Query 014847
Match_columns 417
No_of_seqs 187 out of 1395
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 18:53:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014847.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/014847hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1twf_B DNA-directed RNA polyme 100.0 8E-118 3E-122 1008.7 24.5 378 1-410 745-1221(1224)
2 3h0g_B DNA-directed RNA polyme 100.0 1E-117 5E-122 1000.1 20.6 378 1-410 734-1209(1210)
3 4ayb_B DNA-directed RNA polyme 100.0 6E-112 2E-116 960.1 23.9 377 1-409 647-1120(1131)
4 2a6h_C DNA-directed RNA polyme 100.0 1E-108 5E-113 920.8 21.3 382 1-410 536-1106(1119)
5 3lu0_C DNA-directed RNA polyme 100.0 2E-101 6E-106 860.4 15.9 370 1-406 657-1340(1342)
6 3qqc_A DNA-directed RNA polyme 98.5 3E-08 1E-12 102.3 3.6 58 353-411 7-66 (436)
7 3tbi_B DNA-directed RNA polyme 98.3 9.5E-07 3.3E-11 83.4 8.3 52 108-160 35-108 (228)
8 2bay_A PRE-mRNA splicing facto 15.6 37 0.0013 24.7 0.3 44 269-322 4-50 (61)
9 1qxf_A GR2, 30S ribosomal prot 7.5 1.3E+02 0.0043 22.9 0.8 28 315-342 35-62 (66)
10 1l2m_A REP protein; A+B fold, 7.3 91 0.0031 26.2 -0.0 51 45-95 3-58 (118)
No 1
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Probab=100.00 E-value=8.1e-118 Score=1008.68 Aligned_cols=378 Identities=37% Similarity=0.522 Sum_probs=329.5
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeecccccc---------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCL--------- 71 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~l--------- 71 (417)
|++||||+||+|||||| ||||||||||| |+|||||++.+|+..|+|+..|.|+|||+|||+|..++.+
T Consensus 745 Ps~ILgV~ASlIPF~dH--NqSpRn~yqs~-M~kQA~g~~~~n~~~r~dt~~~~l~ypQkPlV~t~~~~~~~~~elp~G~ 821 (1224)
T 1twf_B 745 PSMILGVAASIIPFPDH--NQSPRNTYQSA-MGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ 821 (1224)
T ss_dssp GGGGSCTTGGGSSSGGG--SCHHHHHHHHH-HGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCE
T ss_pred CccccceeecccCCccc--cccchhhhccc-ccccccccccceeeeecccccceeecCcCCeEEcccccccccccCCCCe
Confidence 89999999999999999 99999999999 8999999999999999999999999999999999877743
Q ss_pred ----------CCC-CCeEEEecceecccceeeEEEEEEEec--------ccccCC---------------CCCCCccccc
Q 014847 72 ----------GRP-EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQVK---------------SRPSDDMLNF 117 (417)
Q Consensus 72 ----------g~n-EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~~~---------------~~~~~g~~~~ 117 (417)
|+| ||||||||+|+|||+|||++|+++... .+.+++ .+|.||++.+
T Consensus 822 N~iVAvm~y~GYN~EDAiIin~~sv~rg~~~s~~~~~y~~~~~~~~~~~~e~~~~P~~~~~~~~~~~~~~~LD~dGiv~~ 901 (1224)
T 1twf_B 822 NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAP 901 (1224)
T ss_dssp EEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCT
T ss_pred eEEEEEecccCcccchhhhhhhhHHhcCCeeEEEEEEEEEEeeeCCCCceeEecCCChhhccCccHHHHhhcccCCccCC
Confidence 444 999999999999999999988776532 111221 2578899999
Q ss_pred cccccccCCeEEEEeccCC---------------ceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEIG---------------ADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~~---------------~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. .|++|||||||++|++ +|+|++++++|.|+||+|.++++++|.+.|||++|+ .|.|+|
T Consensus 902 G~-~V~~gDilvgK~~p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkV~ir~----~R~p~i 976 (1224)
T 1twf_B 902 GV-RVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQI 976 (1224)
T ss_dssp TC-EECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEE----EECCCT
T ss_pred cc-EecCCCEEEEEecCCCccccccccccccCccceeEEEeeCCCCeEEEEEEEEecCCCCEEEEEEEEe----cCCCCc
Confidence 96 8999999999999842 789999999999999999999999999999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||+|| ||||||+|+++||+ ++.|...|+|||++.++++|.
T Consensus 977 GDKfasRHGqKGvis~i~p~eDMPf~~dG~~pDiIiNPhg~PSRMtiGqllE~~lgka~~~~G~~~datpF~~~~~~~i~ 1056 (1224)
T 1twf_B 977 GDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGIS 1056 (1224)
T ss_dssp TCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHH
T ss_pred hhhhhhhccCcceeeeecccccCCcCCCCCCccEEeCCCcCccccccchhHHHHhhHHHHhcCceeecCCCCCccHHHHH
Confidence 999999999999999999 99999999999999 789999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|++ ||+++|+ |.|||| +||++|+++||+|++|||||+|||+||+|||++|||+.
T Consensus 1057 ~~L~~~g~~~~G~---------e~ly~G--------------~TG~~~~~~i~vG~~YyqkL~HmV~DKihaRs~GP~~~ 1113 (1224)
T 1twf_B 1057 KLLREHGYQSRGF---------EVMYNG--------------HTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQV 1113 (1224)
T ss_dssp HHHHTTTSCTTSE---------ECEECT--------------TTCCBCSSCEEEEEEEEEEBSSCGGGTCEEECCCC---
T ss_pred HHHHHcCCCCCCC---------EEeecC--------------CCCCCccceEEEehhHhhcchhhcccCceEEeeCCCcc
Confidence 99999 9988777 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhhc----------ccccccccc---cccCCeeecccCCCCcccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLK----------CKNVANVIQ---RVVGGPYCRICNSADDIIK 381 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~----------c~~~~~~~~---~~~~~~~c~~c~~~~~~~~ 381 (417)
|||||++||+|+|||||||||||||+|||||++|+|||+ |..|+.+.+ ...+.++|+.|.++.++..
T Consensus 1114 lT~QP~~Gr~r~GG~RfGEMErd~L~a~Gaa~~L~ErL~~~SD~~~~~vC~~cG~~~~~~~~~~~~~~c~~c~~~~~i~~ 1193 (1224)
T 1twf_B 1114 LTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQ 1193 (1224)
T ss_dssp -------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEE
T ss_pred cccCCCcccccCCceecchhhhhhHHhccHHHHHHHHHhcCCccceeEeeccCCCeeeecccccCceECCcCCCCCcccc
Confidence 999999999999999999999999999999999999993 444444411 1223467999998889999
Q ss_pred ccChHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847 382 ANVPYGAKLLSQELSFSMGITLKFDTQLS 410 (417)
Q Consensus 382 ~~ipy~~k~l~~EL~~sm~i~~~l~~~~~ 410 (417)
+.+|||||||+||| +||||++++.+++.
T Consensus 1194 ~~iPysfklL~~EL-~sm~i~~~l~~~~~ 1221 (1224)
T 1twf_B 1194 IHIPYAAKLLFQEL-MAMNITPRLYTDRS 1221 (1224)
T ss_dssp EECCHHHHHHHHHH-HHTTBCCEEESCSS
T ss_pred ccCCHhHHHHHHHH-HHCCCeeEEEeccc
Confidence 99999999999999 99999999998853
No 2
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=1.3e-117 Score=1000.10 Aligned_cols=378 Identities=35% Similarity=0.506 Sum_probs=348.9
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeeccccccCCC------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP------ 74 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~lg~n------ 74 (417)
|++|||++||+|||||| ||||||||||| |+|||||++++|++.|+|++.|.|+|||+|||+|+.+|+++++
T Consensus 734 PsmILGIcASiIPFpdH--NQSPRNtYQ~a-MgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~~~elp~G~ 810 (1210)
T 3h0g_B 734 PAMILGILASIIPFPDH--NQSPRNTYQSA-MGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQ 810 (1210)
T ss_dssp GGGSSCSSSTTSSSSTT--SCSHHHHHHHH-HHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTTCTTSCSCC
T ss_pred chhhhhheeecccCccc--cccchhhhhhh-hhcccccccccccccccCccccEeecCcCccccchhHHHhCCCcccCcc
Confidence 89999999999999999 99999999999 8999999999999999999999999999999999999977665
Q ss_pred --------------CCeEEEecceecccceeeEEEEEEEec--------ccccCC---------------CCCCCccccc
Q 014847 75 --------------EDSLVMNQASLECGVFRSESYKAEVDN--------KDIQVK---------------SRPSDDMLNF 117 (417)
Q Consensus 75 --------------EDAiIiNKssidRG~f~s~~Yk~e~~~--------~~~~~~---------------~~~~~g~~~~ 117 (417)
||||||||+|+|||||||++|+++... .+.++. .+|.||++.+
T Consensus 811 NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~ 890 (1210)
T 3h0g_B 811 NAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAP 890 (1210)
T ss_dssp EECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCT
T ss_pred ceEEEEeccCCCChhhheeeehhheecCceEEEEEEEEEEEeeecCCCceeEEcCCCcchhcccchhhHhhcCCCCCcCC
Confidence 999999999999999999998876532 122221 3578999999
Q ss_pred cccccccCCeEEEEeccC---------------CceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeecccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEI---------------GADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACL 182 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~---------------~~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~i 182 (417)
|. .|++|||||||++|+ .+|+|++++++|.|+||+|.++++++|.+.|||++|+ .|.|++
T Consensus 891 G~-~v~~gDiligK~~p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkv~~~~----~R~~~~ 965 (1210)
T 3h0g_B 891 GT-RVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRS----TRIPQI 965 (1210)
T ss_dssp TC-CCCTTCCCCCCCCCC-----------CCCCCCCCCCCCCTTCCCCCCEEEEEECSSSSEEEEEEECC----CBCCCT
T ss_pred CC-EecCCCEEEEEecCCCCCchhhcccccccccceeeEEecCCCCeEEEEEEEEEecCCCeEEEEEEEE----ecCCCc
Confidence 96 799999999999874 2789999999999999999999999999999999999 999999
Q ss_pred ccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHH
Q 014847 183 GDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVIT 235 (417)
Q Consensus 183 GDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~ 235 (417)
|||||||||||||||+|+ |||||++|+++||+ ++.|.+.++|||++.+++++.
T Consensus 966 GDK~a~RhGqKGvi~~i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~~~~~~~ 1045 (1210)
T 3h0g_B 966 GDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVS 1045 (1210)
T ss_dssp TCEEECTTCCCEEEEEEECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSCCHHHHH
T ss_pred hhhhhcccCCCceeeEEeccccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCCcHHHHH
Confidence 999999999999999999 99999999999999 788999999999999999999
Q ss_pred HHHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCC
Q 014847 236 EQHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQP 314 (417)
Q Consensus 236 ~~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~ 314 (417)
+.|++ ||+++|+ +.|||| +||++|+++||+|++|||||+|||+||+|||++||++.
T Consensus 1046 ~~l~~~g~~~~G~---------~~l~~g--------------~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~ 1102 (1210)
T 3h0g_B 1046 KLLRSHGFQSRGF---------EVMYHG--------------HTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQI 1102 (1210)
T ss_dssp HHHHTTTSCTTSC---------BCCBCS--------------SSCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCS
T ss_pred HHHHHcCcCCCCC---------EEEEcC--------------CCCCCccccEEEEehHhhcchhhcccCcEEeccCCCch
Confidence 99999 9988888 999999 99999999999999999999999999999999999999
Q ss_pred cccCCcccccCCCceeeeeccchhhhhcchhhhhhhhh----------cccccccccc--cccCCeeecccCCCCccccc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL----------KCKNVANVIQ--RVVGGPYCRICNSADDIIKA 382 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL----------~c~~~~~~~~--~~~~~~~c~~c~~~~~~~~~ 382 (417)
|||||++||+|+|||||||||||||+|||||++|+||| .|..|+.+.. .....++|+.|.++.++..+
T Consensus 1103 ~t~QP~~gr~~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD~~~~~vC~~cg~~~~~~~~~~~~~c~~c~~~~~i~~~ 1182 (1210)
T 3h0g_B 1103 LTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQV 1182 (1210)
T ss_dssp SSCSBCCSSTTCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTTCCEEEEESSSCCBCCCCSSSCCCCCTTTCCSSCEEEE
T ss_pred hccCCcccccccCCeeeehhhhhhhhhccHHHHHHHHhhcCCCcceeEeecCCCCeeeecccCCceEcCccCCCCcccee
Confidence 99999999999999999999999999999999999999 4444544422 12234789999999999999
Q ss_pred cChHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847 383 NVPYGAKLLSQELSFSMGITLKFDTQLS 410 (417)
Q Consensus 383 ~ipy~~k~l~~EL~~sm~i~~~l~~~~~ 410 (417)
.||||||||+||| +||||+++|.++++
T Consensus 1183 ~~p~~~k~l~~El-~~~~i~~rl~~~~~ 1209 (1210)
T 3h0g_B 1183 YLPYAAKLLFQEL-MSMNIAPRLFTKNH 1209 (1210)
T ss_dssp ECCHHHHHHHHHH-HTTTCCEECCCSTT
T ss_pred cCCHHHHHHHHHH-HhCCCceEEEecCC
Confidence 9999999999999 99999999998865
No 3
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Probab=100.00 E-value=6.2e-112 Score=960.06 Aligned_cols=377 Identities=32% Similarity=0.453 Sum_probs=343.5
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccccchhhcccccccccCccceEeecccccc---------
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCL--------- 71 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n~~~R~D~~~~~l~ypQ~PLV~t~~~d~l--------- 71 (417)
|+.+||++|++|||++| ||||||+|||| |+|||||++.+|+..|.|++.|.|+|||+|||+|+.++.+
T Consensus 647 p~~il~v~a~lipf~~~--NqspRn~yq~~-m~KQa~G~~~~~~~~r~D~~~~~l~ypQ~PlV~t~~~~~~~~~e~p~G~ 723 (1131)
T 4ayb_B 647 SPAILGITASIIPYPEH--NQSPRNTYQSA-MAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGN 723 (1131)
T ss_dssp GGGGSBTTGGGCSSGGG--SCHHHHHHHHH-HGGGBCSCCCGGGGTCCCSEEEEESSCCCCSSBCHHHHHHTCTTSCCSE
T ss_pred cccccccccceeccccc--Cccchheeccc-cccccCCceeecceeeeccccceeecCCccccccchhhhhccCCCCCce
Confidence 67899999999999999 99999999999 8999999999999999999999999999999999877744
Q ss_pred ----------CCC-CCeEEEecceecccceeeEEEEEEE---ec-----cccc---------------CCCCCCCccccc
Q 014847 72 ----------GRP-EDSLVMNQASLECGVFRSESYKAEV---DN-----KDIQ---------------VKSRPSDDMLNF 117 (417)
Q Consensus 72 ----------g~n-EDAiIiNKssidRG~f~s~~Yk~e~---~~-----~~~~---------------~~~~~~~g~~~~ 117 (417)
|+| ||||||||++++||+|||++|+.+. .+ .+.+ -+.+|++|++.+
T Consensus 724 N~lVA~m~w~GYN~EDAIIine~~v~rg~ftSihi~~y~~e~r~~~~g~~e~it~~~p~v~~~~~~~~~~~LDe~Gii~i 803 (1131)
T 4ayb_B 724 NAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSP 803 (1131)
T ss_dssp EEEEEECCCSSCCCTTCEEEEHHHHTTTTTCEEEEEEEEEECCCCTTSCCCCCCCCCSSCSSCCCGGGGTTCCTTSBCCT
T ss_pred eEEEEEEccCCccHHHhhhhhcchhhcccceeeEEEEEEEEEEecCCCCceEEecCCccccccchHHHhhcCCccccccC
Confidence 444 9999999999999999999665433 21 1111 123678999999
Q ss_pred cccccccCCeEEEEeccCC--------------ceeEEEecCCCceeEEEEEEEeCCCCCeEEEEEEeeccccccccccc
Q 014847 118 GKIQSKSGDIVIGKYAEIG--------------ADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLG 183 (417)
Q Consensus 118 g~~~v~~GDiligk~~~~~--------------~d~s~~~k~~e~g~Vd~V~i~~~~~g~~~vkv~ir~~~~~~R~p~iG 183 (417)
|. +|++|||||||++|+. +|+|++++++|.|+||.|.++.+.++++.|||++|+ .|+|+||
T Consensus 804 Ga-~V~~gDilvGKvtP~~~~~~~~~~~~~~~~~d~sl~~~~g~~g~Vd~v~~~~~~~~~~~vkV~i~~----~R~~~vG 878 (1131)
T 4ayb_B 804 EV-EVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRD----LRIPSIG 878 (1131)
T ss_dssp TC-EECTTCEEECCCCCCC-----------CCCCCCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEE----EECCCTT
T ss_pred Cc-EecCCCEEEEEecCCcchhhhhhcCcceeeeeeeEEccCCCceEEEEEEEeeccCCceEEEEEEec----cccCccc
Confidence 96 8999999999999842 799999999999999999999999999999999999 9999999
Q ss_pred cccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecCCCCCCHHHHHH
Q 014847 184 DKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATPFATSTGGVITE 236 (417)
Q Consensus 184 DKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tpF~~~~~~~i~~ 236 (417)
||||||||||||||+|| |||||++|+++||+ ++.|.+.|+|||.....+++.+
T Consensus 879 DK~agRHGnKGvvs~i~p~eDMPf~~dG~~~DiilNP~gvPSRMniGqilE~~~gk~~~~~g~~~~atpf~~~~~e~~~~ 958 (1131)
T 4ayb_B 879 DKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQN 958 (1131)
T ss_dssp CEEEETTSCEEEEEEEECTTTSEEETTSCCCSEECCTTSSTTTTCHHHHHHHHHHHHHHHHCCCCBCCTTSSCCTHHHHH
T ss_pred ccccccccccceeeeecccccCCcCCCCCCccEEECCCCCcccCcHHHHHHHHHHHHHHhCCCceecCccCCCcHHHHHH
Confidence 99999999999999999 99999999999999 8899999999999888899999
Q ss_pred HHHH-hcccccccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCc
Q 014847 237 QHQS-FVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 315 (417)
Q Consensus 237 ~l~~-~~~~~g~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~l 315 (417)
.|.+ ||+++|+ +.|||| +|||+|+++||||++|||||+|||+||+||||+|||++|
T Consensus 959 ~l~~~g~~~~g~---------~~lydG--------------~TGe~~~~~i~vG~~Yy~kL~HmV~DKihaRs~GP~s~~ 1015 (1131)
T 4ayb_B 959 EILKYGYLPDAT---------EVTYDG--------------RTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQIL 1015 (1131)
T ss_dssp HHHHTTSCTTSE---------ECEEET--------------TTCCBCSSCEEEEEEEEEEBSCCHHHHCEEESSCCBCTT
T ss_pred HHHHcCCCCCCC---------EEEeCC--------------CCCCEecCcEEEEhhhhhccchhhccCCEeeccCCCCCc
Confidence 9998 9998888 999999 999999999999999999999999999999999999999
Q ss_pred ccCCcccccCCCceeeeeccchhhhhcchhhhhhhhhccccc----------ccccc--cccCCeeecccCCCCcccccc
Q 014847 316 TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNV----------ANVIQ--RVVGGPYCRICNSADDIIKAN 383 (417)
Q Consensus 316 T~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~----------~~~~~--~~~~~~~c~~c~~~~~~~~~~ 383 (417)
||||++||+++|||||||||||||+|||||++|+|||+-+|| |.+.. ...+..+|+.|.++.++..+.
T Consensus 1016 TqQPl~Gra~~GG~RfGEME~~aL~a~Gaa~~LqE~L~~~SD~~~~~vc~~cG~~~~~~~~~~~~~c~~~~~~~~i~~~~ 1095 (1131)
T 4ayb_B 1016 TRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVT 1095 (1131)
T ss_dssp TCCBCSSGGGTCCCEECHHHHHHHHHHTCHHHHHHHTTTTTCEEEEEECSSSCCBCEEETTTTEEECSSCSSSSCCEEEE
T ss_pred ccCCCCCcccCCCcceeHHHHHHHHHHhHHHHHHHHhhccCCccceeeccCCCceEEEeccCCceeCCccCCCCCccccC
Confidence 999999999999999999999999999999999999955554 33221 223457899999988999999
Q ss_pred ChHhHHHHHHHHHhhcCCeEEEEecc
Q 014847 384 VPYGAKLLSQELSFSMGITLKFDTQL 409 (417)
Q Consensus 384 ipy~~k~l~~EL~~sm~i~~~l~~~~ 409 (417)
+|||||||++|| +||||+++|.+++
T Consensus 1096 iP~sfk~L~~EL-~sm~i~~~l~~~d 1120 (1131)
T 4ayb_B 1096 VSYAFKLLIQEL-MSMIISPRLILED 1120 (1131)
T ss_dssp EEHHHHHHHHHH-HTTTCEEEEEEEE
T ss_pred CCHHHHHHHHHH-HHCCcceEEEecc
Confidence 999999999999 9999999999875
No 4
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Probab=100.00 E-value=1.4e-108 Score=920.76 Aligned_cols=382 Identities=24% Similarity=0.350 Sum_probs=326.5
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCccccccccc-----------------------------------cc
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTN-----------------------------------PN 45 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~~~n-----------------------------------~~ 45 (417)
|++|||++||||||+|| ||||||||||| |+|||||++..| +.
T Consensus 536 P~~ilsv~aslIPF~eh--n~s~R~lmgsn-M~kQAv~l~~~~~p~vgTg~e~~~a~ds~~~~~a~~~G~v~~vd~~~i~ 612 (1119)
T 2a6h_C 536 PKQVFSVNTNLIPFLEH--DDANRALMGSN-MQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIV 612 (1119)
T ss_dssp TTTTSCHHHHTCTTGGG--BCHHHHHHHHH-HHTTBCCBSSCCCCSEECSCHHHHHHHTTCSEECSSSEEEEEECSSBEE
T ss_pred cccccccccccCCCccc--CCCcccccccc-cccccccccccCCCeeeccccceeeeccCceeEeccCCEEEEecCceEE
Confidence 89999999999999999 99999999999 899999987653 33
Q ss_pred hhhc---c----------cccccccCccceEeecc--------cc---------------------ccCCC-CCeEEEec
Q 014847 46 IRVD---T----------LLQQLFYPQRPLFWILI--------SD---------------------CLGRP-EDSLVMNQ 82 (417)
Q Consensus 46 ~R~D---~----------~~~~l~ypQ~PLV~t~~--------~d---------------------~lg~n-EDAiIiNK 82 (417)
.|.| + +|+.++|||+|||++.. +| +.|+| ||||||||
T Consensus 613 ir~~~~~~~~y~L~~~~rsnq~t~~~QkPiV~~g~~v~~g~~ladg~~~~~gel~lG~N~lVA~m~~~GYN~EDAiiine 692 (1119)
T 2a6h_C 613 VRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISE 692 (1119)
T ss_dssp EEETTTEEECCBCCCSEECTTSCEECCEECCCSSCCBCTTCEEEECTTBSSSSBCCSEEEEEECSCCSSTTSSSEEEEET
T ss_pred EEccCCcceeEEeeccccccccccccccceEeeCceeeccceeccccccCCCcccCceeEEEEEecccCCcchhhhhhhh
Confidence 4442 2 34456999999999752 22 23555 99999999
Q ss_pred ceecccceeeEEE---EEEEec-c---ccc-----------CCCCCCCccccccccccccCCeEEEEeccCC--------
Q 014847 83 ASLECGVFRSESY---KAEVDN-K---DIQ-----------VKSRPSDDMLNFGKIQSKSGDIVIGKYAEIG-------- 136 (417)
Q Consensus 83 ssidRG~f~s~~Y---k~e~~~-~---~~~-----------~~~~~~~g~~~~g~~~v~~GDiligk~~~~~-------- 136 (417)
++++||+|+|+++ +++..+ + +.+ -+.+|+||++.+|. +|++|||||||++|++
T Consensus 693 ~~v~rg~~tSihi~~~e~~~r~~~~g~eeit~~ip~~~~~~~~~LD~dGiv~iG~-~V~~gDiLvgK~tP~~~~~~~~ee 771 (1119)
T 2a6h_C 693 ELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGA-EVKPGDILVGRTSFKGESEPTPEE 771 (1119)
T ss_dssp HHHHTTCSEEEEEEEEEEEEECCTTCCCBCCSCCSSSCSGGGSSCCSSSBCCTTC-BCCTTSEEECCEEESSSSSCCHHH
T ss_pred hHHhcCCceEEEEEEEEeeeeecCCCceeeeccCCCcchhhhhccCCCcccCCCC-EECCCCEEEEEecCCccccCChhh
Confidence 9999999999965 444332 1 111 13478899999996 8999999999999753
Q ss_pred --------------ceeEEEecCCCceeEEEEEEEeCCC-CC-------eEEEEEEeeccccccccccccccccccCCce
Q 014847 137 --------------ADHSIKLKHTERGLVLKVLLSSNDD-GK-------NFAVVSIRQSVNMVHSACLGDKFSSMHGQKG 194 (417)
Q Consensus 137 --------------~d~s~~~k~~e~g~Vd~V~i~~~~~-g~-------~~vkv~ir~~~~~~R~p~iGDKfssRHGqKG 194 (417)
+|+|++++++|.|+|++|.++++++ |. +.|||++|+ .|+|++||||||||||||
T Consensus 772 ~ll~aifg~k~~~~rd~Sl~~~~~e~G~V~~V~~~~~~~~g~~l~~~~~~~vkV~i~~----~R~~~vGDKfasRHGqKG 847 (1119)
T 2a6h_C 772 RLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQ----KRKLQVGDKLANRHGNKG 847 (1119)
T ss_dssp HHHHHHHHSCCCCEEECCEECCSSCCCEEEEEEEECSSCSSCCCCTTEEEEEEEEEEE----EEECCTTCEEECTTSCEE
T ss_pred hhhhhhhcccccccceeeEEccCCccEEEEEEEEEccCCCCcccCCCcceEEEEEEcc----cCCcccCchhhhccCCCc
Confidence 5899999999999999999998876 64 789999999 999999999999999999
Q ss_pred eEeeec--------------------------cchhHHHHHhhhhh-hhcCCceeecC-CCCCCHHHHHHHHHHhccccc
Q 014847 195 VLGFLE--------------------------QTPAQLLEAALGKG-ACDGLMSYATP-FATSTGGVITEQHQSFVSQLL 246 (417)
Q Consensus 195 vvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~~~~tp-F~~~~~~~i~~~l~~~~~~~g 246 (417)
|||+|| |||||++|+++||+ +..|.. .+|| |++.+.+++.+.|++.+....
T Consensus 848 Vis~i~p~eDMPf~~dG~~pDiIlNPhgvPSRMtiGqllE~~lG~a~~~~g~~-~atp~F~~~~~~~i~~~L~~~~~~~~ 926 (1119)
T 2a6h_C 848 VVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR-YISPIFDGAKEPEIKELLAQAFEVYF 926 (1119)
T ss_dssp EEEEEECTTTSCBCSSSCBCSEECCSTTTTTTTBTHHHHHHHHHHHHHHTTEE-EECCTTTSCCHHHHHHHHHHHHHHHH
T ss_pred eEEeeeccCCCccccCCCCccEEeCCCcCccccchhhhhHHHhhhHHhhcCCc-eEecccCCCCHHHHHHHHHHhhhhcc
Confidence 999999 99999999999999 556765 4999 999999999998876311000
Q ss_pred ---------------------ccccC--------------CCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeee
Q 014847 247 ---------------------NCIGA--------------RNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWIT 291 (417)
Q Consensus 247 ---------------------~~~~~--------------~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~ 291 (417)
+..++ +..||+.|||| +||++|+++||+|++
T Consensus 927 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~Gk~~lydG--------------~TGe~~~~~I~vG~~ 992 (1119)
T 2a6h_C 927 GKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDG--------------RTGEPIEGPIVVGQM 992 (1119)
T ss_dssp HHHHHHTCCCBHHHHHHHHHHHTTTSSCTTSCHHHHHHHHHHTTEECCBCS--------------SSCCBCSSCEEEEEE
T ss_pred ccccccccccchhhhhhhhhhhcCCcccccccchhhhcccCCCCceEeecC--------------CCCCCccceEEEEhH
Confidence 00023 55788999999 999999999999999
Q ss_pred hhhhccccccccccccccCCCCCcccCCcccccCCCceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeec
Q 014847 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCR 371 (417)
Q Consensus 292 yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~ 371 (417)
|||||+|||+||+|||++|||+.|||||++||+|+|||||||||||||+|||||++|+|||+-+|| ++.+|.. .||.
T Consensus 993 Yy~kL~HmVdDKihaRs~GP~s~lTqQP~~Gra~~GGqRfGEME~~aL~a~GAa~~L~E~L~~kSD-~~~gr~~--~~~~ 1069 (1119)
T 2a6h_C 993 FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD-DIEGRNA--AYEA 1069 (1119)
T ss_dssp EEEEBCCCTTTSCEEESSCCBCSSSCSBCCCSSSCCCEEECHHHHHHHHHTTCSHHHHHHHTTTTT-CHHHHHH--HHHH
T ss_pred HhhcchhhcccCcEEeeccccceeecCCCcccccCCCeeeehhehhhhhhccHHHHHHHHhccCCc-ccccccc--eEEE
Confidence 999999999999999999999999999999999999999999999999999999999999999998 5566653 6898
Q ss_pred ccCCCCccccccChHhHHHHHHHHHhhcCCeEEEEeccC
Q 014847 372 ICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLS 410 (417)
Q Consensus 372 ~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i~~~l~~~~~ 410 (417)
+|. +.++..+.+|||||||++|| +||||++++.+++.
T Consensus 1070 ~~~-~~~i~~~~iP~sfk~L~~EL-~sl~i~~~l~~~~~ 1106 (1119)
T 2a6h_C 1070 IIK-GEDVPEPSVPESFRVLVKEL-QALALDVQTLDEKD 1106 (1119)
T ss_dssp HHT-TCCCCCCCCCHHHHHHHHHH-HHSSCEECCBCSSS
T ss_pred eec-CCccCccCCCHHHHHHHHHH-HhCCCceEEEecCC
Confidence 885 56889999999999999999 99999999987643
No 5
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C*
Probab=100.00 E-value=1.7e-101 Score=860.43 Aligned_cols=370 Identities=24% Similarity=0.324 Sum_probs=324.2
Q ss_pred CcccccccccccCCCCCcCCCcccccccccccCCcccccc-----------------------------------ccccc
Q 014847 1 MSFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFP-----------------------------------TTNPN 45 (417)
Q Consensus 1 p~~ilsi~AslIPF~~h~~NqSpRn~yq~~~M~KQamG~~-----------------------------------~~n~~ 45 (417)
|.+++|++||||||++| |+|+|++|||| |+|||+|+. +.++.
T Consensus 657 P~qivSvaaslIPFLEh--dDAnRaLMGsN-MQRQAVPLl~~e~p~VgTG~E~~~a~dsg~~i~a~~~G~v~~vda~~I~ 733 (1342)
T 3lu0_C 657 TQQVVSVGASLIPFLEH--DDANRALMGAN-MQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIV 733 (1342)
T ss_dssp TTTTSCHHHHSCTTSTT--BCHHHHHHHHH-TTTTBCCCSSCCCCSSBCSCHHHHHHHTTTSCBCSSCBEECCCCSSBCC
T ss_pred HHHhcchhhccCCCccc--CCccccchhhh-ccccccccccCCCCeEecccchheeecCCceEEecCCCEEEEecCCeEE
Confidence 88999999999999999 99999999999 899999998 33344
Q ss_pred hhh--------------------cccccccccCccceEeec--------ccc---------cc------------CCC-C
Q 014847 46 IRV--------------------DTLLQQLFYPQRPLFWIL--------ISD---------CL------------GRP-E 75 (417)
Q Consensus 46 ~R~--------------------D~~~~~l~ypQ~PLV~t~--------~~d---------~l------------g~n-E 75 (417)
.|. .++||.++|+|+|+|++. ++| ++ |+| |
T Consensus 734 Ir~~~~~~~~~~~~~~~y~L~kf~RSNq~Tc~~QrPiV~~G~~V~~GdilADG~st~~GElaLG~N~lVAfMpW~GYNfE 813 (1342)
T 3lu0_C 734 IKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFE 813 (1342)
T ss_dssp EEECSSSSSSSCCEEECCBCCCSCBCSSSCBCCCCBCCCSSCCBCTTCBCBCCSSCSSSSCCCSEECCEECCCCSSTTSS
T ss_pred EEeCCCccccccCcceEEEecccccccccccccccceeecCCEEecCcEecccccccCCeeecccccEEEEecccCcccc
Confidence 444 367899999999999953 333 33 444 9
Q ss_pred CeEEEecceecccceeeEE---EEEEEec---------ccccC------CCCCCCccccccccccccCCeEEEEeccCC-
Q 014847 76 DSLVMNQASLECGVFRSES---YKAEVDN---------KDIQV------KSRPSDDMLNFGKIQSKSGDIVIGKYAEIG- 136 (417)
Q Consensus 76 DAiIiNKssidRG~f~s~~---Yk~e~~~---------~~~~~------~~~~~~g~~~~g~~~v~~GDiligk~~~~~- 136 (417)
||||||++++++|+|||++ |+++..+ .++++ +.+|++|++.+|. +|++|||||||++|++
T Consensus 814 DAIlISErlV~eD~fTSIHIee~e~~aRdtklG~EeiTrdIPnv~e~al~~LDe~GIv~iGa-~V~~GDILVGKvtPkge 892 (1342)
T 3lu0_C 814 DSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGA-EVTGGDILVGKVTPKGE 892 (1342)
T ss_dssp SEEEECTHHHHTTTSCEEEEEEEEEECCEETTEECCCCSCCSSCCHHHHHSBCSSSCBCTTC-CCCTTCEEECCCCBCCT
T ss_pred cchhhhhhhhhcCCceeEEEEEEeeeeeecCCCCceecccCCCCChHHHhcCCCCCCeecCc-EECCCCEEEeccCCCCC
Confidence 9999999999999999994 5555432 11211 3478999999996 8999999999999864
Q ss_pred ---------------------ceeEEEecCCCceeEEEEEEEeCC-----------------------------------
Q 014847 137 ---------------------ADHSIKLKHTERGLVLKVLLSSND----------------------------------- 160 (417)
Q Consensus 137 ---------------------~d~s~~~k~~e~g~Vd~V~i~~~~----------------------------------- 160 (417)
+|+|+++++++.|+|+.|.+++.+
T Consensus 893 ~~~tpEekLLraIFGeka~~vkDtSL~vp~g~~G~Vidv~~f~r~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 972 (1342)
T 3lu0_C 893 TQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLF 972 (1342)
T ss_dssp TTCCHHHHHGGGTSCSSSSSBCCCCEECCTTCCCEEEECCCCCCGGGCCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCChHHHHHHHHhcCcccccccCcEecCCCCcEEEEEEEEEecccccchhhhhHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 699999999999999999888642
Q ss_pred ------------------------------------------------------------------------CCCeEEEE
Q 014847 161 ------------------------------------------------------------------------DGKNFAVV 168 (417)
Q Consensus 161 ------------------------------------------------------------------------~g~~~vkv 168 (417)
...+.|||
T Consensus 973 ~~l~~~l~~~g~t~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~gd~l~~gv~k~VkV 1052 (1342)
T 3lu0_C 973 SRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKV 1052 (1342)
T ss_dssp HHHHHHHHTTSCCHHHHTTSCGGGTTTCCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCSSSSCEEEE
T ss_pred HHHHHHHhhcCCCHHHHhhCCHHHhhccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccCcCCceEEEE
Confidence 02368999
Q ss_pred EEeeccccccccccccccccccCCceeEeeec--------------------------cchhHHHHHhhhhh-hhcCCc-
Q 014847 169 SIRQSVNMVHSACLGDKFSSMHGQKGVLGFLE--------------------------QTPAQLLEAALGKG-ACDGLM- 220 (417)
Q Consensus 169 ~ir~~~~~~R~p~iGDKfssRHGqKGvvs~i~--------------------------MtiGql~E~~~g~~-~~~g~~- 220 (417)
++|+ .|+|++|||||||||||||||+|+ |||||++|+++||+ +..|..
T Consensus 1053 ~ia~----kRk~qvGDK~AgRHGnKGVis~I~p~EDMPf~~dG~~pDIIlNP~gvPSRMnIGqilE~~lG~aa~~~G~~i 1128 (1342)
T 3lu0_C 1053 YLAV----KRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKI 1128 (1342)
T ss_dssp EEEE----EECCCTTCEEECSSSCCEEECCCCCTTTSCEETTEEECSEECCGGGTTSSCBTHHHHHHHHHHGGGTSSTHH
T ss_pred EEEE----eccCCCCCCcccccCCCceEEEEecccCCCCCCCCCCCcEEeCCCCCCCccchhhhhHHhhhHHHHhcCchH
Confidence 9999 999999999999999999999999 99999999999999 444431
Q ss_pred ----------------------------------------------------eeecC-CCCCCHHHHHHHHHH-hccccc
Q 014847 221 ----------------------------------------------------SYATP-FATSTGGVITEQHQS-FVSQLL 246 (417)
Q Consensus 221 ----------------------------------------------------~~~tp-F~~~~~~~i~~~l~~-~~~~~g 246 (417)
..+|| |++.+.++|.+.|.+ ||+++|
T Consensus 1129 ~~~~~~~~~~~~~r~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~aTPvFdga~~~~i~~~L~~aG~~~~G 1208 (1342)
T 3lu0_C 1129 NAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSG 1208 (1342)
T ss_dssp HHTTTHHHHCTTTHHHHHHHTTTTCCCSSSCCTTTSCHHHHHHTTTTTSSCTTCBCCSSSSCCHHHHHHHTSSSSSCSSS
T ss_pred HHHHHhhhhhHHHHHHHHHHhhcccccchhhhhcccchHHHHHHhhhhccCCcccCCCCCCCCHHHHHHHHHHcCCCCCC
Confidence 23888 999999999999998 998877
Q ss_pred ccccCCCCCeeEeeccccceeeccCCCCccccceeeeeeEEEeeehhhhccccccccccccccCCCCCcccCCcccccCC
Q 014847 247 NCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRF 326 (417)
Q Consensus 247 ~~~~~~~~gk~~l~~g~~~~~~~~~~~~~~~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~ 326 (417)
+ +.|||| +||++|+++||||++|||||+|||+||+||||+|||+.+||||++||+++
T Consensus 1209 k---------~~LydG--------------rTGe~f~~~V~vG~~YylKL~HmVdDKiHaRs~GPysllTqQPl~Gkaq~ 1265 (1342)
T 3lu0_C 1209 Q---------IRLYDG--------------RTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1265 (1342)
T ss_dssp C---------BCCBCS--------------SSCSBCSSCBCEECCEEEEBCCCGGGSCCCBSSCCBCSSSCCBCCCSSSC
T ss_pred C---------EEEEcC--------------CCCCCcccceeeeehhHhhhhhccccceEEeccCCCcccccCCCCccccC
Confidence 7 999999 99999999999999999999999999999999999999999999999999
Q ss_pred CceeeeeccchhhhhcchhhhhhhhhcccccccccccccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCCeEEEE
Q 014847 327 GGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFD 406 (417)
Q Consensus 327 GG~RfGEME~d~LiahGas~~L~ErL~c~~~~~~~~~~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i~~~l~ 406 (417)
|||||||||||||+|||||++|+|||+.+|| ++.+|.. .||.+|.. .++..+.+|||||+|++|| +||||++++.
T Consensus 1266 GGqRfGEMEvwaL~a~GAa~~LqE~Lt~kSD-dv~gr~~--~y~~i~~g-~~~~~~~iPesfkvL~~EL-~sl~l~v~l~ 1340 (1342)
T 3lu0_C 1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-DVNGRTK--MYKNIVDG-NHQMEPGMPESFNVLLKEI-RSLGINIELE 1340 (1342)
T ss_dssp CCCCCCHHHHHHHHHSSCSHHHHHHTTTSSS-CHHHHHH--HHHHHTTT-SCCCCCCCCHHHHHHHHHH-HTSSCCEECC
T ss_pred CCeeeehHHHHHHHhccHHHHHHHHhhcCCC-ccccchh--hhhhhcCC-CCCCcCCCCHHHHHHHHHH-HhCCCCeEec
Confidence 9999999999999999999999999999999 6777754 68887754 6788999999999999999 9999999875
No 6
>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=98.53 E-value=3e-08 Score=102.35 Aligned_cols=58 Identities=29% Similarity=0.510 Sum_probs=47.4
Q ss_pred ccccccccccc--ccCCeeecccCCCCccccccChHhHHHHHHHHHhhcCCeEEEEeccCC
Q 014847 353 KCKNVANVIQR--VVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQLSG 411 (417)
Q Consensus 353 ~c~~~~~~~~~--~~~~~~c~~c~~~~~~~~~~ipy~~k~l~~EL~~sm~i~~~l~~~~~~ 411 (417)
+|..|+.+... .....+|+.|.+++.+..+.||||||||+||| +||||.++|.+++.-
T Consensus 7 VC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPYa~KlL~qEL-~smnI~~rl~~~d~~ 66 (436)
T 3qqc_A 7 VCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDEL-KAMVIRPKLNLSEGG 66 (436)
T ss_dssp EETTTCCBCEEETTTTEEECTTTCCSSSEEEEEECHHHHHHHHHH-HHTTBCCEEEEEC--
T ss_pred EeCCCCceeeeccccCccCCCCCCCCCeEEEEEcChHHHHHHHHH-HhCCeeceeeccccc
Confidence 57777765431 22358999999999999999999999999999 999999999998643
No 7
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli}
Probab=98.34 E-value=9.5e-07 Score=83.39 Aligned_cols=52 Identities=25% Similarity=0.470 Sum_probs=47.4
Q ss_pred CCCCCccccccccccccCCeEEEEeccCC----------------------ceeEEEecCCCceeEEEEEEEeCC
Q 014847 108 SRPSDDMLNFGKIQSKSGDIVIGKYAEIG----------------------ADHSIKLKHTERGLVLKVLLSSND 160 (417)
Q Consensus 108 ~~~~~g~~~~g~~~v~~GDiligk~~~~~----------------------~d~s~~~k~~e~g~Vd~V~i~~~~ 160 (417)
.+|.+|++.+|. +|++|||||||++|++ +|+|+++++++.|+|+.|.+++..
T Consensus 35 ~LDe~GIV~iGs-~V~~GDILVGKvTPk~~~~~tpEekLL~aIfg~k~~~vkDtSL~vp~G~~G~VidV~if~r~ 108 (228)
T 3tbi_B 35 KLDESGIVYIGA-EVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRD 108 (228)
T ss_dssp TBCTTSBBCTTC-CCBTTCEEECEEEECCGGGCCHHHHHHHHHHCTTSSCEEECCEECCSSCBEEEEEEEEEEBT
T ss_pred cCCCCCCeecCC-EECCCCEEEeccCCCCCCCCChHHHHHHHHhCCccccceeCcEecCCCCcEEEEEEEEEecC
Confidence 478899999996 8999999999999864 799999999999999999999764
No 8
>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A
Probab=15.58 E-value=37 Score=24.73 Aligned_cols=44 Identities=16% Similarity=0.261 Sum_probs=29.8
Q ss_pred ccCCCCccccceeeeeeEEE---eeehhhhccccccccccccccCCCCCcccCCccc
Q 014847 269 FECPMDWIAFICLVRSLIFT---WITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVAD 322 (417)
Q Consensus 269 ~~~~~~~~~tG~~~~~~if~---G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~G 322 (417)
|-|| +|++.++.++.. |.+|=.+...---++ . ..+++|+||+.-
T Consensus 4 ~~Cp----Is~~~m~dPV~~~~sG~~yer~~I~~~l~~-----~-~~cP~t~~~L~~ 50 (61)
T 2bay_A 4 MLCA----ISGKVPRRPVLSPKSRTIFEKSLLEQYVKD-----T-GNDPITNEPLSI 50 (61)
T ss_dssp CCCT----TTCSCCSSEEEETTTTEEEEHHHHHHHHHH-----H-SBCTTTCCBCCG
T ss_pred EEec----CCCCCCCCCEEeCCCCcEEcHHHHHHHHHh-----C-CCCcCCcCCCCh
Confidence 3467 899999999887 888766543322111 1 249999999864
No 9
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4
Probab=7.48 E-value=1.3e+02 Score=22.92 Aligned_cols=28 Identities=11% Similarity=0.022 Sum_probs=18.9
Q ss_pred cccCCcccccCCCceeeeeccchhhhhc
Q 014847 315 LTGRPVADRKRFGGIEFGEMKCDCLIAH 342 (417)
Q Consensus 315 lT~QP~~Gr~~~GG~RfGEME~d~Liah 342 (417)
+--||+.||++--|.=++..|.--|+-|
T Consensus 35 ~L~~PTGGKA~l~~~i~e~le~~~~~~~ 62 (66)
T 1qxf_A 35 TVAEPTGGKGNIKAEIIEYVDQIELEHH 62 (66)
T ss_dssp EEEECCSSSCEECSEEEECCSCCC----
T ss_pred EEeecCCcceeeehhHHhhhhheeeeec
Confidence 3459999999988887777776555443
No 10
>1l2m_A REP protein; A+B fold, RBD-like fold, viral protein; NMR {Tomato yellow leaf curl sardiniavirus} SCOP: d.89.1.4 PDB: 1l5i_A
Probab=7.33 E-value=91 Score=26.23 Aligned_cols=51 Identities=14% Similarity=-0.035 Sum_probs=36.0
Q ss_pred chhhcccccccccCccceEeeccccc---c--CCCCCeEEEecceecccceeeEEE
Q 014847 45 NIRVDTLLQQLFYPQRPLFWILISDC---L--GRPEDSLVMNQASLECGVFRSESY 95 (417)
Q Consensus 45 ~~R~D~~~~~l~ypQ~PLV~t~~~d~---l--g~nEDAiIiNKssidRG~f~s~~Y 95 (417)
.+|...++|.|.|||-||-+..+.+. + -.|---|.+.+..-+.|-.|...+
T Consensus 3 ~F~i~akn~FLTYp~c~l~Ke~~l~~l~~l~~p~~~~yi~i~rE~H~dG~pHlH~L 58 (118)
T 1l2m_A 3 RFSIKAKNYFLTYPKCDLTKENALSQITNLQTPTNKLFIKICRELHENGEPHLHIL 58 (118)
T ss_dssp CCCCEEEEEEEEETTCCCCHHHHHHHHHHCCCSSCEEEEEEEEEECTTSCEEEEEE
T ss_pred cceeccceeeeeCCCCCCCHHHHHHHHHhhcCCcceeeeeehhhhccCCCeeeEEE
Confidence 46778899999999999976443331 1 111345788888899998887744
Done!