Query 002586
Match_columns 904
No_of_seqs 283 out of 488
Neff 6.1
Searched_HMMs 29240
Date Tue Mar 26 16:35:36 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/002586.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1304-1308//hhsearch_pdb/002586hhsearch_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 1113.1 20.0 623 51-719 31-776 (1022)
2 3lu0_D DNA-directed RNA polyme 1.0 1 1 26.1 3.3 56 536-603 415-473 (1407)
3 1twf_A B220, DNA-directed RNA 1.0 1 1 26.0 2.4 29 809-837 1341-1369(1733)
4 4ayb_A DNA-directed RNA polyme 1.0 1 1 25.7 1.7 54 535-600 410-466 (880)
5 2a6h_D DNA-directed RNA polyme 1.0 1 1 24.9 3.4 53 536-600 694-749 (1524)
6 1hqm_D DNA-directed RNA polyme 1.0 1 1 24.6 -2.1 19 541-559 440-458 (1265)
7 3h0g_A DNA-directed RNA polyme 1.0 1 1 23.5 1.5 18 810-827 1348-1365(1752)
8 1b64_A Elongation factor 1-bet 1.0 1 1 15.5 4.5 58 207-267 21-78 (91)
9 1f60_B Elongation factor EEF1B 1.0 1 1 15.3 3.8 58 207-267 24-81 (94)
10 1gh8_A Translation elongation 1.0 1 1 15.2 3.6 60 207-269 19-78 (89)
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=1113.15 Aligned_cols=623 Identities=20% Similarity=0.270 Sum_probs=469.4
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCHHH--HHHHCCCCCCCCHHHHHHHHHHHHHCCCCC--CCCCHHHHHHHHHHHHCC
Q ss_conf 8893058889999970957941222889--986189999999589999999998402443--690046899999863228
Q 002586 51 ALPYEILFKINLLVQNGCVAGPLLDSNF--YRLVDPYRAPVSISCIEHALDKLYHLKECC--YEPSRWLTDQYRKYMTSR 126 (904)
Q Consensus 51 ~lpf~i~fql~~l~~~g~l~~~~~~~~f--~~~l~~~~~~~~~~~~~~~l~~l~~~~~~~--~~p~~~~~~~~~~~~~~~ 126 (904)
.+||.++|.++-+.+.+-+++.++.... -......+ .. +. .-+.|....... .-|...-...+.... .+
T Consensus 31 ~~P~~~~~e~~R~~~~~~v~~~~~~~~~~~~~~~~~~~-~~--~~---~~~~l~~~~~~~~k~~~e~~~~~~w~~a~-~~ 103 (1022)
T 2j7n_A 31 EAPLAVAWEVTRLFMHCKVDLEDESLGLKYDPSWSTAR-DV--TD---IWKTLYRLDAFRGKPFPEKPPNDVFVTAM-TG 103 (1022)
T ss_dssp TCCHHHHHHHHHHHHHHTCCTTCTTTTCCCCGGGGGCS-SG--GG---GTTTSSCTTTCCCCSCSCCCCHHHHHHHH-HS
T ss_pred CCCHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCCC-CH--HH---HHHHHHHCCCCCCCCCCCCCCCHHHHHHH-HC
T ss_conf 58716789999999847856887123434573334324-89--99---99997507421356588776415999986-13
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEC--------C--CEEEECCCCCCCCCCHHCCCCCCCCCEEEEEEEECCCCCCCCCCCC
Q ss_conf 99999986689991899999991--------7--8035225511254721023376899479999960799766667889
Q 002586 127 SKPSSPAISLDDGLVYVHRVQVT--------P--SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLS 196 (904)
Q Consensus 127 ~~~~~~~~~~~~~~~~v~~v~vT--------P--tri~~~~P~~e~sNRvlR~f~~~~d~FlRV~F~DE~~~~l~~~~~~ 196 (904)
.. + ..|-+-+....++ | .++.|.+|+++.|||+.|+|++ ||||||+|.+++....+. .
T Consensus 104 ~~------~-~~g~~v~~~~~l~~~~~~~~~~~~~~l~L~p~~l~~s~R~~RrfGs--DrFL~V~fp~~~~~~~~~---~ 171 (1022)
T 2j7n_A 104 NF------E-SKGSAVVLSAVLDYNPDNSPTAPLYLVKLKPLMFEQGCRLTRRFGP--DRFFEILIPSPTSTSPSV---P 171 (1022)
T ss_dssp TT------E-ETTEEEEEEEEEEECSCCSTTSCSEEEEECCCEEEECBHHHHHHCG--GGEEEEEEECTTCCCSSS---C
T ss_pred CC------C-CCCCEEEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCEEEEEECC--CEEEEEEECCCCCCCCCC---C
T ss_conf 34------6-5688799998986345666778724899547755777657785278--606999934776544456---6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHH------------------------------------------------HCCEEECCEE
Q ss_conf 8998875201355999999987------------------------------------------------2392873516
Q 002586 197 PRGSSATDITRTRIYTRILSTL------------------------------------------------RNGILIGDRK 228 (904)
Q Consensus 197 ~r~~~~~~~~~~~i~~ri~~~L------------------------------------------------~~Gi~I~gr~ 228 (904)
+... . ....++++..+| .+|+.|++++
T Consensus 172 ~~~~-~----~~~~~~~v~~~l~~~~~~~~gr~~r~f~~~d~~~r~~~~~~~l~~~~~~~~~~~Rv~~f~~~G~~i~~~~ 246 (1022)
T 2j7n_A 172 PVVS-K----QPAAVEEVIQWLTMGQHSLVGRQWRAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDV 246 (1022)
T ss_dssp TTSS-S----SSSCHHHHHHHHHSSCEEETTEEEEEEEEEECC--------------CCCCCEEEEEEEEEEETTCBCCC
T ss_pred CHHC-C----CHHHHHHHHHHHHCCCEEEECCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCC
T ss_conf 1100-2----6578999999871485798435467876202443344310012343235550216899860586126766
Q ss_pred EEEEEECCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCC--CHHHHHHHHCCCCCCCCCCEEEECCCEEEC-CCCCCC
Q ss_conf 89943058978767189997199999999999827987655--898999997032568745213307838981-570024
Q 002586 229 FEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIR--NVAKYAARLGQSFSSSKETLSVHMDEIEII-PDVKIE 305 (904)
Q Consensus 229 y~FLa~S~SqlR~~s~wF~a~~~~~t~~~Ir~wlG~f~~i~--~vaK~aARlgq~FSsT~~ti~i~~~~i~~I-~Di~~~ 305 (904)
|+||++ ||+|++++| ..++++++||+|||+|+.+. +++|||||||||||+|.+++.+.+++|..+ |||+.
T Consensus 247 f~fl~~--s~lre~s~~----~~~ls~~~ir~wmg~f~~n~~q~~aK~aARigq~FS~T~~tv~v~~~~I~~~~dDI~~- 319 (1022)
T 2j7n_A 247 FKTRSV--VPAEEPVEQ----RTEFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLS- 319 (1022)
T ss_dssp C---------------C----CBCCCHHHHHHHHHCGGGCTTSBHHHHHHTTHHHHSBCEEEEECCGGGEEECSSCCBC-
T ss_pred CCCCCC--CCCCCCCCC----CCCCCHHHHHHHCCCHHHCCCCHHHHHHHHHHHHHCCCCCCEEECHHHEEECCCCCCC-
T ss_conf 554444--421124456----6788899999866694344564088999986565158568178655897986785206-
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEECCCCEEEEEECCCCC---CCEEECCCCCCCCC-----CCC
Q ss_conf 5783311256531013999999999909999998258995169538999479999---61562455555546-----788
Q 002586 306 IGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTSS---KKLSLRDSMRKYES-----ELT 377 (904)
Q Consensus 306 ~~g~~~~fTDGvG~IS~~la~~I~~~l~l~~~~PSafQiR~gG~KGvl~vdp~~~---~~I~lR~Sm~KF~s-----~~~ 377 (904)
.+|++|+||||||+||+++|++|++++++ ...|||||||||||||||+|||++. .+|++||||.||++ .++
T Consensus 320 ~~g~g~vFTDGvG~IS~~lA~~I~~~l~l-~~~PSAfQiR~gGaKGvl~vdp~~~~~~~~I~lRpSm~KF~~~~~d~~~~ 398 (1022)
T 2j7n_A 320 PSGTGEVMNDGVGRMSRSVAKRIRDVLGL-GDVPSAVQGRFGSAKGMWVIDVDDTGDEDWIETYPSQRKWECDFVDKHQR 398 (1022)
T ss_dssp TTSSCCBSSTTEEEECHHHHHHHHHHHTC-SSCCSEEEEEETTEEEEEEECTTCCSCCCCEEECTTTBCSCCCCCSGGGS
T ss_pred CCCCCCEECCCCHHHHHHHHHHHHHHCCC-CCCCCEEEEEECCCEEEEEECCCCCCCCCEEEECCCCEEECCCCCCCCCC
T ss_conf 78898751577257529999999998299-99982799975360589997734478864599677512026898885568
Q ss_pred CEEEEEEC-CCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHH-HH-------HHHHHCCHHHHHHHHHHCC---------
Q ss_conf 24596405-764443419899998208999799999999999-99-------9999469999999998639---------
Q 002586 378 KLDVLAWS-KYQPCFLNRQLISLLSTLGIWDEIFEKKQREAV-RQ-------LDAILTDPLKAQEALELMS--------- 439 (904)
Q Consensus 378 ~LeI~~~S-~~~p~~LNrQ~I~iL~~lGV~~evF~~lq~~~l-~~-------l~~~l~d~~~a~~~l~~~~--------- 439 (904)
+|||++|| ++.|++||||+|+||+++||+.++|++++.+.+ +. ...+++++..+..++....
T Consensus 399 ~LEIv~~s~~~~~~~LNRQlI~lL~~lGV~~~~f~~~i~~~~~~~L~~~l~~~~~al~~~~~~r~~l~~~~~~~~~r~~~ 478 (1022)
T 2j7n_A 399 TLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSH 478 (1022)
T ss_dssp EEEEEEECCCCCCCCBCTTTHHHHHHTBSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHSCCHHHHHHH
T ss_pred EEEEEEECCCCCCCEECHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 58997604888874405899999886796779999999999999999999999998538999999998624552100123
Q ss_pred ---------CCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEECCCCEEEEEECCCCCCCCCCCEEEE
Q ss_conf ---------99828999999987999999469999999999999998302311230484125332388899999968999
Q 002586 440 ---------PGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQ 510 (904)
Q Consensus 440 ---------~~~~~~~l~~ll~~Gf~~~~epfl~~~L~~~~~~~l~~lk~K~rI~Vp~s~~l~GV~DetG~L~~gEVfvq 510 (904)
+...++++..|+.+||.|.++||++++++.++..+++.||+|+||+||+|++||||+||||+|+||||||+
T Consensus 479 g~~~~~~glp~s~~~~l~~Ll~aGf~p~~epfL~~~l~~~~~~~l~~LK~k~rI~V~~s~~L~GV~DetG~L~eGEVfv~ 558 (1022)
T 2j7n_A 479 GRVPFLAGLPDSQEETLNFLMNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVG 558 (1022)
T ss_dssp TSCCEETTEESSHHHHHHHHHHTTCCTTTBHHHHHHHHHHHHHHHHHHHHHCCBCCSSEEEEEEEECTTSCCCTTEEEEE
T ss_pred CCCHHHCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCEEEEE
T ss_conf 43012135762269999999975898432399999999999999998888632366662089987668776679837997
Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCEEEE-EEEEEEECCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf 7178633457886434565456522773-159997189889987048997218978778982995699999999876799
Q 002586 511 ISGAGYRQLHGESSLFSSSRSRQRFIVQ-GLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECSGS 589 (904)
Q Consensus 511 ~s~~~~~~~~~~~~~~~~~~~~~~~vi~-G~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~lsGG 589 (904)
++..... + .....++. |+|+|+||||+||||||+++||++|+||||+||||||++|+||+|||||||
T Consensus 559 ~s~~~~~-----------~-~~~~~~l~gg~VlVtRnP~lhPGDIrvv~AV~~PeL~hL~DvIVFp~kG~Rplps~lSGG 626 (1022)
T 2j7n_A 559 FSSKFRD-----------E-EESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVIIFSTKGDVPLAKKLSGG 626 (1022)
T ss_dssp EEEEEEE-----------T-TEEEEEECSEEEEEECSSCCSGGGEEEEEECCCGGGTTCCSEEEECSCSSSCHHHHTTTC
T ss_pred ECCCCCC-----------C-CCCCEEECCCEEEEEECCCCCCCCEEEEEECCCHHHHCCCCEEECCCCCCCCCHHHHCCC
T ss_conf 4355566-----------7-777314217608998577768580027884137333066786980688999985671577
Q ss_pred CCCCCEEEEEECCCCCCCCCCCCCCCCCCCC-------CCC---------C---CCCCHHH-HHHHHHHHHCCCCHHHHH
Q ss_conf 8999838996248889999999999999865-------678---------9---7668889-999999750269088999
Q 002586 590 DLDGDIYFVCWDDELIPPQQDPPMDYTPAQS-------MQL---------D---HDVQIED-VEEYFTNYIVNDSLGIIA 649 (904)
Q Consensus 590 DLDGD~y~ViWD~~Lip~~~~~P~~y~~~~~-------~~l---------~---~~vt~~d-i~~ffv~ym~~d~LG~is 649 (904)
|||||+|||||||+|||++.+.|++..+... ..+ . ++++.+| +.+||+.||++|.||+||
T Consensus 627 DLDGD~Y~ViWD~~Lv~~f~na~~p~~p~~~~y~~k~~~~~~~~~~~~~~g~~~~~~~~~d~i~~ff~~~m~~d~LG~is 706 (1022)
T 2j7n_A 627 DYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDKTTFKQLMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCT 706 (1022)
T ss_dssp CSSSCEEEEECCHHHHHTBCCCCCCCCCCCTTTSEECCCBHHHHHTTTCSSHHHHHHHHHHHHHHHHHHHTSCCHHHHHH
T ss_pred CCCCCEEEEEECHHHCCCCCCCCCCCCCCHHHHCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 87887589982556555656788888875565144454204443302455556673149999999998742743288899
Q ss_pred HHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCHHCH
Q ss_conf 99999862289999996699999998640367988886558--99998899999879999998666660208
Q 002586 650 NAHTVFADREPRKARSEPCLQLAEKFSIAVDFPKTGVPAEI--PPHLYVKEYPDFMEKPDKPTYESQNVIGK 719 (904)
Q Consensus 650 n~Hl~~aD~~~~g~~~~~Cl~LA~l~S~AVD~~KTG~~~~i--p~~l~~~~~Pdfm~k~~~~~Y~S~~iLG~ 719 (904)
|+|+..+|++ .|+.+++|++||+|||+||||||||+++++ ++.++++.+||||+ +++|+|+|++++|+
T Consensus 707 ~~h~~~~~~~-~g~~~~~cl~LA~L~S~AVD~~KtG~pv~~~~~~~lr~~~~p~~m~-~~~p~Y~s~~~~g~ 776 (1022)
T 2j7n_A 707 NYKERLCYIN-NSVSNKPAIILSSLVGNLVDQSKQGIVFNEASWAQLRRELLGGALS-LPDPMYKSDSWLGR 776 (1022)
T ss_dssp HHHHHHHHHH-TCSSSHHHHHHHHHHHHHTTHHHHTEECCHHHHHHHHHHHSCCSSC-CCCCGGGSSSCCSS
T ss_pred HHHHHHHHHC-CCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCC
T ss_conf 9999987650-7999988999999999860856668564733465643864799777-78875114754578
No 2
>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=26.08 Aligned_cols=56 Identities=25% Similarity=0.468 Sum_probs=38.3
Q ss_pred EEEE-EEEEEECCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCCCCEEEEEECCC
Q ss_conf 7731-599971898899870489972189787789829956999999998767--9989998389962488
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVCWDDE 603 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~ViWD~~ 603 (904)
++.| .|+.-|.|+||.--||-++++-.|. +-=|=+|.-|+ +.|+|||+-+|-.=+.
T Consensus 415 vi~gd~VLlNRqPTLHr~sIma~~~~l~~~------------ktirlnp~vC~~yNADFDGDeMnvHvPqs 473 (1407)
T 3lu0_D 415 VIREHPVLLNRAPTLHRLGIQAFEPVLIEG------------KAIQLHPLVCAAYNADFDGDQMAVHVPLT 473 (1407)
T ss_dssp TTTSCCEEEEESSCCSGGGEEEEEEEEESS------------SSEEECTGGGGTTTCCSSSCEEEEECCCS
T ss_pred HHHCEEEEECCCCCCCCCCCEEEEEEECCC------------CEEEECHHHCCCCCCCCCCCEEEEECCCC
T ss_conf 753425665488631224432446786489------------65886765644345773442355423789
No 3
>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=26.02 Aligned_cols=29 Identities=17% Similarity=-0.003 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf 99999999999999996113999935498
Q 002586 809 IGMAVRALRKEARAWFKEKSGSDTEDDAY 837 (904)
Q Consensus 809 i~~~~~~l~~~~r~~f~~~~~~~~~~~~~ 837 (904)
|..+-+.+-+|.+..|...+..-+.-.+.
T Consensus 1341 IEAAR~~Ii~Ei~~V~~~~Gi~Vd~RHl~ 1369 (1733)
T 1twf_A 1341 IEAGRAALYKEVYNVIASDGSYVNYRHMA 1369 (1733)
T ss_dssp HHHHHHHHHHHHHHHHHTTTCCCCHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf 99999999999999986058634623343
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=25.74 Aligned_cols=54 Identities=20% Similarity=0.338 Sum_probs=39.1
Q ss_pred EEEEE-EEEEEECCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCCCCEEEEEE
Q ss_conf 27731-599971898899870489972189787789829956999999998767--9989998389962
Q 002586 535 FIVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVCW 600 (904)
Q Consensus 535 ~vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~ViW 600 (904)
.++.| .|+.-|.|.||.--||=++++-.|. + -=|=||.-|+ ..|+|||+-.|--
T Consensus 410 hl~dgd~VLlNRqPTLHr~si~a~~~~l~~g-k-----------tirlhp~vC~~yNADFDGDeMnvHv 466 (880)
T 4ayb_A 410 HLTDGDVVLFNRQPSLHRISMMAHRVRVLKG-L-----------TFRLNLLVCPPYNADFDGDEMNLHV 466 (880)
T ss_dssp ECCTTCEEEEECSSCCSGGGEEEEEEEECSS-S-----------SEEECGGGHHHHTCCSSSCEEEEEC
T ss_pred EEECCCEEEECCCCCCCCCCEEEEEEECCCC-C-----------EEEECCCCCCCCCCCCCCCEEEEEC
T ss_conf 5216858996378765654513223440567-5-----------3650620035434676666147751
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=24.88 Aligned_cols=53 Identities=28% Similarity=0.582 Sum_probs=38.8
Q ss_pred EEEE-EEEEEECCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCCCCEEEEEE
Q ss_conf 7731-599971898899870489972189787789829956999999998767--9989998389962
Q 002586 536 IVQG-LVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRPHPNECS--GSDLDGDIYFVCW 600 (904)
Q Consensus 536 vi~G-~VlV~RnP~lhPGDIr~v~AV~~P~L~hl~dvIVFp~kG~Rplps~ls--GGDLDGD~y~ViW 600 (904)
++.| .|+.-|.|.||.--||-++++-.|. +-=|=||.-|+ ..|+|||+-.|--
T Consensus 694 vidgd~VLlNRqPTLHRlSIqAf~~kl~~g------------kTiRLhplVC~pyNADFDGDEMnvHv 749 (1524)
T 2a6h_D 694 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEG------------QSIQLHPLVCEAFNADFDGDQMAVHV 749 (1524)
T ss_dssp HSTTCCEEEECSSCCSGGGEEEEEEEEESS------------SCEEECSGGGTTTTCCTTTCEEEEEC
T ss_pred ECCCCEEEECCCCCCCCCCCCEEEEEECCC------------CCCEECHHHCCCCCCCCCCCEEEEEC
T ss_conf 005966787058743425640268897578------------51014723257766775653356762
No 6
>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=24.63 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=6.5
Q ss_pred EEEEECCCCCCCCEEEEEE
Q ss_conf 9997189889987048997
Q 002586 541 VVVAKNPCLHPGDVRVLKA 559 (904)
Q Consensus 541 VlV~RnP~lhPGDIr~v~A 559 (904)
|+.-|.|.||.--||=+++
T Consensus 440 VLlNRqPTLHr~sIma~~~ 458 (1265)
T 1hqm_D 440 VLLNRAPTLHRLGIQAFQP 458 (1265)
T ss_dssp EECCCSSCCSGGGSCEEBC
T ss_pred EEEECCCCCCCCCCCCEEE
T ss_conf 8981686423145421168
No 7
>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=23.46 Aligned_cols=18 Identities=28% Similarity=0.137 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999611
Q 002586 810 GMAVRALRKEARAWFKEK 827 (904)
Q Consensus 810 ~~~~~~l~~~~r~~f~~~ 827 (904)
..+=+.+-+|.+..|...
T Consensus 1348 EAAR~~Ii~Ei~~v~~~~ 1365 (1752)
T 3h0g_A 1348 EATRSALLKELRNVIEFD 1365 (1752)
T ss_dssp HHHHHHHHHHHHTTSCSS
T ss_pred HHHHHHHHHHHHHHHHHC
T ss_conf 999999999999999843
No 8
>1b64_A Elongation factor 1-beta; guanine nucleotide exchange factor, G-protein, translation elongation; NMR {Homo sapiens} SCOP: d.58.12.1
Probab=1.00 E-value=1 Score=15.45 Aligned_cols=58 Identities=10% Similarity=0.211 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHHCCEEECCEEEEEEEECCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCC
Q ss_conf 3559999999872392873516899430589787671899971999999999998279876
Q 002586 207 RTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 267 (904)
Q Consensus 207 ~~~i~~ri~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wF~a~~~~~t~~~Ir~wlG~f~~ 267 (904)
...+.++++.++.+|+..++-..+.+||+ ++.=.+.+.-+.+....+.+-+.+-.|..
T Consensus 21 l~~L~~~Vr~i~~~Gl~wg~~k~~piafG---ikkL~i~~vveDd~v~tD~lee~i~~~ed 78 (91)
T 1b64_A 21 MAKLEECVRSIQADGLVWGSSKLVPVGYG---IKKLQIQCVVEDDKVGTDMLEEQITAFED 78 (91)
T ss_dssp HHHHHHHHHHCCCTTCEEEEEEEEESSSS---CEEEEEEEEECTTSSCHHHHHHHHTTCTT
T ss_pred HHHHHHHHHHHCCCCCEEEEEEEEEEEEE---EEEEEEEEEEECCCCCHHHHHHHHHHCCC
T ss_conf 99999999985748858988899988746---77999999997794484899999985249
No 9
>1f60_B Elongation factor EEF1BA; protein-protein complex, translation; 1.67A {Saccharomyces cerevisiae} SCOP: d.58.12.1 PDB: 1g7c_B* 2b7c_B 2b7b_B 1ije_B* 1ijf_B*
Probab=1.00 E-value=1 Score=15.32 Aligned_cols=58 Identities=7% Similarity=0.165 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHCCEEECCEEEEEEEECCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCC
Q ss_conf 3559999999872392873516899430589787671899971999999999998279876
Q 002586 207 RTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 267 (904)
Q Consensus 207 ~~~i~~ri~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wF~a~~~~~t~~~Ir~wlG~f~~ 267 (904)
...+.+.++.++.+|+..++-..+.+||+ ++.=.+.+.-+.+....+.+-+.+-.|..
T Consensus 24 l~~L~~~Vr~i~~~Gl~wg~~k~~piafG---lkkL~i~~vveDd~~~tD~lee~i~~~ed 81 (94)
T 1f60_B 24 LEEMVANVKAIEMEGLTWGAHQFIPIGFG---IKKLQINCVVEDDKVSLDDLQQSIEEDED 81 (94)
T ss_dssp HHHHHHHHHTCCCTTEEEEEEEEEEEETT---EEEEEEEEEEETTTCCHHHHHHHHHTCTT
T ss_pred HHHHHHHHHHHCCCCCEEEEEEEEEEEEE---EEEEEEEEEEECCCCCHHHHHHHHHHCCC
T ss_conf 99999999985748847878789987614---67899999998785472899999985659
No 10
>1gh8_A Translation elongation factor 1BETA; alpha-beta sandwich, gene regulation, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.58.12.1
Probab=1.00 E-value=1 Score=15.19 Aligned_cols=60 Identities=12% Similarity=0.092 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHCCEEECCEEEEEEEECCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCC
Q ss_conf 355999999987239287351689943058978767189997199999999999827987655
Q 002586 207 RTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREIR 269 (904)
Q Consensus 207 ~~~i~~ri~~~L~~Gi~I~gr~y~FLa~S~SqlR~~s~wF~a~~~~~t~~~Ir~wlG~f~~i~ 269 (904)
...+.+.++.++..|+.+++-..+.+||+ ++.=.+.+.-+.+....+.+-+.+-.|...+
T Consensus 19 l~~L~~~vk~~~~~gl~w~~~k~~piafG---lk~L~i~~vveD~~~~td~lee~i~~~e~Vq 78 (89)
T 1gh8_A 19 LEALKKEIQERIPEGTELHKIDEEPIAFG---LVALNVMVVVGDAEGGTEAAEESLSGIEGVS 78 (89)
T ss_dssp HHHHHHHHHHHSCTTSEECCCCEEECSSS---CEEEEEEEEESSSCGGGGHHHHHHTTSCSSE
T ss_pred HHHHHHHHHHHCCCCCEEEEEEEEEEECC---EEEEEEEEEEECCCCCHHHHHHHHHCCCCCC
T ss_conf 99999999986648857856037877726---2669999999738758289999986469952
Done!