Query psy3023
Match_columns 392
No_of_seqs 137 out of 1630
Neff 8.0
Searched_HMMs 29240
Date Fri Aug 16 23:34:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3023.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/3023hhsearch_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 3.1E-94 1E-98 804.3 24.4 376 3-392 6-392 (1752)
2 1twf_A B220, DNA-directed RNA 100.0 2.8E-89 9.5E-94 765.2 24.1 370 3-392 4-386 (1733)
3 3qqc_A DNA-directed RNA polyme 100.0 1.5E-84 5.3E-89 644.9 20.5 315 9-359 65-394 (436)
4 4ayb_A DNA-directed RNA polyme 100.0 1E-84 3.5E-89 699.4 20.2 343 9-392 2-359 (880)
5 1hqm_D DNA-directed RNA polyme 100.0 2.4E-68 8.4E-73 579.2 -3.0 347 11-386 3-398 (1265)
6 3lu0_D DNA-directed RNA polyme 100.0 4.7E-58 1.6E-62 491.7 10.5 329 9-388 13-384 (1407)
7 2a6h_D DNA-directed RNA polyme 100.0 3.9E-53 1.3E-57 459.9 14.2 143 242-385 509-657 (1524)
8 3hcj_A MSRB, peptide methionin 34.1 11 0.00039 31.2 0.7 10 75-84 104-113 (154)
9 1odh_A MGCM1; transcription fa 29.7 12 0.0004 31.3 0.1 27 64-95 111-139 (174)
10 3e0o_A Peptide methionine sulf 29.2 11 0.00038 31.0 -0.1 14 75-88 95-108 (144)
11 2l1u_A MSRB2, methionine-R-sul 23.2 18 0.00063 29.6 0.2 10 76-85 99-108 (143)
12 1twf_L ABC10-alpha, DNA-direct 22.1 26 0.0009 25.0 0.8 11 62-72 27-37 (70)
13 2k8d_A Peptide methionine sulf 21.6 15 0.00053 30.3 -0.6 10 75-84 115-124 (151)
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=3.1e-94 Score=804.32 Aligned_cols=376 Identities=50% Similarity=0.863 Sum_probs=330.0
Q ss_pred CCCCCCCccccceEEEecCCHHHHHHhhhcccceeCcccccC--CccccCCCCCCCCCCCCCCCccccccCCCCCCCCcc
Q psy3023 3 MADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG--GRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHF 80 (392)
Q Consensus 3 ~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~--~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHf 80 (392)
..+|.+|.++|++|+||++|+|||+++||++ |+++.+||. ++|+.|||||||||+.++...|+|||++..+|||||
T Consensus 6 ~~~s~~~~~~i~~i~Fg~~S~eeI~~~Sv~~--I~~~~~~d~~~~~P~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHF 83 (1752)
T 3h0g_A 6 FSPSSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETMADCPGHF 83 (1752)
T ss_dssp SCCCSSCCCCCCCBEECCCCHHHHHHHCCCC--CCCTTCTTCSSSSSCCSSSSSSSCCCSSSSCCCTTSCCSSSSCCCCC
T ss_pred CCCCcCcceeeeeEEEecCCHHHHHHhCeeE--EecccccccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCcCCCcc
Confidence 4689999999999999999999999999999 999999985 599999999999999999999999999999999999
Q ss_pred eEeecCcchhhhhcHHHHHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHHHHHhhccccCCCCCCCCcCCC
Q psy3023 81 GHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKD 160 (392)
Q Consensus 81 GhI~L~~PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~c~~~~~~~~~~~ 160 (392)
|||||++|||||+||+.|++||+|+|++|++|++++.++++...++. ...++|+++++++|+++..|+.+...+.+..
T Consensus 84 GHIELa~PVfHpgF~~~I~kILr~vC~~C~klll~~~~~~f~~~lrl--rd~k~r~~~V~~~ck~k~~Ce~~~~~~~~~~ 161 (1752)
T 3h0g_A 84 GHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRY--RDPKNRLNAVWNVCKTKMVCDTGLSAGSDNF 161 (1752)
T ss_dssp EECCCCSCBCCHHHHHHHHHHSSSSCTTTCCCSCCSCSHHHHHHHHS--SCTTTTHHHHHHHHHHCCCCCSSTTCCSSCC
T ss_pred eeeecccceEeehhhHHHHHHHHHHHHHhcccccccccHHHHHHHHc--cCHHHHHHHHHHHhccccccCCCCcccccch
Confidence 99999999999999999999999999999999999887766554432 2345678999999998889976432221000
Q ss_pred CCCCccccccCCCCCCCCCCCCCccccccceeeeEeeccccccc-cccccCChHHHHHhhcC-CCCCccc--cccccccc
Q psy3023 161 GAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQ-EKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIRRS 236 (392)
Q Consensus 161 ~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~~~~~-~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~~~ 236 (392)
.......++.|++|++.+|.||+.+++++.+|+...++.. +.+..|+|++|+++|++ |++|+++ +++.+.+
T Consensus 162 ----~~~~~~~~~~~~gCG~~qP~IRKeglkl~~~~k~~k~~~~~~~k~~LtP~eVl~ifk~IsdeD~~lLGl~~~~~r- 236 (1752)
T 3h0g_A 162 ----DLSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYAR- 236 (1752)
T ss_dssp ----CSSCCCCCCSSCSSCCCCCCCEEETTEEECCBCCSSSSCBCSSCCCCCHHHHHHHHHHSCHHHHHHSSCCSSSCC-
T ss_pred ----hcccccccccCCCcCCcCCcEEeeccEEEEEEcccccccccccceecCHHHHHHHHHhcCHHHHHHhCCCccCCC-
Confidence 0000113457999999999999999988888875332211 24568999999999999 9999998 6677777
Q ss_pred CCCCCCccccccccc-----CCceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhcc
Q psy3023 237 GLDLTAEWKHVNEDS-----QEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTD 311 (392)
Q Consensus 237 ~l~~~p~~~il~~l~-----VRP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d 311 (392)
|+||||++|| |||++.++|+...|||||++|++||+.|+.|++....|++..++.+.|++||.+|++|+|
T Consensus 237 -----PewmiL~vLPVpPp~vRPsv~ldg~~~~edDLt~~l~~II~~N~~Lk~~~~~gap~~~~~~~~~~LQ~~v~~~~d 311 (1752)
T 3h0g_A 237 -----PDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSEYEQLLQFHVATYMD 311 (1752)
T ss_dssp -----GGGSSBSSCEECCGGGSCCCCCSSSCCCCCTTTTHHHHHHHHHHHHHGGGGCCSSSTTHHHHHHHHHHHHHHTTC
T ss_pred -----hhheEeeccccCCCCccCceEcCCCccCCChHHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHhhc
Confidence 9999999995 488888888778899999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccCCCC
Q psy3023 312 NDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNM 391 (392)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~~Ni 391 (392)
|+.+|.+.+.+++++|++||+|||+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+||+
T Consensus 312 n~~~~~~~~~~~~~rp~k~~~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~evGvP~~~A~~Lt~Pe~vt~~ni 391 (1752)
T 3h0g_A 312 NEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNI 391 (1752)
T ss_dssp TTCSSCCCCCSSSSCCCCCHHHHHTCSSSSSTTTTSSCCCSSEEEEEEEEETTSCTTBCBCCHHHHTSCCCCCBCCTTTH
T ss_pred CCCCCCccccccCCCCCcchHhhhhcccccccccccccccCCccceeecCCCCcccceeeChHHHHHhcCCCccccHHHH
Confidence 99998876666678999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred C
Q psy3023 392 D 392 (392)
Q Consensus 392 ~ 392 (392)
+
T Consensus 392 ~ 392 (1752)
T 3h0g_A 392 Y 392 (1752)
T ss_dssp H
T ss_pred H
Confidence 3
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=2.8e-89 Score=765.22 Aligned_cols=370 Identities=50% Similarity=0.844 Sum_probs=326.2
Q ss_pred CCCCCCCccccceEEEecCCHHHHHHhhhcccceeCcccccCC--ccccCCCCCCCCCCCCCCCccccccCCCCCCCCcc
Q psy3023 3 MADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEGG--RPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHF 80 (392)
Q Consensus 3 ~~~~~~~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~~--~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHf 80 (392)
.++|+++.++|++|+|+++|+|||++|||.| |+++++|+.+ +|+.|||||||||+.+++..|+|||.+..+|||||
T Consensus 4 ~~~~~~~~~~i~~I~f~l~SpeeIr~~Sv~e--I~~pet~~~~~~~P~~~GL~d~rlG~~~~~~~C~tCg~~~~~C~GHf 81 (1733)
T 1twf_A 4 QQYSSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHF 81 (1733)
T ss_dssp CSCCCSCBCCCCEEECCBCCHHHHHHTCCCC--CCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCTTSCCCCC
T ss_pred CCCCcCCccccceEEEEeCCHHHHHHhCeeE--EecccccccccCCCCcCCCcCcccCcccCCCEeCCCCCCCCcCCCcc
Confidence 5788999999999999999999999999998 9999999866 99999999999999999999999999999999999
Q ss_pred eEeecCcchhhhhcHHHHHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHHHHHhhccccCCCCCCCCcCCC
Q psy3023 81 GHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKD 160 (392)
Q Consensus 81 GhI~L~~PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~c~~~~~~~~~~~ 160 (392)
|||||++||||||||+.++++|+++|++|+++++++.+..++.++.. ...++++++++++|+++..|+.......+
T Consensus 82 GHIELa~PV~HigF~k~i~kiLe~VC~~Cskllld~~~~~~~~~L~~--~~pk~r~~~v~e~ck~k~~Ce~~~~~~~e-- 157 (1733)
T 1twf_A 82 GHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAI--KDSKKRFAAIWTLCKTKMVCETDVPSEDD-- 157 (1733)
T ss_dssp CCEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTC--CSHHHHHHHHHHHHTTCCBCCSEECCSSC--
T ss_pred ceeecccccccHHHHhhHHHHHHHHhHhcceeeeccchHHHHHHHHh--cCHHHHHHHHHHHhcccccccccccchhc--
Confidence 99999999999999999999999999999999999887665554432 13467788899999887788532111100
Q ss_pred CCCCccccccCCCCCCCCCCCCCccccccceeeeEeeccc---cccccccccCChHHHHHhhcC-CCCCccc--cccccc
Q psy3023 161 GAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVN---EDSQEKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIR 234 (392)
Q Consensus 161 ~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~ 234 (392)
+ ...+.|.+|++.++.+++.++++..+|+... +..++.+..++|++|+++|++ +++|+++ ++|.+.
T Consensus 158 ------~--~~~~~~~gCGa~qp~irk~gl~l~~e~k~~~~~~e~~~~~k~~Ltp~eV~eifk~I~deD~~lLgl~p~~~ 229 (1733)
T 1twf_A 158 ------P--TQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFS 229 (1733)
T ss_dssp ------T--TSCEECCSCCCBCCCCEECSSCEEEEECSSSSCTTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTTB
T ss_pred ------c--ccccccCCCCCccHHHHhcCCceEEeecccccccccchhhhccCCHHHHHHHHHhCCHHHHHHhCCCccCC
Confidence 0 1234689999999999999988888887543 222334568999999999999 9999888 566777
Q ss_pred ccCCCCCCcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhh
Q psy3023 235 RSGLDLTAEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATL 309 (392)
Q Consensus 235 ~~~l~~~p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~ 309 (392)
+ |+||||++||| ||++.++|+...|||||++|++||+.|+.|++....|++.+.+.+.|.+||.+|+.|
T Consensus 230 r------PewmiLtvLPVpPp~vRPsv~ldg~~~~edDLT~~l~~II~~N~~Lk~~~~~gap~~ii~e~~~~LQ~~v~~~ 303 (1733)
T 1twf_A 230 R------PEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATY 303 (1733)
T ss_dssp C------GGGGEEEEECCCCTTTSCCCCCSSSCCCCCHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHH
T ss_pred C------hheeeeeeeccCCCCccCceecCCCcccCCHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHH
Confidence 7 99999999955 888888887788999999999999999999999889999999999999999999999
Q ss_pred ccCCCCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccCC
Q psy3023 310 TDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPF 389 (392)
Q Consensus 310 ~d~~~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~~ 389 (392)
|||+.+|.+.+.+++++|++||+|+|+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+|
T Consensus 304 ~dn~~~~~~~~~~~~~rp~k~i~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~L~~~evGvP~~~A~~Lt~Pe~vt~~ 383 (1733)
T 1twf_A 304 MDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPY 383 (1733)
T ss_dssp HCCCSSCCCCCSSCTTCCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTT
T ss_pred hccCccCCCccccCCCccchhHHHHhccccchhhhcccccccCcccceEEeCCCCcccccccCcHHHHHhCCCCccccHH
Confidence 99999988766666789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q psy3023 390 NMD 392 (392)
Q Consensus 390 Ni~ 392 (392)
|++
T Consensus 384 ni~ 386 (1733)
T 1twf_A 384 NID 386 (1733)
T ss_dssp THH
T ss_pred HHH
Confidence 974
No 3
>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=100.00 E-value=1.5e-84 Score=644.94 Aligned_cols=315 Identities=37% Similarity=0.588 Sum_probs=239.3
Q ss_pred CccccceEEEecCCHHHHHHhhhcccceeCcccccC-CccccCCCCCCCCCCCCCCCccccccCCCCCCCCcceEeecCc
Q psy3023 9 PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG-GRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAK 87 (392)
Q Consensus 9 ~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhI~L~~ 87 (392)
..++|++|+||++|+|||+++||++ |+++.+||. |+|+.|||||||||++++...|+|||++..+||||||||||+.
T Consensus 65 ~~~~i~~i~F~~~s~eeI~~~Sv~~--I~~~~~~d~~~~P~~gGl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhIeL~~ 142 (436)
T 3qqc_A 65 GGKVIGSIEFGILSPQEIRKMSAVE--VTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGECPGHFGHIELAR 142 (436)
T ss_dssp --CEEEEEECCBCCHHHHHHTEEEE--CCBCCCCC----CCCSBSSCSSSCCCSSCCCCSSSCCCSSSCCCCEEEEEEEE
T ss_pred ccceeeeeeeccCCHHHHHHhCCeE--EecccccCCCCCccCCCccCccccCCCCCCCCCCCCCCCCcCCCCceeEeech
Confidence 4489999999999999999999999 999999985 9999999999999999999999999999999999999999999
Q ss_pred chhhhhcHHHHHHHHHHhhhcccccccCCCch-HHHHHHHhhhc---chHHHHHHHHHHhhccccCCCCCCCCcCCCCCC
Q psy3023 88 PVFHVGFVTKTIKILRCVCFYCSKLLVSPSHP-KVRDVVLKTKG---QSRRRQAFIYDLCKGKNICEGGDEMDINKDGAE 163 (392)
Q Consensus 88 PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~-~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~c~~~~~~~~~~~~~~ 163 (392)
|||||+|++.+++||+++|++|+++++++.+. ++...++.... ..+.+++.+++.|++..
T Consensus 143 PVfh~gF~~~I~kILr~vC~~C~klll~~~~~~~f~~~lr~~~~~~~~~k~~~~~i~~~~k~~~---------------- 206 (436)
T 3qqc_A 143 PVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEFNEIIKEIHKKAKERM---------------- 206 (436)
T ss_dssp EEECGGGHHHHHHHHHHSCSTTCCCSSCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHTCC----------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHhhhhccccHHHHHHHHHHHcccCC----------------
Confidence 99999999999999999999999999997543 34443432211 23455677777776433
Q ss_pred CccccccCCCCCCCCCCCCCccccccceeeeEeecc-ccccccccccCChHHHHHhhcC-CCCCccc--ccccccccCCC
Q psy3023 164 DPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHV-NEDSQEKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIRRSGLD 239 (392)
Q Consensus 164 ~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~~~~l~ 239 (392)
.|++|++.+|+|++++.... |+.. .++.++.+..|+|++|+++|++ +++|+.+ ++|.+++
T Consensus 207 ----------~C~gCG~~qp~Ir~e~~~~~--~~~~~~~~~~~~k~~LtP~~vl~ifk~IsdeD~~lLGl~~~~~r---- 270 (436)
T 3qqc_A 207 ----------VCPHCGAPQYPIKFEKPTIY--WEIRKDEQGNEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSR---- 270 (436)
T ss_dssp ----------SCC-------CCCBCSSSCE--EEECCC---CCCEEEECHHHHHHHHHHSCTTTGGGSSCCTTTCC----
T ss_pred ----------cCcccCCcCceEEEecceee--eeccccccccccccccCHHHHHHHHHhCCHHHHHHhcccccCCC----
Confidence 46788999999988775433 3321 1222334568999999999999 9999999 7888888
Q ss_pred CCCccccccccc-----CCceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhccCCC
Q psy3023 240 LTAEWKHVNEDS-----QEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDM 314 (392)
Q Consensus 240 ~~p~~~il~~l~-----VRP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~ 314 (392)
|+||||++|| |||++.++|+..+|||||++|.+||++|+.|++....|++.+.+.+.|..||.+|++||||+.
T Consensus 271 --PewmIlt~LPVpPp~vRPsv~~~~g~~~edDLT~kl~~II~~N~~L~~~~~~gap~~~i~~~~~lLQ~~V~~~~dn~~ 348 (436)
T 3qqc_A 271 --PEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDLLQYHVTTYINNEA 348 (436)
T ss_dssp --GGGGEEEEEEECCGGGSCCBCC---CCBCCHHHHHHHHHHHHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHHCTTC
T ss_pred --cceeEeeccccCCCcCcccEEeCCCcCCCChHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhccCCC
Confidence 9999999995 488898887778999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccccCCCchhhHhhhhcccccccccccCCccccCccc-eee
Q psy3023 315 PGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSAR-TVI 359 (392)
Q Consensus 315 ~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaR-SVI 359 (392)
+|.|.+.+++++|++||+|||+|||||||+||||||||||+| |||
T Consensus 349 ~g~~~~~~~~~rp~ksi~~rLkGKeGRfR~NL~GKRVdy~~~~s~~ 394 (436)
T 3qqc_A 349 PGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSGAGSGSVL 394 (436)
T ss_dssp TTCCCCBCTTSCBCCCHHHHHCC-----------------------
T ss_pred CCCCccccCCCCCccchHhhhccccceecCcCCCCCCCcccchhHH
Confidence 998876666789999999999999999999999999999999 999
No 4
>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=1e-84 Score=699.39 Aligned_cols=343 Identities=41% Similarity=0.711 Sum_probs=284.2
Q ss_pred CccccceEEEecCCHHHHHHhhhcccceeCcccccC-CccccCCCCCCCCCCCCCCCccccccCCCCCCCCcceEeecCc
Q psy3023 9 PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG-GRPKLGGLMDPRQGVIDRSSRCQTCAGNMTECPGHFGHIDLAK 87 (392)
Q Consensus 9 ~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~~-~~p~~~Gl~D~rlG~~~~~~~C~TCg~~~~~CpGHfGhI~L~~ 87 (392)
+.++|++|+||++|+|||++|||.| |++|++|+. |+|+.|||||||||+.+++..|+|||.+..+|||||||||||.
T Consensus 2 ~~k~i~~I~f~l~SpeeIr~~S~~e--V~~p~t~n~~g~p~~ggl~D~~lG~~~~~~~C~tCg~~~~~c~ghfGhIeLa~ 79 (880)
T 4ayb_A 2 SEKNIKGIKFGILSPDEIRKMSVTA--IITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGHIELVR 79 (880)
T ss_dssp -CEEEEEEEEECCCHHHHHHHTCSC--BCCSCCCBSSSSSBCSSSSCGGGCCCSSSCCCTTTCCCGGGCCCCCEEEEEEE
T ss_pred CCceeceEEEEeCCHHHHHHhcceE--EeCcceECCCCCccCCCCCChhhCCCCCCCCCCCCCCCCCCCCCCCeeecccc
Confidence 4689999999999999999999988 999999975 9999999999999999999999999999999999999999999
Q ss_pred chhhhhcHHHHHHHHHHhhhcccccccCCCchHH-HHHHHhh-hcc--hHHHH-HHHHHHhhccccCCCCCCCCcCCCCC
Q psy3023 88 PVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKV-RDVVLKT-KGQ--SRRRQ-AFIYDLCKGKNICEGGDEMDINKDGA 162 (392)
Q Consensus 88 PV~hp~f~~~~~~iL~~iC~~C~~l~l~~~~~~~-~~~~~~~-~~~--~~~~~-~~i~~~~~~~~~c~~~~~~~~~~~~~ 162 (392)
||||||||+.+.++|+++|++|+++++++.+.+. ..+.... ... ..+++ +.+.+.+.
T Consensus 80 PV~h~~f~~~i~~lL~~~c~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------ 141 (880)
T 4ayb_A 80 PVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRWPSAARRLTEYVKKTAM------------------ 141 (880)
T ss_dssp EEECGGGTTHHHHHHHTSCTTSSCCCSSCCHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHT------------------
T ss_pred cccchhHHHHHHHHHhCccccccCCcCCHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHhc------------------
Confidence 9999999999999999999999999998865332 1111111 111 11111 11222221
Q ss_pred CCccccccCCCCCCCCCCCCCcccccc-ceeeeEeeccccccccccccCChHHHHHhhcC-CCCCccc--ccccccccCC
Q psy3023 163 EDPNSLQNKKQGHGGCGRYQPNIRRSG-LDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQ-GHGGCGR--YQPNIRRSGL 238 (392)
Q Consensus 163 ~~~~~~~~~~~~~~~C~~~~~~i~~~~-~~~~~~~~~~~~~~~~~~~~l~p~~v~~i~k~-~~~d~~l--l~p~~~~~~l 238 (392)
+...|++|+..+++++... .++.. +.++....++|.+++++|++ +++++.+ +.+...+
T Consensus 142 --------~~~~c~~cg~~~~~i~~~~~~~~~~-------~~~~~~~~l~~~~~~~~l~~i~~~~~~~l~~~~~~~~--- 203 (880)
T 4ayb_A 142 --------KAQVCPHCGEKQFKIKLEKPYNFYE-------ERKEGVAKLTPSDIRERLEKVPESDVEILGYDPTTSR--- 203 (880)
T ss_dssp --------TCSSCTTTTCCCCCCEEEETTEEEE-------EETTEEEECCHHHHHHHHTTCCHHHHHHTTCCTTTCC---
T ss_pred --------ccccchhccchhhhhhhcCcCCHHH-------HHHHHHHhcCHHHHHHHHHHhHHHHHHHhCCCCcCCC---
Confidence 2235677888877765432 22211 12223346899999999999 8888776 5666667
Q ss_pred CCCCcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhccCC
Q psy3023 239 DLTAEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDND 313 (392)
Q Consensus 239 ~~~p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~ 313 (392)
|+||||++||| ||++.++|+...+||+|.+|++||+.|++|++....+++...+.+.|.+||.+|++|+||+
T Consensus 204 ---Pewmil~~lPV~Pp~~RP~v~l~~g~~~~~dl~~~~~~ii~~N~~lk~~~~~~ap~~i~~~~~~~LQ~~V~~l~dn~ 280 (880)
T 4ayb_A 204 ---PEWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNE 280 (880)
T ss_dssp ---SGGGEEEEEEECCSSSSCC-----CCCCCCSSHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHCSC
T ss_pred ---chheEEeeeeCCCCCCCchhhcCCcccccchHHHHHHHHHHhhhhhhhhhhcCCchhHHHHHHHHHHHHHHHHHhcc
Confidence 99999999965 8888888887889999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCccccCCCCC
Q psy3023 314 MPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392 (392)
Q Consensus 314 ~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~Vt~~Ni~ 392 (392)
.+|.+.+..++++|++||+|+|+||+||||+|||||||||||||||||||||++||||||..||++|||||+||+||++
T Consensus 281 ~~g~~~~~~~~~rp~ksl~~~lkgK~GrfR~nl~GKRVd~s~RsVI~~dP~l~~~e~GvP~~~A~~Lt~Pe~vt~~N~~ 359 (880)
T 4ayb_A 281 IPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIE 359 (880)
T ss_dssp CSSSCCCCCTTSCCCCCHHHHHHSSSSTHHHHTSSEECSSEEEEEEEECTTSCSSEEEECHHHHTTSEEEEECCTTTHH
T ss_pred CCCCCccCCCCCCcccchhhhhcccchhhhhcccceeecccCceeeeCCCCccccccCCcHHHHHhCCCCeEEcHHHHH
Confidence 9887765566779999999999999999999999999999999999999999999999999999999999999999974
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=100.00 E-value=2.4e-68 Score=579.25 Aligned_cols=347 Identities=26% Similarity=0.409 Sum_probs=216.0
Q ss_pred cccceEEEecCCHHHHHHhhhcccceeCccccc--CCccccCCCCCCCC-CCCC--------------CCCccccccCCC
Q psy3023 11 RCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQ-GVID--------------RSSRCQTCAGNM 73 (392)
Q Consensus 11 ~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~--~~~p~~~Gl~D~rl-G~~~--------------~~~~C~TCg~~~ 73 (392)
.+|++|+||++|||||++||+.| |++|++|+ .++|..+||+|+|| ||.. ++..|+|||...
T Consensus 3 ~~~~~i~~gl~Spe~Ir~~S~ge--V~~pet~ny~t~kP~~~GLfd~rifGp~k~~~C~Cgkyk~~~~~~~~C~~Cg~~~ 80 (1265)
T 1hqm_D 3 KEVRKVRIALASPEKIRSWSYGE--VEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEV 80 (1265)
T ss_dssp CCBCCCCCCCCCTTTHHHHTTTC--CCCCCC-------------------------------------CCSCSSSSSSSS
T ss_pred cccceEEEecCCHHHHHHhhEEE--EcchhheecCCCcccCCCCcCccccCCCccceecCCCccccCCCCCCCCCCCCcc
Confidence 46899999999999999999988 99999986 59999999999999 7653 667899999999
Q ss_pred CCC---CCcceEeecCcchhhhhcHHH-----------HHHHHHHhhhcccccccCCCchHHHHHHHhhhcchHHHHHHH
Q psy3023 74 TEC---PGHFGHIDLAKPVFHVGFVTK-----------TIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAFI 139 (392)
Q Consensus 74 ~~C---pGHfGhI~L~~PV~hp~f~~~-----------~~~iL~~iC~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~i 139 (392)
.+| |||||||||+.||||+|||+. +.+.|+++|++|+++++++.....+. +. .. .. ...
T Consensus 81 ~~~~vrrg~~GhIeLa~PV~Hi~y~k~~~s~l~~lL~~~~k~le~v~y~~s~v~~~~~~~l~~~-l~---~~--~~-~~~ 153 (1265)
T 1hqm_D 81 TRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDPKGAVLDG-VP---VE--KR-QLL 153 (1265)
T ss_dssp CCSSSCCCSCCCCCCCSCCCSTTSTTHHHHTTTCTTTHHHHTTSSSCCCCSCCCCSSSCCCTTC-CC---CT--TH-HHH
T ss_pred cccccccCccceEEecCceeeeeecccchHHHHHHhcCCHHhhccEeeecceEeecCCchHhhh-cC---HH--HH-HHH
Confidence 999 899999999999999999996 45677888889999987654110000 00 00 00 000
Q ss_pred HHH-hhc-cccC-CC---CCCCCcCC-CCCCCccccccCCCCCCCCCCCCCccccccceeeeEeecccccc-----cccc
Q psy3023 140 YDL-CKG-KNIC-EG---GDEMDINK-DGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDS-----QEKK 207 (392)
Q Consensus 140 ~~~-~~~-~~~c-~~---~~~~~~~~-~~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~~~~~~~~~~-----~~~~ 207 (392)
.+. .+. ...+ .. +.+.+... .+.....+ ........+|+..++.+.. +++..++....++- +..+
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~G~~~~~~~l~~--~~l~~~~~~~~~~~~~~~~~~~~ 230 (1265)
T 1hqm_D 154 TDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-XXXIDARMGAEAIQELLKE--LDLEKLERELLEEMKHPSRARRA 230 (1265)
T ss_dssp TCCCCCCCCCCCCSSCCCCCCCCTTSCCCCCCCCC-CCCCCCCCSHHHHHHHHTH--HHHCHHHHHHHTTTCCSSHHHHH
T ss_pred hhhcccccccccccccccccccccccccccccccc-hhhhhcccCchhHHHHHHh--cCHHHHHHHHHHHHhhccHHHHH
Confidence 000 000 0000 00 00000000 00000000 0000011122222222111 11111111111100 0001
Q ss_pred ccCChHHHHHhhcCCCCCcccccccccccCCCCCCcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHH
Q psy3023 208 IPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNEL 282 (392)
Q Consensus 208 ~~l~p~~v~~i~k~~~~d~~ll~p~~~~~~l~~~p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L 282 (392)
..+.+.++.+.|+. ...+ |+||||++||| ||++.++|+...+||||.+|++||+.|++|
T Consensus 231 ~~~krl~~~~~f~~----------~~~~------Pewmil~~lPVpPp~~RP~v~l~gg~~~~~Dln~~~~~Ii~~N~~L 294 (1265)
T 1hqm_D 231 KARKRLEVVRAFLD----------SGNR------PEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRL 294 (1265)
T ss_dssp HHHHHHHHHHHHHS----------SSCS------SCCSCSSCCCCCSCC------------CCCGGGTHHHHTHHHHHHH
T ss_pred HHhhhhhhhhhhcc----------cCCC------cceEeeeccCCCCCcCccceecCCCceecChhHHHHHHHHHHHHHH
Confidence 12233334444433 2244 99999999975 888888887678999999999999999999
Q ss_pred HHHHhcCCchhhHHHHHHHHHHHHhhhccCCCCCCccccccCCCc-hhhHhhhhcccccccccccCCccccCccceeecC
Q psy3023 283 IRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKP-LKAIKARLKGKEGRIRGNLMGKRVDFSARTVITP 361 (392)
Q Consensus 283 ~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~-~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsP 361 (392)
++....+++...+.+.|.+||.+|++||||+.+|.|. ..++++| ++||+|+|+||+||||+|||||||||||||||||
T Consensus 295 ~~~~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~-~~~~~rp~lksl~~~LkGK~GrfR~NLmGKRVdfSaRSVI~p 373 (1265)
T 1hqm_D 295 KKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPV-TNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVV 373 (1265)
T ss_dssp HTSSSSCCCSTTTSTTTTTTGGGTTTTSSCCSSCCCS-SCSSCCCCCCCSTTTSSSTTCTTTTTTSCCEETTCCCCBEEE
T ss_pred HHHHHcCCchhHHHHHHHHHHHHHHHHhCCCCCCCCc-cCCCCCccccchhhhcccchhhhhhhhcccccCcccceeEec
Confidence 9988889998888889999999999999999988765 3456789 9999999999999999999999999999999999
Q ss_pred CCCCccccccchHHhHhhcccCccc
Q psy3023 362 DPNLRIDQVGVPRSIAQNMTFPEIV 386 (392)
Q Consensus 362 DP~l~ideiGvP~~~A~~LT~Pe~V 386 (392)
||||++||||||..||++||+|+.+
T Consensus 374 dP~L~i~evGvP~~~A~~L~~P~~~ 398 (1265)
T 1hqm_D 374 GPQLKLHQCGLPKRMALELFKPFLL 398 (1265)
T ss_dssp CCSSSSSBCCCBHHHHHHHHHHHHH
T ss_pred CCCcccccccChHHHHHHhCcHHHH
Confidence 9999999999999999999999754
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=4.7e-58 Score=491.65 Aligned_cols=329 Identities=28% Similarity=0.380 Sum_probs=239.0
Q ss_pred CccccceEEEecCCHHHHHHhhhcccceeCccccc--CCccccCCCCCCCC-CCCC--------------CCCccccccC
Q psy3023 9 PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQ-GVID--------------RSSRCQTCAG 71 (392)
Q Consensus 9 ~~~~i~~i~F~~~s~eeI~~~Sv~~~~i~~~~~~~--~~~p~~~Gl~D~rl-G~~~--------------~~~~C~TCg~ 71 (392)
....+++|+++++|||+|++||+-| |+.|++++ ..+|..+||+|+|+ ||.. ++..|++||.
T Consensus 13 ~~~~~~~i~i~laSpe~I~~ws~GE--V~kpetinyrt~kPe~dGLFcerIFGp~kd~eC~Cgkyk~~~~~g~~C~~Cgv 90 (1407)
T 3lu0_D 13 KTEEFDAIKIALASPDMIRSWSFGE--VKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGV 90 (1407)
T ss_dssp -CCCCCCEEECCCCHHHHHHHBCSC--CCSCCCCCSSCCSCCSSSSSCTTTTCCSSSSCCSSCSCCSTTCSSSCCSSSCC
T ss_pred ccCccceEEEEeCCHHHHHhhcCeE--ECCccccccCCCCCCCCCccchhhcCCCcCcEEeCccccccccCCCCCCCCCC
Confidence 4468999999999999999999966 99999864 69999999999999 9873 4568999999
Q ss_pred CCCCCC---CcceEeecCcchhhhhcHHHH----HHHHHHhhhcccccccC-------CCchHHHHHHHhhhcchHHHHH
Q psy3023 72 NMTECP---GHFGHIDLAKPVFHVGFVTKT----IKILRCVCFYCSKLLVS-------PSHPKVRDVVLKTKGQSRRRQA 137 (392)
Q Consensus 72 ~~~~Cp---GHfGhI~L~~PV~hp~f~~~~----~~iL~~iC~~C~~l~l~-------~~~~~~~~~~~~~~~~~~~~~~ 137 (392)
...+|. .|||||+|+.||.|+|||+.+ -.+|.+.|..|.+++-- +....+ .+... +.
T Consensus 91 evt~~~vRr~rmGhI~La~PV~Hiwy~k~~ps~i~~lL~~~~k~le~viy~~~~iv~~~~~~~l----~~~~~-----~~ 161 (1407)
T 3lu0_D 91 EVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNL----ERQQI-----LT 161 (1407)
T ss_dssp CCCCTTHHHHCBCEEEEEEEECCTHHHHSSSCTTTTTTTSCSSTTHHHHSSSCCCEECCSSSCS----CSSCC-----CC
T ss_pred ccccCcchhhhcceeeecCceeEeeeccCCchHHHHHhCCCHHHhhhheecceeEeecCCCCcc----chhcc-----cC
Confidence 999997 999999999999999999965 66787777777665432 211100 00000 00
Q ss_pred HHHHHhhccccCCCCCCCCcCCCCCCCccccccCCCCCCCCCCCCCccccccceeee-------EeeccccccccccccC
Q psy3023 138 FIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTA-------EWKHVNEDSQEKKIPL 210 (392)
Q Consensus 138 ~i~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~i~~~~~~~~~-------~~~~~~~~~~~~~~~l 210 (392)
+ +.+.....|.. +..... .+..+....+. ..++.. +|+.... .+..+..+
T Consensus 162 ~--~~~~~~~~~~~----~~~~~~--------------~Gaeai~~lL~--~~dl~~~~~~l~~~~~~~~~-~~k~~~~~ 218 (1407)
T 3lu0_D 162 E--EQYLDALEEFG----DEFDAK--------------MGAEAIQALLK--SMDLEQECEQLREELNETNS-ETKRKKLT 218 (1407)
T ss_dssp S--TTCCCCCSSSC----CCCCEE--------------CSSHHHHHHHH--TCCHHHHHHTHHHHHHHCCC-TTTTTTTT
T ss_pred H--HHHHHHHHhhc----hhhhcc--------------ccHHHHHHHHH--hcCHHHHHHHHHHHHHhccc-HHHHHHHH
Confidence 0 00110001100 000000 00000100000 011110 1111100 01112233
Q ss_pred ChHHHHHhhcCCCCCcccccccccccCCCCCCcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHH
Q psy3023 211 TGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRN 285 (392)
Q Consensus 211 ~p~~v~~i~k~~~~d~~ll~p~~~~~~l~~~p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~ 285 (392)
...++.+.|..+ ..+ |+||||++||| ||++.++|+...+||||.+|++||+.|++|++.
T Consensus 219 krl~~v~~F~~s----------~~r------Pewmil~~lPVpPp~lRP~v~l~gg~~~~~DLn~ly~~II~~N~~Lk~~ 282 (1407)
T 3lu0_D 219 KRIKLLEAFVQS----------GNK------PEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRL 282 (1407)
T ss_dssp TSSTTHHHHHSS----------SCC------GGGSSEEEEECCCSTTSCCCBCSTTCBCCCTTTTTHHHHHHTTTTTGGG
T ss_pred HHHHHHHHHHhc----------CCC------HHHhhhheeecCCCCCCCcEEeCCCccccCchHHHHHHHHHHHHHHHHH
Confidence 334444445442 234 99999999965 888999887788999999999999999999998
Q ss_pred HhcCCchhhHHHHHHHHHHHHhhhccCCCCCCccccccCCCchhhHhhhhcccccccccccCCccccCccceeecCCCCC
Q psy3023 286 ESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNL 365 (392)
Q Consensus 286 ~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~~~~~~~~~~~~~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l 365 (392)
...+++...+.+.|.+||.+|++|+||+.+|.+.. .++++|++||+|+|+||+||||+|||||||||||||||||||||
T Consensus 283 ~~~~ap~~ii~~~~~~LQ~~V~~l~Dn~~~g~~~~-~~~~rplksl~qrLkGKeGrfR~NLmGKRVDfSaRSVIspdP~L 361 (1407)
T 3lu0_D 283 LDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAIT-GSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYL 361 (1407)
T ss_dssp TSSCCCTTTHHHHHHHHHHHHHHHHCSSSSCCCCB-TTBCCCCCCTTHHHHTSSSTHHHHTTCCCCSSBCEEEEEECSSC
T ss_pred HHcCCcHHHHHHHHHHHHHHHHHhcCCCCCCCccc-CCCCCcccchHHHhccccchhhcccccCCCCCcCceEEeCCCCc
Confidence 88999999999999999999999999999886543 34678999999999999999999999999999999999999999
Q ss_pred ccccccchHHhHhhcccCccccC
Q psy3023 366 RIDQVGVPRSIAQNMTFPEIVTP 388 (392)
Q Consensus 366 ~ideiGvP~~~A~~LT~Pe~Vt~ 388 (392)
++||||||..||++||+|+.++.
T Consensus 362 ~i~evGvP~~~A~~L~~Pf~i~~ 384 (1407)
T 3lu0_D 362 RLHQCGLPKKMALELFKPFIYGK 384 (1407)
T ss_dssp CTTEEEEESHHHHHHTCHHHHHH
T ss_pred cceeeeCCHHHHHHhcchHHHHH
Confidence 99999999999999999987754
No 7
>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=3.9e-53 Score=459.92 Aligned_cols=143 Identities=32% Similarity=0.527 Sum_probs=133.9
Q ss_pred CcccccccccC-----CceeeecCCcccchhhHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhhhccCCCCC
Q psy3023 242 AEWKHVNEDSQ-----EKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPG 316 (392)
Q Consensus 242 p~~~il~~l~V-----RP~~~~~~~~~~eddlT~~l~~II~~n~~L~~~~~~g~~~~~~~~~~~~LQ~~v~~~~d~~~~~ 316 (392)
|+||||++||| ||++.++|+...+||||.+|++||+.|++|++....+++..++.+.|.+||.+|++||||+.+|
T Consensus 509 Pewmil~vlPVpPp~lRP~v~ldgg~~~~sDLn~ly~~II~~Nn~Lk~~~~~gap~~ii~~e~~~LQ~~V~~liDN~~~g 588 (1524)
T 2a6h_D 509 PEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRG 588 (1524)
T ss_dssp TTTTEEEEEEECCSTTSCEEECSTTCEEECTHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCSSSSS
T ss_pred ccEEEEecccCCCCCCCCceecCCCceecchHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 99999999965 8889998877789999999999999999999988889999999999999999999999999988
Q ss_pred CccccccCCCc-hhhHhhhhcccccccccccCCccccCccceeecCCCCCccccccchHHhHhhcccCcc
Q psy3023 317 LPRAMQKSGKP-LKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385 (392)
Q Consensus 317 ~~~~~~~~~~~-~~gi~q~L~~K~G~fR~nlmGKRVnfsaRSVIsPDP~l~ideiGvP~~~A~~LT~Pe~ 385 (392)
.|.. ..+++| ++||+|+|+||+||||+|||||||||||||||||||||++||||||..||++||+|+.
T Consensus 589 ~p~~-~~~~Rp~lKslsq~LkGKeGRFRqNLlGKRVDySgRSVI~pdP~L~l~evGvP~~mA~eLt~Pf~ 657 (1524)
T 2a6h_D 589 APVT-NPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFL 657 (1524)
T ss_dssp CCBC-SSSCCCBCCCHHHHHSTTTCHHHHHHHCEEESSEEEEEEEECTTSCTTEEEEEHHHHHHHTHHHH
T ss_pred CCcc-CCCCCCcCcchhhhccccccccccccccccccccCcceEecCCCccccccCCcHHHHHHhccHHH
Confidence 7653 446789 9999999999999999999999999999999999999999999999999999999974
No 8
>3hcj_A MSRB, peptide methionine sulfoxide reductase; methionine sulfoxide reductase B, oxidized form, oxidoreductase; 1.66A {Xanthomonas campestris PV} PDB: 3hci_A*
Probab=34.09 E-value=11 Score=31.23 Aligned_cols=10 Identities=40% Similarity=1.026 Sum_probs=7.4
Q ss_pred CCCCcceEee
Q psy3023 75 ECPGHFGHID 84 (392)
Q Consensus 75 ~CpGHfGhI~ 84 (392)
.|-||.||+=
T Consensus 104 ~Cg~HLGHVF 113 (154)
T 3hcj_A 104 RCDSHLGHVF 113 (154)
T ss_dssp TTCCEEEEEE
T ss_pred CCCCccCCcc
Confidence 4558999974
No 9
>1odh_A MGCM1; transcription factor/DNA, transcription factor, DNA-binding domain, protein/DNA complex; 2.85A {Mus musculus} SCOP: d.239.1.1
Probab=29.73 E-value=12 Score=31.26 Aligned_cols=27 Identities=33% Similarity=0.688 Sum_probs=21.2
Q ss_pred CccccccCC--CCCCCCcceEeecCcchhhhhcH
Q psy3023 64 SRCQTCAGN--MTECPGHFGHIDLAKPVFHVGFV 95 (392)
Q Consensus 64 ~~C~TCg~~--~~~CpGHfGhI~L~~PV~hp~f~ 95 (392)
..|+-|... ...|.||-|| ||+|.|..
T Consensus 111 k~CpnC~g~L~~~~Crgh~Gy-----PVThFWrh 139 (174)
T 1odh_A 111 KSCPNCNGPLKLIPCRGHGGF-----PVTNFWRH 139 (174)
T ss_dssp SBCSSSCCBEEEECCCTBTTB-----CCEEEEEE
T ss_pred CCCCCCCcceeeEeccCcCCC-----cceEEEEE
Confidence 368888755 4699999987 99998753
No 10
>3e0o_A Peptide methionine sulfoxide reductase MSRB; oxidoreductase; 2.60A {Bacillus subtilis} SCOP: b.88.1.3 PDB: 1xm0_A 2kzn_A
Probab=29.18 E-value=11 Score=30.96 Aligned_cols=14 Identities=29% Similarity=0.536 Sum_probs=9.0
Q ss_pred CCCCcceEeecCcc
Q psy3023 75 ECPGHFGHIDLAKP 88 (392)
Q Consensus 75 ~CpGHfGhI~L~~P 88 (392)
.|-||.||+=---|
T Consensus 95 ~Cg~HLGHVF~DGP 108 (144)
T 3e0o_A 95 TADSHLGHVFNDGP 108 (144)
T ss_dssp TTCCEEEEEESCCS
T ss_pred CCCCccCCccCCCC
Confidence 45589999743334
No 11
>2l1u_A MSRB2, methionine-R-sulfoxide reductase B2, mitochondria; methionine sulfoxide reductase, oxidoreductase; NMR {Mus musculus}
Probab=23.24 E-value=18 Score=29.59 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=7.1
Q ss_pred CCCcceEeec
Q psy3023 76 CPGHFGHIDL 85 (392)
Q Consensus 76 CpGHfGhI~L 85 (392)
|-||.||+==
T Consensus 99 Cg~HLGHVF~ 108 (143)
T 2l1u_A 99 CEAHLGHVFP 108 (143)
T ss_dssp SCCCCEEEEC
T ss_pred CCCcCCcccC
Confidence 4489999743
No 12
>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...
Probab=22.12 E-value=26 Score=24.97 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=8.9
Q ss_pred CCCccccccCC
Q psy3023 62 RSSRCQTCAGN 72 (392)
Q Consensus 62 ~~~~C~TCg~~ 72 (392)
-...|..||..
T Consensus 27 v~Y~C~~CG~~ 37 (70)
T 1twf_L 27 LKYICAECSSK 37 (70)
T ss_dssp CCEECSSSCCE
T ss_pred EEEECCCCCCc
Confidence 44689999987
No 13
>2k8d_A Peptide methionine sulfoxide reductase MSRB; thermophilic, Zn binding, metal-binding, oxidoreductase; NMR {Methanothermobacter thermautotrophicusorganism_taxid}
Probab=21.61 E-value=15 Score=30.33 Aligned_cols=10 Identities=40% Similarity=1.029 Sum_probs=7.2
Q ss_pred CCCCcceEee
Q psy3023 75 ECPGHFGHID 84 (392)
Q Consensus 75 ~CpGHfGhI~ 84 (392)
.|-||.||+=
T Consensus 115 ~Cg~HLGHVF 124 (151)
T 2k8d_A 115 RCDAHLGHVF 124 (151)
T ss_dssp TEEEEEEEEE
T ss_pred CCCCcCCccc
Confidence 3458999974
Done!