Query 001771
Match_columns 1015
No_of_seqs 277 out of 467
Neff 5.4
Searched_HMMs 29240
Date Tue Mar 26 15:48:25 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001771.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1070-1073//hhsearch_pdb/001771hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2j7n_A RNA-dependent RNA polym 1.0 1 1 1036.8 51.5 565 235-867 132-777 (1022)
2 2j7n_A RNA-dependent RNA polym 1.0 1 1 30.1 -2.8 95 257-376 197-302 (1022)
3 3lu0_D DNA-directed RNA polyme 1.0 1 1 29.3 4.4 44 217-265 428-471 (1407)
4 4ayb_A DNA-directed RNA polyme 1.0 1 1 28.3 5.1 69 645-732 400-470 (880)
5 2a6h_D DNA-directed RNA polyme 1.0 1 1 28.3 4.4 57 659-731 694-752 (1524)
6 1twf_A B220, DNA-directed RNA 1.0 1 1 28.0 5.2 15 18-32 98-112 (1733)
7 1hqm_D DNA-directed RNA polyme 1.0 1 1 28.0 -2.2 12 536-547 615-626 (1265)
8 3h0g_A DNA-directed RNA polyme 1.0 1 1 26.2 4.2 10 471-482 867-876 (1752)
9 3pih_A Uvrabc system protein A 1.0 1 1 13.3 -1.2 33 48-80 38-70 (916)
10 3og6_A Interleukin-29; helical 1.0 1 1 12.1 2.8 10 991-1000 175-184 (196)
No 1
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A
Probab=1.00 E-value=1 Score=1036.84 Aligned_cols=565 Identities=20% Similarity=0.205 Sum_probs=450.7
Q ss_pred EEEECCCEECCCCCEEECCCCCCCEEEEEEECCCCCCC--CC--CCCCCHHHHHHHHHHCC-EEECCEEEEEEEEECCCC
Q ss_conf 07961983236886471204998579999804898987--89--99600489999998729-298585788989834886
Q 001771 235 NCTFKGPYLNQTRTHLQRELGDDNILLVKFDEELGGHR--SS--NNWNDSYSKYNEIAREG-ILVGLRCYHFFVFKDGGK 309 (1015)
Q Consensus 235 ~~~~~gP~le~snr~lrr~~g~d~FLrV~F~ee~~~~~--~~--~~~~~~~~r~~~~L~~G-i~I~gR~y~FLafs~S~~ 309 (1015)
++.|.+|+++.|||+.|| ||+||||+|+|+++..... +. .......+++.++|.+| +.++||.|++|...+.+.
T Consensus 132 ~l~L~p~~l~~s~R~~Rr-fGsDrFL~V~fp~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~gr~~r~f~~~d~~~ 210 (1022)
T 2j7n_A 132 LVKLKPLMFEQGCRLTRR-FGPDRFFEILIPSPTSTSPSVPPVVSKQPAAVEEVIQWLTMGQHSLVGRQWRAFFAKDAGY 210 (1022)
T ss_dssp EEEECCCEEEECBHHHHH-HCGGGEEEEEEECTTCCCSSSCTTSSSSSSCHHHHHHHHHSSCEEETTEEEEEEEEEECC-
T ss_pred EEEECCCCCCCCCEEEEE-ECCCEEEEEEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCEEEECCEEEEEEECCCCC
T ss_conf 899547755777657785-2786069999347765444566110026578999999871485798435467876202443
Q ss_pred CCCCCCC--------CCCCCEEEEEECCCHHHHCCC-----------CCCCCCHHCHHHHHHHCCCCCCC--CCHHHHHH
Q ss_conf 5567999--------999827999941870222036-----------54334612199998501687888--85547998
Q 001771 310 EEKKKDP--------STSPVKCYFVRMESSAFIDMG-----------YQYILSGKTVHEARYMFMHVRTV--SSVANYMS 368 (1015)
Q Consensus 310 re~~k~~--------S~s~~~~~F~~~~s~w~~~~~-----------~P~~~~~~ti~~~r~~f~~i~~~--~~vaK~aA 368 (1015)
|.+.|++ +....+||||++++..+.... .+....++++.++|.||++|+.+ ++++||||
T Consensus 211 r~~~~~~~l~~~~~~~~~~~Rv~~f~~~G~~i~~~~f~fl~~s~lre~s~~~~~ls~~~ir~wmg~f~~n~~q~~aK~aA 290 (1022)
T 2j7n_A 211 RKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQRTEFKVSQMLDWLLQLDNNTWQPHLKLFS 290 (1022)
T ss_dssp -------------CCCCCEEEEEEEEEEETTCBCCCC-------------CCBCCCHHHHHHHHHCGGGCTTSBHHHHHH
T ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHCCCCHHHHHHH
T ss_conf 34431001234323555021689986058612676655444442112445667888999998666943445640889999
Q ss_pred HHHCCCCCCCCCEEECCCEEEEEE-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCHHHCCCCCCCCCCCCCC
Q ss_conf 622002676222142333008980-5866778899742238972111343121348999860010001236788854210
Q 001771 369 RLSLILSKTMKLEVDFSRINIERI-EDEPCRDKDGNVVYKDGEALIHTDGTGFISEDLALKCPTYVYKEKCTNDDSTERS 447 (1015)
Q Consensus 369 Rlgq~FSsT~~~~V~~~~~~i~~I-~DI~~~d~~g~dv~~~g~~y~fTDGvG~IS~~lA~~I~~~i~k~~~l~~~~~~~k 447 (1015)
|||||||+|.+ +|.+.+.+|..+ |||+.. +|.+|+||||||+||++||++|+..+ +
T Consensus 291 Rigq~FS~T~~-tv~v~~~~I~~~~dDI~~~---------~g~g~vFTDGvG~IS~~lA~~I~~~l----~--------- 347 (1022)
T 2j7n_A 291 RIQLGLSKTYA-IMTLEPHQIRHHKTDLLSP---------SGTGEVMNDGVGRMSRSVAKRIRDVL----G--------- 347 (1022)
T ss_dssp TTHHHHSBCEE-EEECCGGGEEECSSCCBCT---------TSSCCBSSTTEEEECHHHHHHHHHHH----T---------
T ss_pred HHHHHHCCCCC-CEEECHHHEEECCCCCCCC---------CCCCCEECCCCHHHHHHHHHHHHHHC----C---------
T ss_conf 86565158568-1786558979867852067---------88987515772575299999999982----9---------
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEECCCCCCC--EEEECCCCEEEECCCCCCCCCCCCEEE
Q ss_conf 124543200231112478889999147998637997600689925999998--066189831110599989887764179
Q 001771 448 IDRKELEANFSDVARTESHYGEPPLLMQVRLFYNGTAVKGTLLLNKKLPPQ--TIQIRPSMIKVKADRDLSDGQTFNSLE 525 (1015)
Q Consensus 448 ~~~~~~~~~f~~~~~~~~~~~~~PSAfQiR~~y~G~GaKGvL~vdp~l~~~--~I~lRpSm~KF~~~~~~~~~~~~~~LE 525 (1015)
+...|||||||+ || |||||+|||++.+. +|+|||||+||+++.. ++.+++||
T Consensus 348 -------------------l~~~PSAfQiR~--gG--aKGvl~vdp~~~~~~~~I~lRpSm~KF~~~~~---d~~~~~LE 401 (1022)
T 2j7n_A 348 -------------------LGDVPSAVQGRF--GS--AKGMWVIDVDDTGDEDWIETYPSQRKWECDFV---DKHQRTLE 401 (1022)
T ss_dssp -------------------CSSCCSEEEEEE--TT--EEEEEEECTTCCSCCCCEEECTTTBCSCCCCC---SGGGSEEE
T ss_pred -------------------CCCCCCEEEEEE--CC--CEEEEEECCCCCCCCCEEEECCCCEEECCCCC---CCCCCEEE
T ss_conf -------------------999982799975--36--05899977344788645996775120268988---85568589
Q ss_pred EEEECCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH-HH-------HHHHCCHHHHHHHHHH----------C---
Q ss_conf 9830389865434598999770799997999999999999-99-------9671299999999842----------2---
Q 001771 526 VVKTSNQPRKTYLSRNLIALLSYGGVPEIFFLDILRNALD-DA-------RGVFSNKRNALKVSFN----------Y--- 584 (1015)
Q Consensus 526 Iv~~S~~p~~~~LNRqlI~iL~~lGVp~~vF~~Lq~~~l~-~l-------~~~~~~~~~Al~~l~~----------~--- 584 (1015)
||++|++|.+++||||+|+||+++||+.++|++++.+.+. .+ ..++.++..+...+.. .
T Consensus 402 Iv~~s~~~~~~~LNRQlI~lL~~lGV~~~~f~~~i~~~~~~~L~~~l~~~~~al~~~~~~r~~l~~~~~~~~~r~~~g~~ 481 (1022)
T 2j7n_A 402 VRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRV 481 (1022)
T ss_dssp EEEECCCCCCCCBCTTTHHHHHHTBSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHSCCHHHHHHHTSC
T ss_pred EEEECCCCCCCEECHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 97604888874405899999886796779999999999999999999999998538999999998624552100123430
Q ss_pred ---CCC--CHHHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHH-CCCEECCCCCEEEEECCCCCCCCCCEEEEEECC
Q ss_conf ---999--94689999999399-99957999999999999997662-258141893126763299889899728998226
Q 001771 585 ---GGM--DYDFTSARMILSGI-SLDEPYLQHRLSILMKEEKKSLQ-AGKLPVTESYYLMGTVDPTGILKSNEVCIILKD 657 (1015)
Q Consensus 585 ---~~~--d~~~~~~~ll~aGf-p~~epfl~~~L~~~~~~~l~~Lk-k~rIpV~~s~~l~GV~DetG~L~eGEVfv~~s~ 657 (1015)
+++ ..++.+..|+.+|| |.++|||++++..++..+++.|| ++||||++|++||||+||||+|+||||||+++.
T Consensus 482 ~~~~glp~s~~~~l~~Ll~aGf~p~~epfL~~~l~~~~~~~l~~LK~k~rI~V~~s~~L~GV~DetG~L~eGEVfv~~s~ 561 (1022)
T 2j7n_A 482 PFLAGLPDSQEETLNFLMNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFSS 561 (1022)
T ss_dssp CEETTEESSHHHHHHHHHHTTCCTTTBHHHHHHHHHHHHHHHHHHHHHCCBCCSSEEEEEEEECTTSCCCTTEEEEEEEE
T ss_pred HHHCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCEEEEEECC
T ss_conf 12135762269999999975898432399999999999999998888632366662089987668776679837997435
Q ss_pred ---------CEEECEEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf ---------24524049998489888897269999505854221268650899289999994421128999998279971
Q 001771 658 ---------GQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIAGGDFDGDMYFVSR 728 (1015)
Q Consensus 658 ---------~~i~G~~VlV~RnP~lhPGDIrvv~AV~~P~L~~~v~~lkdVIVFp~kG~Rplps~lSGGDLDGD~Y~ViW 728 (1015)
.+|.|.+|||+||||+||||||+++||++|+|| ||+|||||||+|+|||||||||||||||+|||||
T Consensus 562 ~~~~~~~~~~~l~gg~VlVtRnP~lhPGDIrvv~AV~~PeL~----hL~DvIVFp~kG~Rplps~lSGGDLDGD~Y~ViW 637 (1022)
T 2j7n_A 562 KFRDEEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELH----SLKDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCW 637 (1022)
T ss_dssp EEEETTEEEEEECSEEEEEECSSCCSGGGEEEEEECCCGGGT----TCCSEEEECSCSSSCHHHHTTTCCSSSCEEEEEC
T ss_pred CCCCCCCCCEEECCCEEEEEECCCCCCCCEEEEEECCCHHHH----CCCCEEECCCCCCCCCHHHHCCCCCCCCEEEEEE
T ss_conf 556677773142176089985777685800278841373330----6678698068899998567157787887589982
Q ss_pred CCCCCCCCCCCCCCCCCCCC-CCCCCCCCCC---------C---HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 82111122221000013789-8556567458---------9---689889999999710467888202035499999987
Q 001771 729 NPELLKHFKESERWMSTSKN-LSANKRLIDF---------S---LEELESELFKLFLNTRFCPSNAKSLAADCWQAVMDR 795 (1015)
Q Consensus 729 D~~Li~~f~~~~p~~~~~~P-~y~~~~p~~~---------~---~~~~~~~~f~~Fl~~~y~~~d~LG~isn~Hl~~aD~ 795 (1015)
||+||++|+|++.. ..+.+ .|..+....+ + +++...+++++|+. .||.+|.||+|||+|+..+|+
T Consensus 638 D~~Lv~~f~na~~p-~~p~~~~y~~k~~~~~~~~~~~~~~g~~~~~~~~~d~i~~ff~-~~m~~d~LG~is~~h~~~~~~ 715 (1022)
T 2j7n_A 638 DPEIVDGFVNAEMP-LEPDLSRYLKKDKTTFKQLMASHGTGSAAKEQTTYDMIQKSFH-FALQPNFLGMCTNYKERLCYI 715 (1022)
T ss_dssp CHHHHHTBCCCCCC-CCCCCTTTSEECCCBHHHHHTTTCSSHHHHHHHHHHHHHHHHH-HHTSCCHHHHHHHHHHHHHHH
T ss_pred CHHHCCCCCCCCCC-CCCCHHHHCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHH
T ss_conf 55655565678888-8875565144454204443302455556673149999999998-742743288899999998765
Q ss_pred HCCCCCCHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 413799616899741199999999995232688889984347--878999899877578999941236720165
Q 001771 796 FLTLGDESAEEKAAMKENMLRLINIYYDALDAPKKSGIKVEV--PEDLKVEKFPCYMRRDESVSFESTSVLGTI 867 (1015)
Q Consensus 796 ~~~~g~~~~~e~g~~~~~Cl~LA~L~S~AVD~pK~TG~~v~l--p~~L~~~~~PdFM~k~~~~~Y~S~kiLGkL 867 (1015)
.. |+.+++|++||+|||+|||||| ||+++++ ++.|+++.+||||+ ..+++|+|++++|+.
T Consensus 716 ~~----------g~~~~~cl~LA~L~S~AVD~~K-tG~pv~~~~~~~lr~~~~p~~m~-~~~p~Y~s~~~~g~~ 777 (1022)
T 2j7n_A 716 NN----------SVSNKPAIILSSLVGNLVDQSK-QGIVFNEASWAQLRRELLGGALS-LPDPMYKSDSWLGRG 777 (1022)
T ss_dssp HT----------CSSSHHHHHHHHHHHHHTTHHH-HTEECCHHHHHHHHHHHSCCSSC-CCCCGGGSSSCCSSS
T ss_pred CC----------CCCCHHHHHHHHHHHHHHCCCC-CCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCC
T ss_conf 07----------9999889999999998608566-68564733465643864799777-788751147545788
No 2
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA polymerase, hydrolase; 2.30A {Neurospora crassa} PDB: 2j7o_A
Probab=1.00 E-value=1 Score=30.08 Aligned_cols=95 Identities=9% Similarity=-0.050 Sum_probs=58.5
Q ss_pred CCEEEEEEECCCCCCCCC-------CCC-CCHHHHHHHHHHCCEEECCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf 857999980489898789-------996-004899999987292985857889898348865567999999827999941
Q 001771 257 DNILLVKFDEELGGHRSS-------NNW-NDSYSKYNEIAREGILVGLRCYHFFVFKDGGKEEKKKDPSTSPVKCYFVRM 328 (1015)
Q Consensus 257 d~FLrV~F~ee~~~~~~~-------~~~-~~~~~r~~~~L~~Gi~I~gR~y~FLafs~S~~re~~k~~S~s~~~~~F~~~ 328 (1015)
.|..|+-|.++.+-+... .+. ..++.|+..++.+|+.+++++|+|+++ ||+||+ ++|
T Consensus 197 gr~~r~f~~~d~~~r~~~~~~~l~~~~~~~~~~~Rv~~f~~~G~~i~~~~f~fl~~--s~lre~---------s~~---- 261 (1022)
T 2j7n_A 197 GRQWRAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSV--VPAEEP---------VEQ---- 261 (1022)
T ss_dssp TEEEEEEEEEECC--------------CCCCCEEEEEEEEEEETTCBCCCC------------------------C----
T ss_pred CCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC--CCCCCC---------CCC----
T ss_conf 35467876202443344310012343235550216899860586126766554444--421124---------456----
Q ss_pred CCHHHHCCCCCCCCCHHCHHHHHHHCCCC--CC-CCCHHHHHHHHHCCCCC
Q ss_conf 87022203654334612199998501687--88-88554799862200267
Q 001771 329 ESSAFIDMGYQYILSGKTVHEARYMFMHV--RT-VSSVANYMSRLSLILSK 376 (1015)
Q Consensus 329 ~s~w~~~~~~P~~~~~~ti~~~r~~f~~i--~~-~~~vaK~aARlgq~FSs 376 (1015)
.. .++...|++|+|.|..+ .. .+-.|+.+--++....+
T Consensus 262 ----~~------~ls~~~ir~wmg~f~~n~~q~~aK~aARigq~FS~T~~t 302 (1022)
T 2j7n_A 262 ----RT------EFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAI 302 (1022)
T ss_dssp ----CB------CCCHHHHHHHHHCGGGCTTSBHHHHHHTTHHHHSBCEEE
T ss_pred ----CC------CCCHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf ----67------888999998666943445640889999865651585681
No 3
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=1.00 E-value=1 Score=29.28 Aligned_cols=44 Identities=7% Similarity=-0.060 Sum_probs=23.0
Q ss_pred CCCCCCEEEEEEEEECCCEEEECCCEECCCCCEEECCCCCCCEEEEEEE
Q ss_conf 5699942799999942970796198323688647120499857999980
Q 001771 217 KWDSGKTHMYHCHISTKGNCTFKGPYLNQTRTHLQRELGDDNILLVKFD 265 (1015)
Q Consensus 217 ~~~~g~~~v~~~~vtp~~~~~~~gP~le~snr~lrr~~g~d~FLrV~F~ 265 (1015)
..+--.+.-+++.+.+-+++.++......-| .-|.|| =|-|-++
T Consensus 428 TLHr~sIma~~~~l~~~ktirlnp~vC~~yN---ADFDGD--eMnvHvP 471 (1407)
T 3lu0_D 428 TLHRLGIQAFEPVLIEGKAIQLHPLVCAAYN---ADFDGD--QMAVHVP 471 (1407)
T ss_dssp CCSGGGEEEEEEEEESSSSEEECTGGGGTTT---CCSSSC--EEEEECC
T ss_pred CCCCCCCEEEEEEECCCCEEEECHHHCCCCC---CCCCCC--EEEEECC
T ss_conf 3122443244678648965886765644345---773442--3554237
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=1.00 E-value=1 Score=28.34 Aligned_cols=69 Identities=22% Similarity=0.120 Sum_probs=46.6
Q ss_pred CCCCCEEEEEECCCEEECEEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCC--CCCCCCC
Q ss_conf 98997289982262452404999848988889726999950585422126865089928999999442112--8999998
Q 001771 645 ILKSNEVCIILKDGQVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGD 722 (1015)
Q Consensus 645 ~L~eGEVfv~~s~~~i~G~~VlV~RnP~lhPGDIrvv~AV~~P~L~~~v~~lkdVIVFp~kG~Rplps~lS--GGDLDGD 722 (1015)
.|++|.+... ..+.|..||.-|.|.||.--||=++++-.|. +-=|=||.-|+ ..|+|||
T Consensus 400 ~l~~g~~V~r---hl~dgd~VLlNRqPTLHr~si~a~~~~l~~g----------------ktirlhp~vC~~yNADFDGD 460 (880)
T 4ayb_A 400 TLAPGYVVER---HLTDGDVVLFNRQPSLHRISMMAHRVRVLKG----------------LTFRLNLLVCPPYNADFDGD 460 (880)
T ss_dssp HCCTTCEEEE---ECCTTCEEEEECSSCCSGGGEEEEEEEECSS----------------SSEEECGGGHHHHTCCSSSC
T ss_pred HCCCCCEEEE---EEECCCEEEECCCCCCCCCCEEEEEEECCCC----------------CEEEECCCCCCCCCCCCCCC
T ss_conf 6065646755---5216858996378765654513223440567----------------53650620035434676666
Q ss_pred EEEEEECCCC
Q ss_conf 2799718211
Q 001771 723 MYFVSRNPEL 732 (1015)
Q Consensus 723 ~Y~ViWD~~L 732 (1015)
+-.|--=+.+
T Consensus 461 eMnvHvPqS~ 470 (880)
T 4ayb_A 461 EMNLHVPQSE 470 (880)
T ss_dssp EEEEECCCSH
T ss_pred EEEEECCCCH
T ss_conf 1477516888
No 5
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=1.00 E-value=1 Score=28.29 Aligned_cols=57 Identities=25% Similarity=0.257 Sum_probs=41.2
Q ss_pred EEECEEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCC--CCCCCCCEEEEEECCC
Q ss_conf 452404999848988889726999950585422126865089928999999442112--8999998279971821
Q 001771 659 QVSWEKVLVYRNPGLHFGDIHVLKATYVKELEDFVGTSKYAIFFPCNGPRSLADEIA--GGDFDGDMYFVSRNPE 731 (1015)
Q Consensus 659 ~i~G~~VlV~RnP~lhPGDIrvv~AV~~P~L~~~v~~lkdVIVFp~kG~Rplps~lS--GGDLDGD~Y~ViWD~~ 731 (1015)
++.|..||.-|.|.||.--||=++++-.|. +-=|=||.-|+ +.|+|||+-.|--=+.
T Consensus 694 vidgd~VLlNRqPTLHRlSIqAf~~kl~~g----------------kTiRLhplVC~pyNADFDGDEMnvHvPqS 752 (1524)
T 2a6h_D 694 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEG----------------QSIQLHPLVCEAFNADFDGDQMAVHVPLS 752 (1524)
T ss_dssp HSTTCCEEEECSSCCSGGGEEEEEEEEESS----------------SCEEECSGGGTTTTCCTTTCEEEEECCCS
T ss_pred ECCCCEEEECCCCCCCCCCCCEEEEEECCC----------------CCCEECHHHCCCCCCCCCCCEEEEECCCC
T ss_conf 005966787058743425640268897578----------------51014723257766775653356762787
No 6
>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=1.00 E-value=1 Score=28.02 Aligned_cols=15 Identities=7% Similarity=0.171 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHCC
Q ss_conf 599999999988079
Q 001771 18 SVEQLISKIYTEQNK 32 (1015)
Q Consensus 18 ~~~~~~~~~~~~~~~ 32 (1015)
.+-..|+.+|-.-.+
T Consensus 98 ~i~kiLe~VC~~Csk 112 (1733)
T 1twf_A 98 KIKKVCECVCMHCGK 112 (1733)
T ss_dssp HHHHHHHHBCTTTCC
T ss_pred HHHHHHHHHHHHCCE
T ss_conf 589999877675160
No 7
>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=1.00 E-value=1 Score=27.96 Aligned_cols=12 Identities=33% Similarity=0.227 Sum_probs=5.5
Q ss_pred CCCCHHHHHHHH
Q ss_conf 434598999770
Q 001771 536 TYLSRNLIALLS 547 (1015)
Q Consensus 536 ~~LNRqlI~iL~ 547 (1015)
....||++..+.
T Consensus 615 t~~Gr~if~~~l 626 (1265)
T 1hqm_D 615 TNPGRILFARIV 626 (1265)
T ss_dssp CCHHHHHHHHHH
T ss_pred CCCCCEEEEEEC
T ss_conf 068856776203
No 8
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=1.00 E-value=1 Score=26.20 Aligned_cols=10 Identities=20% Similarity=0.311 Sum_probs=5.6
Q ss_pred CCEEEEEECCCC
Q ss_conf 914799863799
Q 001771 471 PLLMQVRLFYNG 482 (1015)
Q Consensus 471 PSAfQiR~~y~G 482 (1015)
=+.+||+ ||+
T Consensus 867 g~ivQF~--YGe 876 (1752)
T 3h0g_A 867 GDIIQFA--YGE 876 (1752)
T ss_dssp SCEEESS--SSS
T ss_pred CCEEEEE--CCC
T ss_conf 9489874--677
No 9
>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}
Probab=1.00 E-value=1 Score=13.28 Aligned_cols=33 Identities=15% Similarity=0.201 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 278999999861163202234799999630157
Q 001771 48 EDAALDVLRTIASDKIKYSFSGYINYLVKKRNN 80 (1015)
Q Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (1015)
--+|++||-+-+.-+++-|||.|..-|..+...
T Consensus 38 SsLafdtl~aegqrry~es~s~y~r~~l~~~~~ 70 (916)
T 3pih_A 38 SSLAMDTIYAEGQRRYLESLSTYARQFLGNLKK 70 (916)
T ss_dssp HHHHTTTHHHHHHHHHHTTSCCC--------CC
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCC
T ss_conf 999999999999999987535999975234789
No 10
>3og6_A Interleukin-29; helical bundle, fibronectin type III domain, beta-sandwich, signaling, membrane; HET: BMA NAG; 2.10A {Homo sapiens} PDB: 3og4_A*
Probab=1.00 E-value=1 Score=12.11 Aligned_cols=10 Identities=20% Similarity=0.335 Sum_probs=3.9
Q ss_pred HHHHHHHHCC
Q ss_conf 9998884099
Q 001771 991 RKFYARRQGD 1000 (1015)
Q Consensus 991 ~~ik~~~~~~ 1000 (1015)
.+++++++++
T Consensus 175 rDL~CvA~gd 184 (196)
T 3og6_A 175 RDLKYVADGN 184 (196)
T ss_dssp THHHHHHHSC
T ss_pred HHHHHHCCCC
T ss_conf 0122334787
Done!