Query 020936
Match_columns 319
No_of_seqs 106 out of 1085
Neff 6.7
Searched_HMMs 29240
Date Mon Mar 25 10:21:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020936.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/020936hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2pa8_D DNA-directed RNA polyme 100.0 7.2E-69 2.5E-73 499.4 24.4 255 10-297 1-257 (265)
2 3h0g_C DNA-directed RNA polyme 100.0 5.3E-69 1.8E-73 503.9 12.7 251 8-297 3-260 (297)
3 1twf_C B44.5, DNA-directed RNA 100.0 2.4E-66 8.3E-71 491.4 17.6 252 7-297 3-259 (318)
4 1bdf_A RNA polymerase alpha su 100.0 1.3E-49 4.5E-54 363.2 16.8 216 3-297 5-232 (235)
5 2a6h_A DNA-directed RNA polyme 100.0 4.1E-49 1.4E-53 373.1 13.3 211 8-299 7-229 (315)
6 3lu0_A DNA-directed RNA polyme 100.0 7E-42 2.4E-46 324.4 10.1 224 2-299 4-235 (329)
7 2pa8_L DNA-directed RNA polyme 95.7 0.011 3.9E-07 45.5 4.5 39 10-49 1-39 (92)
8 1xpp_A TA1416, DNA-directed RN 95.1 0.021 7.2E-07 45.9 4.6 40 7-47 8-47 (115)
9 3h0g_K DNA-directed RNA polyme 92.3 0.09 3.1E-06 42.7 3.4 37 261-297 65-101 (123)
10 2pa8_L DNA-directed RNA polyme 92.3 0.14 4.8E-06 39.3 4.3 36 262-297 49-84 (92)
11 1twf_K B13.6, DNA-directed RNA 92.1 0.086 2.9E-06 42.6 3.0 36 8-43 17-52 (120)
12 1twf_K B13.6, DNA-directed RNA 90.7 0.29 9.8E-06 39.5 4.7 36 262-297 67-102 (120)
13 1xpp_A TA1416, DNA-directed RN 86.4 0.56 1.9E-05 37.5 3.6 35 262-297 59-93 (115)
14 3h0g_K DNA-directed RNA polyme 85.9 0.49 1.7E-05 38.3 3.1 35 10-44 16-52 (123)
15 1jnr_B Adenylylsulfate reducta 60.1 5.4 0.00019 32.7 2.9 39 211-249 20-58 (150)
16 3gyx_B Adenylylsulfate reducta 57.5 5.7 0.0002 33.2 2.6 39 211-249 19-57 (166)
17 1dax_A Ferredoxin I; electron 34.4 25 0.00084 23.4 2.5 40 209-249 14-55 (64)
18 1xer_A Ferredoxin; electron tr 32.9 13 0.00045 27.5 0.9 41 209-249 48-94 (103)
19 3i9v_9 NADH-quinone oxidoreduc 28.9 20 0.00069 29.3 1.5 48 209-260 56-116 (182)
20 3eun_A Ferredoxin; electron tr 23.8 1.1E+02 0.0038 21.3 4.6 38 209-249 11-54 (82)
21 3mm5_B Sulfite reductase, diss 22.8 35 0.0012 32.0 2.1 40 210-250 214-253 (366)
22 3isy_A Bsupi, intracellular pr 21.2 3E+02 0.01 21.5 8.3 64 103-170 19-87 (120)
23 1xhj_A Nitrogen fixation prote 20.2 1.8E+02 0.0061 21.6 5.1 39 11-49 29-74 (88)
No 1
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D
Probab=100.00 E-value=7.2e-69 Score=499.42 Aligned_cols=255 Identities=29% Similarity=0.458 Sum_probs=231.9
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceecc-ccceeeec
Q 020936 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSER-AMSMRFSR 88 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~-~~~~~~~~ 88 (319)
++|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+|||+||||||||+++++ .+.|.|+.
T Consensus 1 ~~i~i~~~~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~Ntsvl~DE~v~Hr~~~Ip~~~edv~k~~~~~~ 80 (265)
T 2pa8_D 1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPE 80 (265)
T ss_dssp -CEEEEEECSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGG
T ss_pred CeEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEeCCCccccHHHHHhhcCCcCcccCchhhccccc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999997 45688888
Q ss_pred cC-CCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEE
Q 020936 89 DC-DACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRA 167 (319)
Q Consensus 89 ~c-~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~ 167 (319)
+| .|+ ++|+.|+++|+|+++| ++++++|||+||++.++.+ ++++|+|+|+||++||+|+|++
T Consensus 81 ~~~~~~---~~~~~~~~~~~l~~~~-~~g~~~V~a~Di~~~~~~v-------------~~~~~~i~I~~L~~g~~l~~e~ 143 (265)
T 2pa8_D 81 ECIECT---ENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPSV-------------VPISGDIPIVLLGTNQKISLEA 143 (265)
T ss_dssp GCTTCC---SSCTTTEEEEEEEEEC-CSSCEEEEGGGCEESSTTC-------------CBSCSCCEEEEECTTCEEEEEE
T ss_pred cccccc---cCCCCcEEEEEEEEEe-cCCCcEEEhhhcccCCCCc-------------eecCCCcEEEEeCCCCEEEEEE
Confidence 88 554 3799999999999999 6799999999999755555 5667789999999999999999
Q ss_pred EEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHH
Q 020936 168 IARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247 (319)
Q Consensus 168 ~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~ 247 (319)
+|+||+||+||||+|+++++|++.|.+.++ . .+..|.+.||.+++.+|+. ...+.+..+|++|.+|.+.
T Consensus 144 ~~~~G~G~~~ak~~pv~t~~yr~~p~I~i~-~--------~C~~C~~~CP~g~I~id~~--~~v~~d~~~C~~C~~C~~v 212 (265)
T 2pa8_D 144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEIL-A--------NCEKAVNVCPEGVFELKDG--KLSVKNELSCTLCEECLRY 212 (265)
T ss_dssp EEEEECTTTCGGGCCEEEEEEEEEEEEEEC-S--------CCTTHHHHCTTCCEEEETT--EEEESCGGGCCCCCHHHHH
T ss_pred EEecCccccccCcccceeeeeccccchhhh-h--------hHHHHHHhCcccCeEecCC--eeEEeccccCCCchHHHHh
Confidence 999999999999999999999999999987 2 3567888999999999863 2446688999999999998
Q ss_pred HhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 248 ~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
+ +++|.+.+++++|+|+|||+|+++|++++.+|+++|++||+.|.
T Consensus 213 C-----p~aI~~~~~~d~~i~~VEt~Gsl~Pee~v~~A~~iL~~~~~~~~ 257 (265)
T 2pa8_D 213 C-----NGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELE 257 (265)
T ss_dssp H-----TTSEEEEEEEEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred C-----CCceEEEecCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7 35899999999999999999999999999999999999999987
No 2
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=5.3e-69 Score=503.92 Aligned_cols=251 Identities=37% Similarity=0.615 Sum_probs=214.4
Q ss_pred CCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccc----
Q 020936 8 RFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS---- 83 (319)
Q Consensus 8 ~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~---- 83 (319)
++|+|+|.++++++++|.|+|+++|+||||||+|||||||+||+.|+|++|||||+||+|||||||||++++++..
T Consensus 3 ~~p~I~i~~~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt~AI~~V~I~~NtSvl~DE~laHrlglIP~v~edv~e~~~~ 82 (297)
T 3h0g_C 3 SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPV 82 (297)
T ss_dssp -CCSBCCCCBCSSEEEEEECSCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSS
T ss_pred CCCeEEEEEccCCEEEEEEECCChhHHHHHHHHHHHcCccceEEEEEEEeCCccccccceeeeeccCCcccccccccccc
Confidence 4689999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred -eeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCc--eeeccccCCCCCCCCCCCCCeEEEEeCCC
Q 020936 84 -MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHS--VVPVDFVDPAGYDSTDQQRGIIIVKLRRG 160 (319)
Q Consensus 84 -~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~--~~Pv~~~~~~~~~~~~~~~~I~I~kL~~g 160 (319)
|+|+.+|.|.+ .|+.|+++|+|+++|+++.+++|||+||++.+.. +.|+.. ++.+++|+|+||++|
T Consensus 83 ~l~~k~~c~~~~---~~~~~~v~l~L~v~g~~~~~~~Vta~Dl~~~~~~~~~~pv~~--------~~~n~di~IakL~~g 151 (297)
T 3h0g_C 83 GLEYTRNCDCDQ---YCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILA--------DPKSRGPLICKLRKE 151 (297)
T ss_dssp CCCCSSSCSSSS---SCGGGSCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCC--------STTSCCSEEEEECSS
T ss_pred eeEecccccccc---CCCCceEEEEEEEEeccCCCceEEcccccccCcccccccccc--------cCCCCCeEEEEECCC
Confidence 89999998753 7999999999999998888999999999986543 334443 457899999999999
Q ss_pred CEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccc
Q 020936 161 QELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240 (319)
Q Consensus 161 q~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~ 240 (319)
|+|+|+|+|+||+||+|||||||++|+|||+|.|+|++...+ . ..++.+.||.+++..-. .+. .
T Consensus 152 q~l~le~~a~kG~G~~HAKwsPv~~~~y~~~P~i~l~~~~~~-~----e~~~~~~~P~~~~~~~~-------~~~-~--- 215 (297)
T 3h0g_C 152 QEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYW-F----ENDADAEWPKSKNADWE-------EPP-R--- 215 (297)
T ss_dssp CCEEEEEEEEEECGGGCTTSCCBCCCCCCSSSSCSSCCSCCC-C----SSCSTTTSCCCGGGTTC-------CCC-S---
T ss_pred CEEEEEEEEECCEeccccccCcceEEEEEeccceEEcccccc-c----cchhHhhCCccccceee-------ccc-c---
Confidence 999999999999999999999999999999999999864211 0 01344677876543210 000 0
Q ss_pred hHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 241 ~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
....+.+..++|+|+|+|||+|+|+|++||.+|+++|++||+.|.
T Consensus 216 ------------~~~~~~~~~~~dkfif~VET~Gsl~p~eiv~~A~~iL~~kl~~f~ 260 (297)
T 3h0g_C 216 ------------EGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLV 260 (297)
T ss_dssp ------------CCSCCCSSCCCCCEEEEEEBCSSSCTTTTTHHHHHHHHHHHHHHH
T ss_pred ------------ccccccccccCCEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 013466778999999999999999999999999999999999998
No 3
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...
Probab=100.00 E-value=2.4e-66 Score=491.45 Aligned_cols=252 Identities=42% Similarity=0.670 Sum_probs=213.2
Q ss_pred CCCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccccceee
Q 020936 7 QRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRF 86 (319)
Q Consensus 7 ~~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~~~~~~ 86 (319)
.+.|+|++.++++++++|.|+|+++||||||||||||||||+||+.|+|++|||||+||+|||||||||+++++++.|+|
T Consensus 3 ~~~p~I~i~~~~~~~~kF~leG~~~tlaNALRRiLLSevPg~AI~~V~I~~NTSvl~DE~vaHrlglIP~v~eDvk~l~~ 82 (318)
T 1twf_C 3 EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY 82 (318)
T ss_dssp CCSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTGGGSCC
T ss_pred ccCCeEEEEEecCCEEEEEEEccChhHHHHHHHHHHHcCccceEEEEEEEeCCcccccceeEeecccCCCcccChhheEE
Confidence 35588999999999999999999999999999999999999999999999999999999999999999999999988999
Q ss_pred eccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCC---ce--eeccccCCCCCCCCCCCCCeEEEEeCCCC
Q 020936 87 SRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH---SV--VPVDFVDPAGYDSTDQQRGIIIVKLRRGQ 161 (319)
Q Consensus 87 ~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~---~~--~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq 161 (319)
+.+|.|++ .|+.|+++|+|+++|+.+++++|||+||+.... .. .|.-. ++.+|+|+||||++||
T Consensus 83 ~~~~~~~~---~c~~~~v~l~L~v~c~~~g~~~Vta~Di~~~~~~~~~~~~~p~v~--------ei~npdi~IakL~~gq 151 (318)
T 1twf_C 83 SRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQ--------DKEGNGVLICKLRKGQ 151 (318)
T ss_dssp TTTSSSSS---CCTTTEEEEEEEEECCSSSCEEEEGGGEEECSCCTTCSEEEECCC--------STTSCCSEEEEECTTC
T ss_pred eecccccc---CCCCceEEEEEEEEecCCCCeeEEhHhccccCccccccccCCCcc--------ccCCCCeEEEEECCCC
Confidence 99998853 799999999999999999999999999986431 00 01110 3678999999999999
Q ss_pred EEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCccccch
Q 020936 162 ELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYD 241 (319)
Q Consensus 162 ~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~ 241 (319)
+|+|+|+|+||+||+|||||||++++|+|+|.+++++. .+++..|+. ..+.++.+|.|+
T Consensus 152 ~L~me~~a~kG~G~~hAk~sPva~~~y~~~P~~~~~~~------------------~~~i~~D~~---~~f~pv~~v~~~ 210 (318)
T 1twf_C 152 ELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHT------------------DYWYEQDSA---KEWPQSKNCEYE 210 (318)
T ss_dssp EEEEEEEEEEECTTTCGGGCCEEEEEEEECSSTTSCCS------------------CCCCSSCHH---HHSCCCGGGTTS
T ss_pred EEEEEEEEEcCcccccccccccccceeccccccccccc------------------ccccccCch---hhCCCCcceeEE
Confidence 99999999999999999999999999999999877431 111112210 024556677777
Q ss_pred HHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 242 DEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 242 ~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.++. ....|...+++|||+|+|||+|+|+|++||.+|+++|++||+.|.
T Consensus 211 ve~~-------~~~rv~~~~d~dkfif~VET~Gsi~Peeav~~A~kIL~~kl~~f~ 259 (318)
T 1twf_C 211 DPPN-------EGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASIL 259 (318)
T ss_dssp CCCC-------SSSCCCTTCCCCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred eccc-------ccccccccccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 6531 012455678999999999999999999999999999999999997
No 4
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Probab=100.00 E-value=1.3e-49 Score=363.17 Aligned_cols=216 Identities=21% Similarity=0.255 Sum_probs=182.0
Q ss_pred CCCCCCCCcEEEEEecCceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCccee
Q 020936 3 GASYQRFPKVKIRELKDDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTS 78 (319)
Q Consensus 3 ~~~~~~~~~iei~~~~~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~ 78 (319)
|..|..+.+|++.+.++++++|.++ |++.++||||||+|||||||+||+.|+| |.++||||+||+++
T Consensus 5 ~~~~~~p~~i~i~~~~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~V~I---------e~v~He~~~Ipgv~ 75 (235)
T 1bdf_A 5 VTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEI---------DGVLHEYSTKEGVQ 75 (235)
T ss_dssp SSCSCCCCEEEEEESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEE---------TTCCSTTCCCTTBS
T ss_pred hhhhcCCceEEEEEccCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEEEEE---------cceeeccccCCCcc
Confidence 4566676669999999999999997 9999999999999999999999999999 45999999999999
Q ss_pred ccc-------cceeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCC
Q 020936 79 ERA-------MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151 (319)
Q Consensus 79 ~~~-------~~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~ 151 (319)
+++ +.+.++.+ ..|+++++|+++ ||+.|||+||.. ++.+ ++++|+
T Consensus 76 Edv~~iilNlk~i~~~~~----------~~~~~~~~L~v~----gp~~VtA~Di~~-~~~v-------------~ivnpd 127 (235)
T 1bdf_A 76 EDILEILLNLKGLAVRVQ----------GKDEVILTLNKS----GIGPVTAADITH-DGDV-------------EIVKPQ 127 (235)
T ss_dssp SCHHHHHHHHHTCCEECS----------SCSEEEEEEEEE----SSEEEEGGGBCC-CSSC-------------EESCTT
T ss_pred CCHHHHhhchheeEEecc----------CCceEEEEEEEe----cCeEEEhHhCCC-CCCC-------------EEcCCC
Confidence 884 45666543 247899999999 889999999984 2223 567788
Q ss_pred eEEEEeCC-CCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCce
Q 020936 152 IIIVKLRR-GQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQV 230 (319)
Q Consensus 152 I~I~kL~~-gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~ 230 (319)
++||||++ ||+|+|+|+|.+|+||+||||+- .+. .+.||.|++.+|+.
T Consensus 128 ~~IatL~~~g~~l~~e~~~~kG~Gy~~ak~si-------------~~~--------------~~~~~~g~i~iD~~---- 176 (235)
T 1bdf_A 128 HVICHLTDENASISMRIKVQRGRGYVPASTRI-------------HSE--------------EDERPIGRLLVDAC---- 176 (235)
T ss_dssp CEEEEECSTTCEEEEEEEEEECCSEECGGGTC--------------------------------CCCCSCCBCCEE----
T ss_pred eEEEEECCCCCEEEEEEEEEecccceeccccc-------------ccc--------------cccCCCcEEEECCC----
Confidence 99999999 99999999999999999999961 000 14689999999863
Q ss_pred eecCCccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 231 YVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 231 ~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
+.++.+++|+.+.. .+...+++|+|+|+|||+|+++|++||.+|+++|++||+.|.
T Consensus 177 -f~pv~~v~y~ve~~----------~v~~~~~~d~li~eIeT~Gsi~P~eal~~A~~iL~~~~~~f~ 232 (235)
T 1bdf_A 177 -YSPVERIAYNVEAA----------RVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 232 (235)
T ss_dssp -CCSEEEEEEECCBC----------CCSSCSSEEEEEEEEEECSSSCHHHHHHHHHHHHHHHGGGGC
T ss_pred -CCcEEEEEEEccCc----------cccccccCcEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 56778888886621 244457889999999999999999999999999999999885
No 5
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...
Probab=100.00 E-value=4.1e-49 Score=373.08 Aligned_cols=211 Identities=18% Similarity=0.295 Sum_probs=184.9
Q ss_pred CCCcEEEEEecCceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcceeccc--
Q 020936 8 RFPKVKIRELKDDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERA-- 81 (319)
Q Consensus 8 ~~~~iei~~~~~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~~~~~-- 81 (319)
.+|+|++.+.++++++|.++ |++.|+||||||+|||||||+||+.|+|++ ++||||+||++++++
T Consensus 7 ~~p~i~i~~~~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~AI~~V~I~~---------v~He~~~Ipgv~Edv~e 77 (315)
T 2a6h_A 7 KAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIED---------VLHEFSTIPGVKEDVVE 77 (315)
T ss_dssp SCCEEEEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESS---------CCSTTCBCTTBSSBHHH
T ss_pred cCCeEEEEEccCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCceEEEEEEEec---------chhccCCCCCccCCHHH
Confidence 45889999999999999996 999999999999999999999999999998 999999999999884
Q ss_pred -----cceeeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEEE
Q 020936 82 -----MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVK 156 (319)
Q Consensus 82 -----~~~~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~k 156 (319)
+.+.|+.+| |..|+++++|+++ ||+.|||+||.. ++.+ ++++|+++|||
T Consensus 78 IilNlk~i~~~~~~--------~~~~~~~~~L~v~----gp~~VtA~Di~~-~~~v-------------~ivnpd~~Iat 131 (315)
T 2a6h_A 78 IILNLKELVVRFLN--------PSLQTVTLLLKAE----GPKEVKARDFLP-VADV-------------EIMNPDLHIAT 131 (315)
T ss_dssp HHHHHHTCCEEECS--------TTCSBCCEEEEEE----SSCEEEGGGSCC-CTTE-------------EESCTTCEEEE
T ss_pred HhhhhheEEEeccc--------CCCCeEEEEEEEe----cCeeEEhhhCCc-CCCc-------------EEcCCCeEEEE
Confidence 467777765 2357899999999 889999999984 2333 56678899999
Q ss_pred eCCCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecCCc
Q 020936 157 LRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAE 236 (319)
Q Consensus 157 L~~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~~~ 236 (319)
|++||+|+|+++|.+|+||+||||++ +.||.|+|.+|+. +.+++
T Consensus 132 L~~g~~l~me~~~~kG~Gy~~ak~~~-------------------------------~~~p~g~i~iDa~-----f~pv~ 175 (315)
T 2a6h_A 132 LEEGGRLNMEVRVDRGVGYVPAEKHG-------------------------------IKDRINAIPVDAV-----FSPVR 175 (315)
T ss_dssp BCSSCEEEEEEEEEEEESEECHHHHC-------------------------------CCSSTTCEECCEE-----CCCEE
T ss_pred ECCCCEEEEEEEEEecCCccccccCc-------------------------------ccCCcceEeecCC-----CCCce
Confidence 99999999999999999999999994 2478999999873 68889
Q ss_pred cccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc-cC
Q 020936 237 AYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR-LS 299 (319)
Q Consensus 237 ~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~-~~ 299 (319)
+|+|+.++.+ +...+++|+|+|+|||+|+++|++||.+|+++|++||+.|. +.
T Consensus 176 ~v~y~ve~~r----------v~~~~~~dkli~eIeT~Gsi~P~eal~~A~~iL~~~l~~f~~~~ 229 (315)
T 2a6h_A 176 RVAFQVEDTR----------LGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 229 (315)
T ss_dssp EEEEEEEECC----------BTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC
T ss_pred eEEEEeeeee----------ecccccccEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Confidence 9999887532 22357899999999999999999999999999999999997 54
No 6
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A
Probab=100.00 E-value=7e-42 Score=324.39 Aligned_cols=224 Identities=21% Similarity=0.265 Sum_probs=185.8
Q ss_pred CCCCCCCCCcEEEEEecCceEEEEEE----ecCcchhhHHHHHHHhhcCcceEEEEEEeeCcccccchhhhhhhcCCcce
Q 020936 2 DGASYQRFPKVKIRELKDDYAKFELR----DTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLT 77 (319)
Q Consensus 2 ~~~~~~~~~~iei~~~~~~~~~f~l~----g~~~s~aNaLRRillseVPt~AId~V~I~~NtSvl~DE~laHRLgLIPi~ 77 (319)
.|..+..+..+++.+.++.+++|.++ |++.++||||||+|||+|||+||+.|+|++ ++||||+||++
T Consensus 4 ~~~~~~~p~~~~v~~~~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~g---------v~Hefs~Ipgv 74 (329)
T 3lu0_A 4 SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG---------VLHEYSTKEGV 74 (329)
T ss_dssp STTTSSSCCCCCEEECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESS---------CSSTTCCCTTB
T ss_pred hhhhccCCceEEEEEcCCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEeC---------ccccccccccc
Confidence 46678888888999999999999999 999999999999999999999999999977 99999999999
Q ss_pred eccccce--eeeccCCCCCCCCCCCCceEEEEEEEEeccCCCceeeccCeeeCCCceeeccccCCCCCCCCCCCCCeEEE
Q 020936 78 SERAMSM--RFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIV 155 (319)
Q Consensus 78 ~~~~~~~--~~~~~c~~~~~~~~~~~c~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~ 155 (319)
.+++..+ +++ .|.+. .|..|+++++|+++ ||+.|||+||.+ ++.+ ++++|+++||
T Consensus 75 ~Edv~eiilNlK-~i~~k----~~~~~~~~~~L~~~----Gp~~VtA~DI~~-~~~v-------------eivnpd~~Ia 131 (329)
T 3lu0_A 75 QEDILEILLNLK-GLAVR----VQGKDEVILTLNKS----GIGPVTAADITH-DGDV-------------EIVKPQHVIC 131 (329)
T ss_dssp SSCHHHHHHHHH-SCCCE----ESSCSCEEEEECCC----SSSCEETTSSCC-CSSE-------------ECSCTTCEEE
T ss_pred cCCHHHHHhhhc-cceEe----cCCCceEEEEEEEe----CCeEEEeeeecc-CCCC-------------EEeCCCcEEE
Confidence 9987542 333 34332 24578899999987 899999999986 2333 5778899999
Q ss_pred EeC-CCCEEEEEEEEEecccccccccCccceeecccccccccchhhhhhhhHHhhhhhhccCCCeeEEeCCCCCceeecC
Q 020936 156 KLR-RGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVD 234 (319)
Q Consensus 156 kL~-~gq~I~le~~a~kG~Gk~HAKw~Pvs~~~y~~~p~i~i~~~~~~~~~~~~~~~~~~~cp~~v~~id~~~~~~~~~~ 234 (319)
+|+ +||+|+|+++|.+|+||.+|.++... + ....|.|++.+|+. ++|
T Consensus 132 tL~~~~~~L~me~~i~~G~GY~~a~~~~~~----~-----------------------~~~~~ig~i~iDa~-----fsP 179 (329)
T 3lu0_A 132 HLTDENASISMRIKVQRGRGYVPASTRIHS----E-----------------------EDERPIGRLLVDAC-----YSP 179 (329)
T ss_dssp CBCSSCCCCCEEEEEEEESSEECTTTSCCC----S-----------------------TTSSSCCCEECCEE-----CCC
T ss_pred EEccCCcEEEEEEEEECcccceechhcccc----c-----------------------cccCcCceEeeCCC-----CCc
Confidence 999 99999999999999999999987210 0 01246789999873 889
Q ss_pred CccccchHHHHHHHhhcCCCCcEEEeeeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc-cC
Q 020936 235 AEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR-LS 299 (319)
Q Consensus 235 ~~~~~~~~e~~~~~~~~~~~~~i~v~~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~-~~ 299 (319)
+++++|..|..+ +...+++|+++|+|||||+++|++|+.+|+++|+++|..|. +.
T Consensus 180 V~~Vny~Ve~~r----------vgq~td~dkL~leI~TdGsi~P~eAl~~Aa~iL~~~l~~f~~~~ 235 (329)
T 3lu0_A 180 VERIAYNVEAAR----------VEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR 235 (329)
T ss_dssp EEEEEEEEEEEC----------CSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC
T ss_pred eeeEEEEEeccc----------cCCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 999999877321 11235679999999999999999999999999999999997 44
No 7
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L
Probab=95.67 E-value=0.011 Score=45.55 Aligned_cols=39 Identities=13% Similarity=0.336 Sum_probs=33.3
Q ss_pred CcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCcce
Q 020936 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIA 49 (319)
Q Consensus 10 ~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt~A 49 (319)
++++|.+.+++.++|.+.|-|.+++|+||-.|+.. |..-
T Consensus 1 Meikvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~-p~V~ 39 (92)
T 2pa8_L 1 MEIRILKSESNYLELEIEGEDHTLGNLIAGTLRRI-SGVS 39 (92)
T ss_dssp CEEEEEEEETTEEEEEEETCCHHHHHHHHHHHHTS-TTEE
T ss_pred CceEEEecCCCeEEEEEecCchhHHHHHHHHHhcC-CCee
Confidence 46899999999999999999999999999988764 5433
No 8
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2
Probab=95.14 E-value=0.021 Score=45.88 Aligned_cols=40 Identities=8% Similarity=0.175 Sum_probs=34.2
Q ss_pred CCCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHhhcCc
Q 020936 7 QRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPT 47 (319)
Q Consensus 7 ~~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRillseVPt 47 (319)
.+.+++++.+.+++.++|.+.|-|.+|+|+||-.|+.. |.
T Consensus 8 ~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkd-p~ 47 (115)
T 1xpp_A 8 TAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKD-DQ 47 (115)
T ss_dssp -CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTC-TT
T ss_pred ccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcC-CC
Confidence 34588999999999999999999999999999987764 44
No 9
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=92.34 E-value=0.09 Score=42.67 Aligned_cols=37 Identities=19% Similarity=0.420 Sum_probs=34.2
Q ss_pred eeCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 261 ~~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
.-.+++.|.|.|+|..+|.++|.+|++-|.+.|+.|.
T Consensus 65 Ple~~~~lrIqT~~~~~p~eaL~~al~~L~~~~~~l~ 101 (123)
T 3h0g_K 65 PLNHNFILRVQTVEDCSPKQVIVDAAKSLITHLEEIK 101 (123)
T ss_dssp TTSCEEEEEEECCSSSCSHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999999999999999999886
No 10
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L
Probab=92.33 E-value=0.14 Score=39.34 Aligned_cols=36 Identities=22% Similarity=0.318 Sum_probs=33.1
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
-.+++.|.|.|+|..+|.++|.+|++-|.+.++.|.
T Consensus 49 l~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 84 (92)
T 2pa8_L 49 LSDKIIVKILTDGSITPKDALLKAIENIRGMTSHYI 84 (92)
T ss_dssp TSCCEEEEEEECSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 368899999999999999999999999999998775
No 11
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Probab=92.14 E-value=0.086 Score=42.59 Aligned_cols=36 Identities=11% Similarity=0.173 Sum_probs=29.3
Q ss_pred CCCcEEEEEecCceEEEEEEecCcchhhHHHHHHHh
Q 020936 8 RFPKVKIRELKDDYAKFELRDTDASMANALRRVMIA 43 (319)
Q Consensus 8 ~~~~iei~~~~~~~~~f~l~g~~~s~aNaLRRills 43 (319)
+++++++...+++.++|.+.|-|.|++|+||-.|+.
T Consensus 17 ~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk 52 (120)
T 1twf_K 17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLN 52 (120)
T ss_dssp CSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTT
T ss_pred ceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhh
Confidence 345666666678899999999999999999988775
No 12
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Probab=90.70 E-value=0.29 Score=39.49 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=33.5
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
-.+++.|.|.|+|..+|.++|++|++-|.+.++.|.
T Consensus 67 l~~~~~lrIqT~~~~~p~eaL~~a~~~L~~~~~~l~ 102 (120)
T 1twf_K 67 FFARFKLRIQTTEGYDPKDALKNACNSIINKLGALK 102 (120)
T ss_dssp TSCEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 368999999999999999999999999999998886
No 13
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2
Probab=86.40 E-value=0.56 Score=37.51 Aligned_cols=35 Identities=11% Similarity=0.078 Sum_probs=32.3
Q ss_pred eCCEEEEEEEeCcccCHHHHHHHHHHHHHHHhcccc
Q 020936 262 KEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297 (319)
Q Consensus 262 ~~d~f~f~IET~Gsl~p~~il~~A~~iL~~kl~~l~ 297 (319)
-.+++.|.|.|+|.. |.++|.+|++-|.+.|+.|.
T Consensus 59 le~~~~lrIqT~~~~-p~eaL~~al~~L~~~~~~l~ 93 (115)
T 1xpp_A 59 VIDNPQIYVRVKSGK-PQSAIKRAVRKLSKLYEDLG 93 (115)
T ss_dssp TTSCCEEEEEESSSC-HHHHHHHHHHHHHHHHHHHH
T ss_pred CCCccEEEEEeCCCC-hHHHHHHHHHHHHHHHHHHH
Confidence 368899999999998 99999999999999999887
No 14
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=85.85 E-value=0.49 Score=38.28 Aligned_cols=35 Identities=26% Similarity=0.376 Sum_probs=28.5
Q ss_pred CcEEEEE--ecCceEEEEEEecCcchhhHHHHHHHhh
Q 020936 10 PKVKIRE--LKDDYAKFELRDTDASMANALRRVMIAE 44 (319)
Q Consensus 10 ~~iei~~--~~~~~~~f~l~g~~~s~aNaLRRillse 44 (319)
.+|++.. ..++.++|.+.|-|.|++|+||-.|+..
T Consensus 16 ~Kv~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~ 52 (123)
T 3h0g_K 16 PKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSD 52 (123)
T ss_dssp CSCCEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGS
T ss_pred cceEEecCCCCCceEEEEEeCCCcchHHHHHHHHhcC
Confidence 3455554 4578999999999999999999988764
No 15
>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*
Probab=60.07 E-value=5.4 Score=32.67 Aligned_cols=39 Identities=10% Similarity=0.112 Sum_probs=30.3
Q ss_pred hhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020936 211 SWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 211 ~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
.+.+.||.+.+.++..+......+...|..|..|+..+.
T Consensus 20 ~C~~~CP~~ai~~~~~~~~~~~id~~~C~~Cg~Cv~~CP 58 (150)
T 1jnr_B 20 ACEYICPNDLMTLDKEKMKAYNREPDMCWECYSCVKMCP 58 (150)
T ss_dssp HHHHHCTTSCEEEETTTTEEEESCGGGCCCCCHHHHHCT
T ss_pred cchhhcCccCeEEecCCceeeeeCcccCcCHhHHHHhCC
Confidence 678899999998876543444556788999999999874
No 16
>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}
Probab=57.51 E-value=5.7 Score=33.16 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=30.7
Q ss_pred hhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHh
Q 020936 211 SWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 211 ~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~ 249 (319)
.++..||.+++.++..+......+...|..|..|...+.
T Consensus 19 ~C~~~CP~~ai~~~~~~~~~~~~d~~~C~~Cg~Cv~~CP 57 (166)
T 3gyx_B 19 ACMYICPNDLMILDPEEMKAFNQEPEACWECYSCIKICP 57 (166)
T ss_dssp HHHHHCTTSCEEEETTTTEEEESCGGGCCCCCHHHHHCS
T ss_pred hhHHhCCccccEEecCCceeEecCcccCcccChHhHhCC
Confidence 678899999998876544444566789999999998874
No 17
>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A
Probab=34.35 E-value=25 Score=23.38 Aligned_cols=40 Identities=28% Similarity=0.447 Sum_probs=26.5
Q ss_pred hhhhhccCCCeeEEeCCCCCceeecC--CccccchHHHHHHHh
Q 020936 209 KQSWVESSPTKVFDIDPNTGQVYVVD--AEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~~~~~~~--~~~~~~~~e~~~~~~ 249 (319)
+..+...|| ++|.++...+...+.+ ...|..|..|.+.+.
T Consensus 14 Cg~C~~~CP-~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP 55 (64)
T 1dax_A 14 CESCVEIAP-GAFAMDPEIEKAYVKDVEGASQEEVEEAMDTCP 55 (64)
T ss_dssp CCHHHHHCT-TTEEECSSSSSEEECCGGGSCHHHHHHHHHHSS
T ss_pred chHHHHhCC-ccEeEcCCCCEEEEecCCCcchhHHHHHHHhCC
Confidence 446777899 7888865323333333 567888989988763
No 18
>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A
Probab=32.89 E-value=13 Score=27.47 Aligned_cols=41 Identities=17% Similarity=0.280 Sum_probs=28.0
Q ss_pred hhhhhccCCCeeEEeCCCCC------ceeecCCccccchHHHHHHHh
Q 020936 209 KQSWVESSPTKVFDIDPNTG------QVYVVDAEAYTYDDEVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~------~~~~~~~~~~~~~~e~~~~~~ 249 (319)
+..+...||.+++.++...+ .....+...|..|..|...+.
T Consensus 48 Cg~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~C~~Cg~C~~~CP 94 (103)
T 1xer_A 48 DGSCINACPVNVFQWYDTPGHPASEKKADPVNEQACIFCMACVNVCP 94 (103)
T ss_dssp CCHHHHHCTTCCCEEEECTTCSSCSEEEECTTGGGCCCCCHHHHHCT
T ss_pred hhhHHHHcCccCeecccccCccccccceeecCcccccChhhHHHhcc
Confidence 45678899988887643211 122345678999999998874
No 19
>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9*
Probab=28.90 E-value=20 Score=29.29 Aligned_cols=48 Identities=10% Similarity=0.193 Sum_probs=31.2
Q ss_pred hhhhhccCCCeeEEeCCCCC-------------ceeecCCccccchHHHHHHHhhcCCCCcEEEe
Q 020936 209 KQSWVESSPTKVFDIDPNTG-------------QVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIY 260 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~-------------~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~v~ 260 (319)
+..|...||.+.+.++.... .....+..+|+.|..|...+.. +++.+.
T Consensus 56 C~~C~~~CP~~ai~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~C~~~CP~----~Ai~~~ 116 (182)
T 3i9v_9 56 CSLCAAACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPT----GAIVLG 116 (182)
T ss_dssp CCHHHHHCTTCCEEEEEECCCSSSCSSSSSCEEEEEEEETTTCCCCCHHHHHCSS----SCEEEC
T ss_pred cccchhhCCcccEEeecccccccccccccccccceeecCCCcCcChhChhhhCCc----cceEec
Confidence 45677889988876542110 1224467889999999988742 455554
No 20
>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} SCOP: d.58.1.1 PDB: 1blu_A 3exy_A
Probab=23.85 E-value=1.1e+02 Score=21.29 Aligned_cols=38 Identities=8% Similarity=0.054 Sum_probs=28.0
Q ss_pred hhhhhccCCCeeEEeCCCCCceeecCCccccchH------HHHHHHh
Q 020936 209 KQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDD------EVIKKAE 249 (319)
Q Consensus 209 ~~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~------e~~~~~~ 249 (319)
+..+...||.+.+.++.. .+ ..+..+|..|. .|...+.
T Consensus 11 C~~C~~~CP~~ai~~~~~--~~-~i~~~~C~~C~~~~~~~~C~~~CP 54 (82)
T 3eun_A 11 CDVCEPECPNGAISQGDE--TY-VIEPSLCTECVGHYETSQCVEVCP 54 (82)
T ss_dssp CCTTGGGCTTCCEEECSS--SE-EECGGGCCTTTTTCSSCHHHHHCT
T ss_pred ccchHHHCChhheEcCCC--ce-EEchhhcCCCCCCCCccHHHHhCC
Confidence 446778899999988643 22 34567899998 8998874
No 21
>3mm5_B Sulfite reductase, dissimilatory-type subunit BET; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B* 3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*
Probab=22.81 E-value=35 Score=31.98 Aligned_cols=40 Identities=23% Similarity=0.255 Sum_probs=31.6
Q ss_pred hhhhccCCCeeEEeCCCCCceeecCCccccchHHHHHHHhh
Q 020936 210 QSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEA 250 (319)
Q Consensus 210 ~~~~~~cp~~v~~id~~~~~~~~~~~~~~~~~~e~~~~~~~ 250 (319)
..+++.||.+.+..+..++.+ ..+..+|..|..|...+..
T Consensus 214 ~~Cv~~CP~~AI~~~~~~~~~-~id~~~C~~Cg~C~~~CP~ 253 (366)
T 3mm5_B 214 PSTVAACPTGALKPDMKNKTI-KVDVEKCMYCGNCYTMCPG 253 (366)
T ss_dssp HHHHHTCTTCCEEEETTTTEE-EECGGGCCCCCHHHHHCTT
T ss_pred cchhccCCccceEecCCCCeE-EEehhhCCCcchHHHhCCH
Confidence 568899999999887544444 4566889999999999865
No 22
>3isy_A Bsupi, intracellular proteinase inhibitor; intracellular proteinase inhibitor bsupi, beta sandwich, GRE structural genomics; HET: PG4; 2.61A {Bacillus subtilis}
Probab=21.16 E-value=3e+02 Score=21.54 Aligned_cols=64 Identities=11% Similarity=0.158 Sum_probs=40.3
Q ss_pred eEEEEEEEEeccCCCceeecc-----CeeeCCCceeeccccCCCCCCCCCCCCCeEEEEeCCCCEEEEEEEEE
Q 020936 103 SVEFHLRAKCHSDQTLDVTSK-----DLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIAR 170 (319)
Q Consensus 103 ~v~~~L~v~~~~~~~~~V~s~-----Dl~~~~~~~~Pv~~~~~~~~~~~~~~~~I~I~kL~~gq~I~le~~a~ 170 (319)
++.|.|.++|+++.++++.-. |+...|..-..++.- +++....+-+--.+|.||+.+..+....
T Consensus 19 ~v~~~ltv~N~s~~~v~l~f~Sgq~~Df~v~d~~G~~Vwrw----S~~~~FtQa~~~~tl~pGE~~~f~~~w~ 87 (120)
T 3isy_A 19 QIKFNMSLKNQSERAIEFQFSTGQKFELVVYDSEHKERYRY----SKEKMFTQAFQNLTLESGETYDFSDVWK 87 (120)
T ss_dssp CEEEEEEEEECSSSCEEEEESSSCCEEEEEECTTCCEEEET----TTTCCCCCCCEEEEECTTCEEEEEEEES
T ss_pred eEEEEEEEEcCCCCcEEEEeCCCCEEEEEEECCCCCEEEEc----cccchhhhhhceEEECCCCEEEEEEEeC
Confidence 889999999998877765543 444433211233321 1113344456677999999999977644
No 23
>1xhj_A Nitrogen fixation protein NIFU; alpha-beta, NIFU-like, structural genomics, protein structur initiative, NESG, PSI; NMR {Staphylococcus epidermidis} SCOP: d.52.8.1
Probab=20.22 E-value=1.8e+02 Score=21.62 Aligned_cols=39 Identities=18% Similarity=0.439 Sum_probs=32.4
Q ss_pred cEEEEEecCceEEEEEEec-------CcchhhHHHHHHHhhcCcce
Q 020936 11 KVKIRELKDDYAKFELRDT-------DASMANALRRVMIAEVPTIA 49 (319)
Q Consensus 11 ~iei~~~~~~~~~f~l~g~-------~~s~aNaLRRillseVPt~A 49 (319)
.|++...++..+.+.|.|. +.++-+++.+.|...+|.+.
T Consensus 29 dvelv~v~~g~V~V~L~GaC~gCpss~~TLk~gIE~~L~~~vPev~ 74 (88)
T 1xhj_A 29 DCTLVDVEDGIVKLQLHGACGTCPSSTITLKAGIERALHEEVPGVI 74 (88)
T ss_dssp EEEEEECCSSEEEEEEESSCCSSCHHHHHHHHHHHHHHHHHSTTCC
T ss_pred eEEEEEEECCEEEEEEeecCCCCcchHHHHHHHHHHHHHHhCCCce
Confidence 4888888888999999864 23788999999999999754
Done!