.-.++..+..+...|.-||+ .+..|..||..+|+-.
T Consensus 41 ~v~L~~~~G~~W~v~~~~~~~~~~l~~GW~~Fv~~~~L~~GD~lvF~~~ 89 (104)
T 1yel_A 41 TVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQFIYD 89 (104)
T ss_dssp EEEEEETTSCEEEEEEEEETTEEEECTTHHHHHHHHTCCTTCEEEEEEC
T ss_pred EEEEECCCCCEEEEEEEEECCcEEEccChHHHHHHcCCCCCCEEEEEEc
Confidence 44444 688888887766666778999998 5889999999999864
No 17
>4i1k_A B3 domain-containing transcription factor VRN1; B3 domain beta-barrel, DNA binding protein; 1.60A {Arabidopsis thaliana}
Probab=33.97 E-value=17 Score=30.66 Aligned_cols=55 Identities=18% Similarity=0.286 Sum_probs=36.9
Q ss_pred ceEEEeccCeEEeeccCCCCCCccccCCcE---EeeeccccceeEeecCCC---cccccee
Q psy1131 15 AKYIVRDNGERIDLRFHPKPSDLHLQCGYK---VERHIRDGDLVIFNRQPT---LHKMSMM 69 (353)
Q Consensus 15 a~~vi~~~g~r~~l~~~~~~~~~~l~~g~~---verhl~d~~~~~~~~~~~---l~r~~~m 69 (353)
...+.++.|+.-.++...+.+...|.-||+ .+..|..||+.+|+--.. .|+.++.
T Consensus 80 ~~i~L~~~gk~W~v~~~~~~~~~~ls~GW~~Fv~dn~L~~GD~cvFeli~~~~~~f~V~If 140 (146)
T 4i1k_A 80 GFIKVQLAEKQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAF 140 (146)
T ss_dssp SEEEEEETTEEEEEEEEEETTEEEECTTHHHHHHHTTCCTTCEEEEEECSSSSCEEEEEEE
T ss_pred eEEEEEECCcEEEEEEEEeCCcEEECCchHHHHHHcCCCCCCEEEEEEecCCceEEEEEEE
Confidence 466677777555544433334567899998 688999999999986542 3444443
No 18
>2k8f_B Cellular tumor antigen P53; complex of P53 and P300, acetylation, bromodomain, cell cycle, chromosomal rearrangement, citrullination; NMR {Homo sapiens}
Probab=28.37 E-value=24 Score=22.98 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=24.9
Q ss_pred eeEEeecCChhHHHHHHHHhcCCCeeecCC
Q psy1131 297 EMNLHVPQSMETRAEVENIHVTPRQIITPQ 326 (353)
Q Consensus 297 em~~~~p~s~~a~~E~~~l~~~~~~~~s~~ 326 (353)
++.+..|+|.++-.++..|+ .+++++||-
T Consensus 7 d~siepPLSQETFsdLW~LL-P~~~ilspl 35 (39)
T 2k8f_B 7 DPSVEPPLSQETFSDLWKLL-PENNVLSPL 35 (39)
T ss_dssp CSSCCCCCSCHHHHHHHHTC-SSSCCCCCC
T ss_pred ccccCCCccHHHHHHHHHhC-CcccccccC
Confidence 46788999999999999984 788999874
Done!