Query psy6965
Match_columns 1764
No_of_seqs 314 out of 1070
Neff 1.9
Searched_HMMs 29240
Date Fri Aug 16 23:19:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6965.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/6965hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 1.1E-66 3.6E-71 647.6 14.1 275 1386-1682 1179-1457(1752)
2 1twf_A B220, DNA-directed RNA 100.0 4E-63 1.4E-67 615.6 15.8 278 1385-1687 1175-1456(1733)
3 4ayb_C DNA-directed RNA polyme 100.0 6.7E-48 2.3E-52 419.2 13.6 220 1420-1678 173-392 (395)
4 2a6h_D DNA-directed RNA polyme 99.9 2.3E-27 8E-32 291.6 3.7 113 1560-1674 1329-1481(1524)
5 1hqm_D DNA-directed RNA polyme 99.9 1.4E-26 4.6E-31 283.2 6.4 116 1560-1678 1070-1225(1265)
6 3lu0_D DNA-directed RNA polyme 99.9 1.3E-26 4.5E-31 282.5 4.8 162 1497-1672 1154-1364(1407)
7 3h0g_A DNA-directed RNA polyme 99.2 5.2E-12 1.8E-16 159.7 2.8 113 1-117 1212-1329(1752)
8 1twf_A B220, DNA-directed RNA 98.8 1.2E-09 4.2E-14 138.4 4.0 108 2-116 1210-1322(1733)
9 3qqc_A DNA-directed RNA polyme 96.3 0.00065 2.2E-08 77.4 -0.1 41 1625-1665 391-431 (436)
10 4ayb_C DNA-directed RNA polyme 80.7 1.3 4.3E-05 49.1 4.7 88 2-118 182-269 (395)
11 3i1m_R 30S ribosomal protein S 20.7 22 0.00076 32.9 0.2 33 1589-1621 15-48 (75)
No 1
>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=1.1e-66 Score=647.56 Aligned_cols=275 Identities=48% Similarity=0.767 Sum_probs=247.6
Q ss_pred CCChhH--HhhccCcchhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEEE
Q psy6965 1386 MQDEED--AVDKMEDDMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFIR 1461 (1764)
Q Consensus 1386 m~DEE~--al~k~~~~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRIR 1461 (1764)
+|+|++ .++.+++ |++|||+| | +|.+++|++.+|+++|.+ |+.+ ++|+++++|+++++||||
T Consensus 1179 ~~~~~~~~~~~~~~~--~~~rl~l~----------~~~~~~~~l~~~~I~~~i~~~~~~~--~~v~~~d~~~~~~~i~i~ 1244 (1752)
T 3h0g_A 1179 IPDEEVEENLYKQSP--WLLRLELD----------RAKMLDKKLSMSDVAGKIAESFERD--LFTIWSEDNADKLIIRCR 1244 (1752)
T ss_dssp TTCSSTTCSSCSCCC--CEEEEECC----------TTSSTTTTCCHHHHTTSGGGSSTTS--CCEECCCTTCSSCEEEEC
T ss_pred cchhhhhcccccccc--eeEEEEec----------HHHHHHcCCCHHHHHHHHHhhccCC--eeEeecCCCccceeEEEE
Confidence 555543 3566888 99999999 8 999999999999999988 7765 999999999999999999
Q ss_pred EecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeec
Q psy6965 1462 IMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDG 1541 (1764)
Q Consensus 1462 I~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDG 1541 (1764)
+....+.+.++ + ....+++.||++++.++|.+++|+|||||+||++++ +++.+++++|++....+|+|.|+|
T Consensus 1245 ~~~~~~~~~~~-~--~~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv~i~~-----~~~~~~~~~g~~~~~~~~~l~teG 1316 (1752)
T 3h0g_A 1245 IIRDDDRKAED-D--DNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMME-----HKIVRQIEDGTFERADEWVLETDG 1316 (1752)
T ss_dssp CCCCSCCCCCS-S--CCCSCSCHHHHHHHHHHTTCCCSSCCTTCCCCCEEE-----EEEEEECSSSCEEEEEEEEEECCS
T ss_pred ecccccccccc-c--cccccHHHHHHHHHHhhccceEEecCCCccEEEEec-----ccceeecCCCcccccceEEEEecc
Confidence 87643221110 0 112346689999999999999999999999999975 234446777877777899999999
Q ss_pred cchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeeccccccccc
Q psy6965 1542 TSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1621 (1764)
Q Consensus 1542 TNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGIN 1621 (1764)
+||++||++++||++||+||||+||++||||||||++|++||++||++||+|||||||+||||+||++|+++|||||||+
T Consensus 1317 ~nL~~v~~~~gVD~~rt~sNdI~ei~~vlGIEAAR~~Ii~Ei~~v~~~~G~~Vd~RHl~LlaD~MT~~G~~~~itR~Gi~ 1396 (1752)
T 3h0g_A 1317 INLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGIN 1396 (1752)
T ss_dssp CCCSTTTSSSSCCTTTCCCSCHHHHHHHSCHHHHHHHHHHHHHTTSCSSSCCCCHHHHHHHHHHHTSSSSCCCCCTTSCS
T ss_pred cCHHHHhCcCCCccccCeeCCHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccCCeEEeechhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChhhhh
Q psy6965 1622 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 1682 (1764)
Q Consensus 1622 R~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~ekLk 1682 (1764)
+.++|||+|||||+|++||++||++|++|+|+|||||||+||++|+|||+|||+++.++|+
T Consensus 1397 ~~~~s~l~~aSFE~T~~~L~~Aa~~g~~D~l~gvse~Ii~G~~~~~GTG~fdll~~~~~l~ 1457 (1752)
T 3h0g_A 1397 RAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDIYLDQDMLM 1457 (1752)
T ss_dssp CCCSHHHHHHHHSCCTHHHHHHGGGTCCBCCCCSTTGGGTCSCCCSBTTSCEECCCHHHHH
T ss_pred cCCCCHHHHhhHHHHHHHHHHHHHhcCcccccChhHHhhcCCCcCCccceEEEEeCHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999
No 2
>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=4e-63 Score=615.58 Aligned_cols=278 Identities=40% Similarity=0.664 Sum_probs=239.9
Q ss_pred CCCChhH--HhhccCcchhhhHhhhccccchhhHHHH-HHhcCCCCccchHHHHhc-cCCCCcEEEEeccCCccceEEEE
Q psy6965 1385 KMQDEED--AVDKMEDDMFLRCIEANMLSDMTLQFIR-IMNSDDSKMQDEEDAVDK-MEDDMFLRCIEANMLSDMTLQFI 1460 (1764)
Q Consensus 1385 ~m~DEE~--al~k~~~~~~L~~iE~nm~~d~~l~~~R-~MiDkdLtM~~iaekI~~-f~dd~DL~VIfSDDNAEKLVIRI 1460 (1764)
++|+|+. ..+.+++ |+++||++ | +|.++++++.+|+++|.+ |+.+ +.|+++++|++++++|+
T Consensus 1175 ~i~~~d~~~~~~~~~~--~~lrl~l~----------~~~~~~~~l~~~~I~~~i~~~~~~~--~~~~~~d~~~~~~~~~i 1240 (1733)
T 1twf_A 1175 SLLDEEAEQSFDQQSP--WLLRLELD----------RAAMNDKDLTMGQVGERIKQTFKND--LFVIWSEDNDEKLIIRC 1240 (1733)
T ss_dssp CC----------CCCS--EEEEEEEC----------HHHHHHTTCCHHHHHHHHHHHHGGG--EEEEECCTTSSSCEEEE
T ss_pred cccHHhhcchhhhccc--ceeEEEec----------HHHHHhcCCCHHHHHHHHHHhhCCC--cceecCCcccchhheee
Confidence 4665555 4677888 99999999 8 888999999999999988 8755 99999999999999999
Q ss_pred EEecCCCCccchhhhhhhchhhhHHHHHHHHhhccCceeccccCcceEEecccccCCCceEEEcCCCcccccceEEEEee
Q psy6965 1461 RIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETD 1540 (1764)
Q Consensus 1461 RI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETD 1540 (1764)
|+...++ +. ++ +..+++.||++++.++|.+++|+|||||+||++++ .+++++.++|.++...+|+|+|+
T Consensus 1241 ~~~~~~~-~~---~~--~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~i~~-----~~~~~~~~~g~~~~~~~~~L~te 1309 (1733)
T 1twf_A 1241 RVVRPKS-LD---AE--TEAEEDHMLKKIENTMLENITLRGVENIERVVMMK-----YDRKVPSPTGEYVKEPEWVLETD 1309 (1733)
T ss_dssp EEC----------------CCTTHHHHHHHHHHHHHCEEESCTTCCCEEEEE-----EEEEEECTTSSEEEEEEEEEEEE
T ss_pred eeccCcc-cc---cc--ccchhHHHHHHHHHHhhhheEEecCCCccEEEEec-----ccceeecCCCccccCcceEEEee
Confidence 9876431 10 00 12234579999999999999999999999999864 25677888887766789999999
Q ss_pred ccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccc
Q psy6965 1541 GTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGI 1620 (1764)
Q Consensus 1541 GTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGI 1620 (1764)
|+||++||++++||++|||||||++|++||||||||++|++||++||++||++||+|||+||||+||++|+++|||||||
T Consensus 1310 G~nL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~LlaD~MT~~G~~~~itR~Gi 1389 (1733)
T 1twf_A 1310 GVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGF 1389 (1733)
T ss_dssp SCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSS
T ss_pred cccHHHHhccCCcccccceeccHHHHHHHhhHHHHHHHHHHHHHHHHhhcCccccchhhhhhhhhhccCceecccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecChhhhhccccc
Q psy6965 1621 NRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCKDGIEI 1687 (1764)
Q Consensus 1621 NR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~ekLkdAiE~ 1687 (1764)
++.++|||++||||+|+++|++||++|+.|.|+|||||||+||++|+|||+|||+++.++|+++++.
T Consensus 1390 ~~~~~S~L~~aSFE~T~~~L~~Aa~~g~~D~l~gvsenII~G~~~~~GTG~FdLl~~~~~~~~~~~~ 1456 (1733)
T 1twf_A 1390 NRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPE 1456 (1733)
T ss_dssp SCSSCCTTSSCCSSCSHHHHHHHHHHTCEECCCSHHHHHHTTCCCSSGGGSSEEEECSCCC------
T ss_pred cccCCCchhhcchhhhHHHHHHHHhccCcCcccccccccccCCCCCCCCccEEEEEchhhccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999998864
No 3
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=100.00 E-value=6.7e-48 Score=419.21 Aligned_cols=220 Identities=31% Similarity=0.494 Sum_probs=185.5
Q ss_pred HHhcCCCCccchHHHHhccCCCCcEEEEeccCCccceEEEEEEecCCCCccchhhhhhhchhhhHHHHHHHHhhccCcee
Q psy6965 1420 IMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTL 1499 (1764)
Q Consensus 1420 ~MiDkdLtM~~iaekI~~f~dd~DL~VIfSDDNAEKLVIRIRI~~ded~k~eeeee~vD~~EDDvFLRrIEanMLsdItL 1499 (1764)
.+.++.+++.++..++.+.+.. .+.+..++ ...+++++.+... . ..|.++... +.++.|
T Consensus 173 ~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~--v-------------~~l~~~~~~-~~~~~i 231 (395)
T 4ayb_C 173 MLKDKGVTVDDVKKAINRLKLG-EFVIDESE----GNTLNISFANIDS--I-------------AALFKLRDK-ILNTKI 231 (395)
T ss_dssp GGBTTBCHHHHHHHHHHHSCCS-SEEEEECS----SEEEEEECCSSCC--C-------------CCTHHHHHH-HHHHCC
T ss_pred hhhhcCccHHHHHHHHhhhccC-cEEEeccc----CcEEEeecCCCch--H-------------HHHHHHHhh-ccccEE
Confidence 5667788889999999884332 24444433 3345555433211 0 012223222 336789
Q ss_pred ccccCcceEEecccccCCCceEEEcCCCcccccceEEEEeeccchhhhccCCCcccccccccCHHHHHHHhcHHHHHHHH
Q psy6965 1500 QGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSV 1579 (1764)
Q Consensus 1500 RGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVLETDGTNL~EVLS~pgVDptRTySNDI~EILeVLGIEAARkAI 1579 (1764)
+||+||.|+.+.. ...+|++.|+|+|+.++|.+++||+++++||||++|+++|||||||++|
T Consensus 232 ~gi~gi~r~~~~~------------------~~~~~~~~t~g~~l~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~i 293 (395)
T 4ayb_C 232 KGIKGIKRAIVQK------------------KGDEYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREII 293 (395)
T ss_dssp CSSSSCCEEEEEE------------------ETTEEEEEEESCCHHHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHH
T ss_pred ecccceeEEEEec------------------cCCEEEEEecCCCceeeeEeecccccccccCcchhhhhhhhHHHHHHHH
Confidence 9999999987643 1147999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCCcccchhhHHHHHHHHhccCeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCe
Q psy6965 1580 EKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENI 1659 (1764)
Q Consensus 1580 InEIrnVFSfYGIYVNyRHLSLLADvMT~RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENI 1659 (1764)
++|+++||+.||++||+|||.||||+||++|++++++|||+++...|||++||||||+++|++||++|++|+|+||||||
T Consensus 294 v~Ei~~V~~~~Gv~In~rHi~li~d~Mt~~G~~~~igr~g~s~~t~S~LsaASFqeTt~vLteAAi~Gk~D~L~GlkENV 373 (395)
T 4ayb_C 294 IREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENI 373 (395)
T ss_dssp HHHHHHHHHTTSCCCCHHHHHHHHHHHHGGGSCCCSSSSSHHHHCSCHHHHHHHSCTHHHHHHHHHTTCBCCCCSHHHHH
T ss_pred HHhHHHHHhccCceechHHhhhhhhhhhccceEeccCcccccCCCCCHHHHhcChhHHHHHHHHHhcCCCCCCCChHHHe
Confidence 99999999999999999999999999999999999999999998899999999999999999999999999999999999
Q ss_pred eccCCCCCCcceeEeecCh
Q psy6965 1660 IMGQLPRMGTGCFDLLLDA 1678 (1764)
Q Consensus 1660 ILGQLIPVGTGsFDLLLD~ 1678 (1764)
|+||++|+|||+|||++++
T Consensus 374 IvGklipaGTG~f~l~~~p 392 (395)
T 4ayb_C 374 IIGHPIKLGTGMVELTMRP 392 (395)
T ss_dssp HHTCCCSSGGGTCEEEECS
T ss_pred ecCCCCCCCcCceEEEecc
Confidence 9999999999999999874
No 4
>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=99.93 E-value=2.3e-27 Score=291.63 Aligned_cols=113 Identities=27% Similarity=0.424 Sum_probs=106.8
Q ss_pred ccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhcc------------------------------
Q psy6965 1560 SNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK------------------------------ 1609 (1764)
Q Consensus 1560 SNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~R------------------------------ 1609 (1764)
|||+++|++++||||||++|++||++||+.||++||.|||+||||+||++
T Consensus 1329 ~~~~~dil~v~Giea~~~~iv~Eiq~Vyr~QGv~I~dKHIevIvrqM~~kv~i~~~Gdt~~l~Ge~v~~~~~~~~n~~~~ 1408 (1524)
T 2a6h_D 1329 AIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLI 1408 (1524)
T ss_dssp BCCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTSEEEEEECSSSCSSCEEEHHHHHHHHHHHHTT
T ss_pred CCCchhheeecCHHHHHHHHHHHHHHHHHhcCcccchhHHHHHHHHHhceeEEecCCCccCCCCceeeHHHHHHHHHHHH
Confidence 48899999999999999999999999999999999999999999999664
Q ss_pred ----------CeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEe
Q psy6965 1610 ----------GHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDL 1674 (1764)
Q Consensus 1610 ----------G~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDL 1674 (1764)
|.++||||+|+++ .|+|++||||||+++|++||++|++|+|+|++||||+|+++|+|||+|.+
T Consensus 1409 ~~g~~~a~~~~~llGITkasL~t--~SfLsaASFqeTtrvLt~AAi~Gk~D~L~GlkENVIiG~lIPaGTG~~~~ 1481 (1524)
T 2a6h_D 1409 AEGKTPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFV 1481 (1524)
T ss_dssp SCSCCCCEEEECCCCHHHHHHSC--SCHHHHHHSSCHHHHHHHHHHTTEEEECCSHHHHHHTTCCCSSSTTCTTT
T ss_pred HcCCCcceeeeeeeeeeeccccc--CChhhhcChHHHHHHHHHHHhcCCCCCCCCcHHHeeecCCccCCcCchhh
Confidence 4578999999984 79999999999999999999999999999999999999999999998754
No 5
>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=99.92 E-value=1.4e-26 Score=283.24 Aligned_cols=116 Identities=28% Similarity=0.451 Sum_probs=107.2
Q ss_pred ccCHHHHHHHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhc-------------------------------
Q psy6965 1560 SNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTA------------------------------- 1608 (1764)
Q Consensus 1560 SNDI~EILeVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~------------------------------- 1608 (1764)
+|++++|++++||||+|++|++||++||+.||++||.|||+||||+||+
T Consensus 1070 ~~~~~eil~v~Giea~~~~lv~EIq~vyr~QGv~I~dkHievivrqM~~kv~i~~~g~t~~l~Ge~v~~~~~~~~n~~~~ 1149 (1265)
T 1hqm_D 1070 AIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLI 1149 (1265)
T ss_dssp BSHHHHHHHTTHHHHHHHHHHHHHHHHHHTTSCCCCSSTHHHHHHHHTTEECBSSCCSSCCSCCCEEGGGTTTTTTTTTT
T ss_pred CccHHHHHHHhhHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHHHHhcceEEecCCCcCCCCCceecHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999999999965
Q ss_pred ---------cCeecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCcceeEeecCh
Q psy6965 1609 ---------KGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDA 1678 (1764)
Q Consensus 1609 ---------RG~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsFDLLLD~ 1678 (1764)
+|.++||||+|+++ .|+|++||||||+++|++||++|++|+|+|++||||+|+++|+|||. ..+.+.
T Consensus 1150 ~~g~~~~~~~~~llGITkasl~t--~SflsaASFqeTt~vL~~AAi~gk~D~L~GlkEnVIiG~lipaGTG~-~~~~~~ 1225 (1265)
T 1hqm_D 1150 AEGKVPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS-DFVRFT 1225 (1265)
T ss_dssp C---CCCCBCCCCCCTHHHHTSC--SCHHHHTTSTTHHHHHHHHHHSCCCCTTCSSHHHHHHTCCCSSGGGC-TTSCCC
T ss_pred hcCCCcceeeeeeecceeccccc--CChhhccchHHHHHHHHHHHHcCCCCcCCCcHHheeeCCcccCCcCc-hhhhcc
Confidence 45688999999984 69999999999999999999999999999999999999999999994 334443
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=99.92 E-value=1.3e-26 Score=282.54 Aligned_cols=162 Identities=28% Similarity=0.447 Sum_probs=130.3
Q ss_pred ceeccccCcceEEecccccCCCceEEEcCCCcccccceEEE---------EeeccchhhhccCCCcccccccccCHHHHH
Q psy6965 1497 MTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLL---------ETDGTSLMKVLSERDVDPVRTFSNDICEIF 1567 (1764)
Q Consensus 1497 ItLRGIPGIkKVfI~ePetdkKKRIVITEDGefkak~EWVL---------ETDGTNL~EVLS~pgVDptRTySNDI~EIL 1567 (1764)
..|..|.|+-+. . ..++++.+++++++.+- ...+|.+ +.+-+.-++.|+.+.++| ++|+
T Consensus 1154 a~i~ei~G~v~~--~-~~~~~~~~~~i~~~~g~-~~~~y~i~~~~~~~v~~gd~v~~G~~l~~G~~~p--------~dil 1221 (1407)
T 3lu0_D 1154 AILAEISGIVSF--G-KETKGKRRLVITPVDGS-DPYEEMIPKWRQLNVFEGERVERGDVISDGPEAP--------HDIL 1221 (1407)
T ss_dssp CCCCSSCSCCEE--C-CCCSSCEEEECCCSSCC-TTCEEEECSSSCCCCCSSSCCCTTCCCSSSCCCH--------HHHH
T ss_pred eEEeccceEEEE--e-eccCCceEEEEEeCCCC-eeEEEEccCCceeeecCCCEEcCCCCccCCCCCH--------HHHH
Confidence 344555555432 1 13345566777654211 1234433 334445677888877777 5999
Q ss_pred HHhcHHHHHHHHHHHHHHhhccCCcccchhhHHHHHHHHhccC-------------------------------------
Q psy6965 1568 QVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKG------------------------------------- 1610 (1764)
Q Consensus 1568 eVLGIEAARkAIInEIrnVFSfYGIYVNyRHLSLLADvMT~RG------------------------------------- 1610 (1764)
+++||||+|++|++|+++||+.||++||+|||++|+++||+++
T Consensus 1222 ~v~Giea~~~ylv~Evq~VYr~QGV~IndKHIEvIvrqM~~kv~I~d~Gdt~fl~Ge~vd~~~~~~~N~~~~~~g~~pa~ 1301 (1407)
T 3lu0_D 1222 RLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGAT 1301 (1407)
T ss_dssp HHSCHHHHHHHTTTTTHHHHHHHTCCCCSHHHHTTTGGGTSBCEESSCSSSCSCCCCBSHHHHHHHHHHHTTSSSCCCCC
T ss_pred HhhCHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHHHhCceEEeeCCCcccCCcceecHHHHHHHHHHHHHcCCCCce
Confidence 9999999999999999999999999999999999999999872
Q ss_pred ---eecccccccccccCCChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCCCCCccee
Q psy6965 1611 ---HLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCF 1672 (1764)
Q Consensus 1611 ---~LmgITRHGINR~dTSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLIPVGTGsF 1672 (1764)
.|+||||++++. .|+|++||||||+++|++||++|++|+|+|++||||+|+++|+|||..
T Consensus 1302 ~~p~llGITkasl~t--~SflSaASFQeTtkvLteAAi~Gk~D~L~GlkENVIvG~lIPaGTG~~ 1364 (1407)
T 3lu0_D 1302 YSRDLLGITKASLAT--ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYA 1364 (1407)
T ss_dssp EECCCCCTTTTTTSC--SCTTTGGGSSCHHHHHHHHHHTCCEECCCSSHHHHTTTCCCTTTTTST
T ss_pred eeeeeeceeeccccC--CCchhhcchhhHHHHHHHHHhcCCCCcCCCcccceEecccccCCcCch
Confidence 468999999974 799999999999999999999999999999999999999999999964
No 7
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.17 E-value=5.2e-12 Score=159.70 Aligned_cols=113 Identities=32% Similarity=0.526 Sum_probs=90.4
Q ss_pred ChHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccc-----
Q psy6965 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR----- 75 (1764)
Q Consensus 1 MEdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP----- 75 (1764)
+++|+++|.+.|+++++|+++|+|+++++||||+.+..+..++ + + ....+++.||++||.++|.+++|||||
T Consensus 1212 ~~~I~~~i~~~~~~~~~v~~~d~~~~~~~i~i~~~~~~~~~~~-~-~-~~~~~~~~~l~~l~~~~l~~~~i~Gi~~I~rv 1288 (1752)
T 3h0g_A 1212 MSDVAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAE-D-D-DNMIEEDVFLKTIEGHMLESISLRGVPNITRV 1288 (1752)
T ss_dssp HHHHTTSGGGSSTTSCCEECCCTTCSSCEEEECCCCCSCCCCC-S-S-CCCSCSCHHHHHHHHHHTTCCCSSCCTTCCCC
T ss_pred HHHHHHHHHhhccCCeeEeecCCCccceeEEEEeccccccccc-c-c-cccccHHHHHHHHHHhhccceEEecCCCccEE
Confidence 3579999999999999999999999999999999864321111 0 0 112346789999999999999999999
Q ss_pred ccccccCccccchhhhcccCcceEEecccchhhhccccccEE
Q psy6965 76 IMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIR 117 (1764)
Q Consensus 76 ~Ir~d~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~ 117 (1764)
.|++..+...+++|+|.+ .++|+|+|+|+||.+||+++||-
T Consensus 1289 ~i~~~~~~~~~~~g~~~~-~~~~~l~teG~nL~~v~~~~gVD 1329 (1752)
T 3h0g_A 1289 YMMEHKIVRQIEDGTFER-ADEWVLETDGINLTEAMTVEGVD 1329 (1752)
T ss_dssp CEEEEEEEEECSSSCEEE-EEEEEEECCSCCCSTTTSSSSCC
T ss_pred EEecccceeecCCCcccc-cceEEEEecccCHHHHhCcCCCc
Confidence 444544444567788887 78999999999999999999983
No 8
>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=98.81 E-value=1.2e-09 Score=138.42 Aligned_cols=108 Identities=29% Similarity=0.405 Sum_probs=84.4
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccccc----
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIM---- 77 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~I---- 77 (1764)
++|+++|.+.|+.+++|+++|+||+++++|+|+...++. . + + ++.+++.||++|+.++|.+++|+|||.|
T Consensus 1210 ~~I~~~i~~~~~~~~~~~~~d~~~~~~~~~i~~~~~~~~-~--~--~-~~~~~~~~l~~l~~~~l~~~~v~Gi~~I~r~~ 1283 (1733)
T 1twf_A 1210 GQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSL-D--A--E-TEAEEDHMLKKIENTMLENITLRGVENIERVV 1283 (1733)
T ss_dssp HHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------------CCTTHHHHHHHHHHHHHCEEESCTTCCCEE
T ss_pred HHHHHHHHHhhCCCcceecCCcccchhheeeeeccCccc-c--c--c-ccchhHHHHHHHHHHhhhheEEecCCCccEEE
Confidence 579999999999999999999999999999999764321 0 0 0 1224568999999999999999999944
Q ss_pred -ccccCccccchhhhcccCcceEEecccchhhhccccccE
Q psy6965 78 -NSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFI 116 (1764)
Q Consensus 78 -r~d~rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V 116 (1764)
++..+...+++|.|.+ .++|+|+|+|+||.+||++++|
T Consensus 1284 i~~~~~~~~~~~g~~~~-~~~~~L~teG~nL~~vl~~~~V 1322 (1733)
T 1twf_A 1284 MMKYDRKVPSPTGEYVK-EPEWVLETDGVNLSEVMTVPGI 1322 (1733)
T ss_dssp EEEEEEEEECTTSSEEE-EEEEEEEEESCCHHHHTTSTTB
T ss_pred EecccceeecCCCcccc-CcceEEEeecccHHHHhccCCc
Confidence 4333333467777866 7899999999999999999996
No 9
>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=96.28 E-value=0.00065 Score=77.36 Aligned_cols=41 Identities=41% Similarity=0.623 Sum_probs=29.9
Q ss_pred CChhhhhhhHHHHHHHHHHhhcCCCCCCCccccCeeccCCC
Q psy6965 1625 TGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLP 1665 (1764)
Q Consensus 1625 TSPLmRASFEETVEILtEAAIfGEvD~LRGVSENIILGQLI 1665 (1764)
.|+|.+++||.|..+|.+|+.+|+.|.++||.|||++||.-
T Consensus 391 ~s~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (436)
T 3qqc_A 391 GSVLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQKH 431 (436)
T ss_dssp --------CCCCHHHHHHHHHHTCEEECCSSCCTTSCC---
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHhhhcccc
Confidence 59999999999999999999999999999999999999853
No 10
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=80.74 E-value=1.3 Score=49.10 Aligned_cols=88 Identities=15% Similarity=0.132 Sum_probs=56.0
Q ss_pred hHHHHHHHhccCCCceEEeccCCccceEEEEEEeecCCCcccchhhhhccchhHHHHHHHHHhhccCccccccccccccc
Q psy6965 2 EAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRIMNSDD 81 (1764)
Q Consensus 2 EdIAEKIKEEFGDDL~VIfSDDNAEKLVIRIRIVndeDdkdDeEEDevDkmEDDvFLRRLESNMLSdLTLRGIP~Ir~d~ 81 (1764)
.+|...|...+.++..+..++. ..++++..+... ...|.++...++ +..++||+.+....
T Consensus 182 ~~i~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~---------------v~~l~~~~~~~~-~~~i~gi~gi~r~~ 241 (395)
T 4ayb_C 182 DDVKKAINRLKLGEFVIDESEG----NTLNISFANIDS---------------IAALFKLRDKIL-NTKIKGIKGIKRAI 241 (395)
T ss_dssp HHHHHHHHHSCCSSEEEEECSS----EEEEEECCSSCC---------------CCCTHHHHHHHH-HHCCCSSSSCCEEE
T ss_pred HHHHHHHhhhccCcEEEecccC----cEEEeecCCCch---------------HHHHHHHHhhcc-ccEEecccceeEEE
Confidence 4577778887777777665543 344444332110 012334444444 57899999665432
Q ss_pred CccccchhhhcccCcceEEecccchhhhccccccEEE
Q psy6965 82 SKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFIRI 118 (1764)
Q Consensus 82 rk~~~Et~~f~K~~kEWVLdTdGtNL~eVLTlp~V~~ 118 (1764)
.. .+ .++|++.|+|+||.++|.+++|.+
T Consensus 242 ~~--------~~-~~~~~~~t~g~~l~~~~~~~~vd~ 269 (395)
T 4ayb_C 242 VQ--------KK-GDEYIILTDGSNLSGVLSVKGVDI 269 (395)
T ss_dssp EE--------EE-TTEEEEEEESCCHHHHTTSTTCCT
T ss_pred Ee--------cc-CCEEEEEecCCCceeeeEeecccc
Confidence 11 12 579999999999999999999854
No 11
>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R 3sfs_R* 3uoq_R* 4gaq_R* 4gas_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R ...
Probab=20.72 E-value=22 Score=32.93 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=25.9
Q ss_pred cCCc-ccchhhHHHHHHHHhccCeeccccccccc
Q psy6965 1589 FYGL-YVNYRHLALLCDVMTAKGHLMAITRHGIN 1621 (1764)
Q Consensus 1589 fYGI-YVNyRHLSLLADvMT~RG~LmgITRHGIN 1621 (1764)
..|+ +|||+.+.||..++|.+|.+.|=...|+.
T Consensus 15 ~~~~~~iDYknv~lL~~Fis~~GkIlprr~TGlc 48 (75)
T 3i1m_R 15 AEGVQEIDYKDIATLKNYITESGKIVPSRITGTR 48 (75)
T ss_dssp -----CCSTTCHHHHGGGBCTTCCBCCHHHHCCC
T ss_pred cCCCCcCCcCCHHHHHHHcCcCCCCcCccccccC
Confidence 3455 69999999999999999999987666764
Done!