Query 000247
Match_columns 1790
No_of_seqs 385 out of 950
Neff 3.7
Searched_HMMs 29240
Date Tue Mar 26 18:09:46 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000247.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_23-27//hhsearch_pdb/000247hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2exu_A Transcription initiatio 1.0 1 1 219.3 7.7 104 211-314 80-193 (200)
2 3h7h_B Transcription elongatio 1.0 1 1 214.1 6.8 103 221-323 2-106 (106)
3 3p8b_B Transcription antitermi 1.0 1 1 191.6 13.2 128 225-357 3-130 (152)
4 2jvv_A Transcription antitermi 1.0 1 1 148.7 5.3 131 224-357 6-168 (181)
5 2e70_A Transcription elongatio 1.0 1 1 144.0 8.3 52 658-709 16-67 (71)
6 1m1h_A Transcription antitermi 1.0 1 1 139.3 10.1 136 224-359 10-237 (248)
7 2oug_A Transcriptional activat 1.0 1 1 138.1 -10.4 130 225-357 2-149 (162)
8 3lpe_A Putative transcription 1.0 1 1 135.7 11.6 89 219-312 4-92 (92)
9 2xhc_A Transcription antitermi 1.0 1 1 107.3 10.8 46 659-704 298-345 (352)
10 1nz8_A Transcription antitermi 1.0 1 1 96.3 8.1 87 224-313 1-115 (119)
No 1
>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=219.25 Aligned_cols=104 Identities=34% Similarity=0.559 Sum_probs=97.6
Q ss_pred HHCCCCC--CCCCC------CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCC--CCCCCEEEEEEECCCCCEEEEEECCC
Q ss_conf 1011112--79999------99939999912723699999999999963048--99875889998179985799995050
Q 000247 211 KMLEREY--HMPCP------EDPTIWKVKCMAGRERQSAFCLMQKFVDLQSL--GSKMQIISAFAVDHIKGFIFIEADKQ 280 (1790)
Q Consensus 211 ~~VpQq~--LLPSV------kDPkLWaVKCK~GkEReVV~sLmkKii~lq~~--g~pL~I~SVFvpd~lKGYIYVEA~kq 280 (1790)
+.+||+. |||+. +||+||+|||++|+||+||++||+|+++++++ +.+|+|+|||+|++|||||||||+++
T Consensus 80 G~LPq~i~~lLp~y~~r~~S~DP~iw~Vkc~~G~Er~va~~l~~K~~~~~~~~~~~~l~I~Si~~~d~lkGYIyVEA~~~ 159 (200)
T 2exu_A 80 GRLPAEVVELLPHYKPRDGSGSATIWGVRCRPGKEKELIRKLLKKKFNLDRAMGKKKLKILSIFQRDNYTGRIYIEAPKQ 159 (200)
T ss_dssp SCCCHHHHTTCTTCCCTTSCSCCCEEEEEECTTCHHHHHHHHHHHHHHHHHHSCSSCCCCCEEECCTTSTTEEEEECSCH
T ss_pred CCCCHHHHHHCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEECCH
T ss_conf 76868899638776677767888779996579869999999999999865015799863799995489857999997988
Q ss_pred HHHHHHHCCCCCEEECEECCCCHHHHHHHHHCCC
Q ss_conf 0499983399977821101179989999762043
Q 000247 281 CDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQI 314 (1790)
Q Consensus 281 ~dV~eAI~GI~gVy~sK~vlVPIkEM~dLLkvkk 314 (1790)
.+|.+||+||++||..++.|||++||++||+++-
T Consensus 160 ~~V~~ai~Gi~~vy~~~~~lVPi~Em~dll~v~~ 193 (200)
T 2exu_A 160 SVIEKFCNGVPDIYISQKLLIPVQELPLLLKPNL 193 (200)
T ss_dssp HHHHHHHTTCTTEEEEEEEECCGGGHHHHHCSSC
T ss_pred HHHHHHHHHHHHHHCCCCEEECHHHHHHHHHHHH
T ss_conf 9999999604444237845764899676754455
No 2
>3h7h_B Transcription elongation factor SPT5; helices surrounding beta sheet, activator, ME binding, nucleus, repressor, transcription regulation; 1.55A {Homo sapiens}
Probab=1.00 E-value=1 Score=214.08 Aligned_cols=103 Identities=33% Similarity=0.602 Sum_probs=98.0
Q ss_pred CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEEC--EE
Q ss_conf 9999939999912723699999999999963048998758899981799857999950500499983399977821--10
Q 000247 221 CPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYS--RL 298 (1790)
Q Consensus 221 SVkDPkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~I~SVFvpd~lKGYIYVEA~kq~dV~eAI~GI~gVy~s--K~ 298 (1790)
||+||+||+|||++|+|++||++||+|+++++.+..+|+|+|||+|+++||||||||+++.+|.+||+|+++||.. ++
T Consensus 2 sv~Dp~i~~Vk~~~G~Er~va~~L~~k~~~~~~~~~~l~I~Si~~~~~lkGyIyVEA~~~~~V~~ai~gi~~v~~~~~~~ 81 (106)
T 3h7h_B 2 SHMDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYWNQ 81 (106)
T ss_dssp --CCCEEEEEECCTTCHHHHHHHHHHHHHHHTTSSSCCCCCEEEECTTCCSEEEEEESSHHHHHHHHTTCGGGGGGSSCC
T ss_pred CCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCEEEEEEECCHHHHHHHHHCCCCEECCCCCC
T ss_conf 98899789999789838999999999999863359986369999628984699999698899999985345141023324
Q ss_pred CCCCHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 1179989999762043655545798
Q 000247 299 APVPKNEVSHLLSAQIKRNEVSEGT 323 (1790)
Q Consensus 299 vlVPIkEM~dLLkvkkks~dLkvGd 323 (1790)
.+||++||+++|++++....|++|+
T Consensus 82 ~lVpi~Em~~~L~~~k~~~~l~~G~ 106 (106)
T 3h7h_B 82 QMVPIKEMTDVLKVVKEVANLGSGC 106 (106)
T ss_dssp EECCGGGTTGGGCCEEC--------
T ss_pred EEECHHHHHHHCCCCCCCCCCCCCC
T ss_conf 0776999997667576525678998
No 3
>3p8b_B Transcription antitermination protein NUSG; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} PDB: 3qqc_D
Probab=1.00 E-value=1 Score=191.62 Aligned_cols=128 Identities=26% Similarity=0.425 Sum_probs=117.1
Q ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEECEECCCCHH
Q ss_conf 93999991272369999999999996304899875889998179985799995050049998339997782110117998
Q 000247 225 PTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKN 304 (1790)
Q Consensus 225 PkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~I~SVFvpd~lKGYIYVEA~kq~dV~eAI~GI~gVy~sK~vlVPIk 304 (1790)
-+||+|+|++|+|+.|+.+|++++... +|+|++||+|..|||||||||.+.++++++|+++++|+.....|||.+
T Consensus 3 ~~WYvv~~~~g~E~~v~~~L~~~~~~~-----~l~i~~v~vp~~fPGYVfVe~~~~~~~~~~v~~t~gV~~fvg~~v~~~ 77 (152)
T 3p8b_B 3 GKIFAVRVTHGQEETTAKLIYSKVRTY-----NLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFK 77 (152)
T ss_dssp CEEEEEEECTTCHHHHHHHHHHHHHHH-----TCCCCEEEECTTCCSEEEEEESSHHHHHHHHTTCTTEEEECSSCBCGG
T ss_pred CEEEEEEEECCHHHHHHHHHHHHHHHC-----CCCEEEEEEECCCCCEEEEEEECHHHHHHHHHCCCCEEEECCCCCCHH
T ss_conf 549999997897999999999987436-----983899996658991999999853999999868998787478888999
Q ss_pred HHHHHHHCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCEEEEEEECCC
Q ss_conf 99997620436555457988999167689982899999489987999990167
Q 000247 305 EVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1790)
Q Consensus 305 EM~dLLkvkkks~dLkvGdwVRIKrGpYKGDLAQVveVDenk~kV~VKLIPRI 357 (1790)
||.+||...+....|++|++|||++|||+|++|+|++|+.++.+|+|.|.+.-
T Consensus 78 Ei~~il~~~~~~~~~~~Gd~VrI~~Gpf~g~~g~V~~vd~~k~~v~V~v~~~g 130 (152)
T 3p8b_B 78 EIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAI 130 (152)
T ss_dssp GTGGGCCCSCTTTTCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEESSCS
T ss_pred HHHHHHCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCEEEEEEEECC
T ss_conf 99998672776556778999999440589978999999289889999999336
No 4
>2jvv_A Transcription antitermination protein NUSG; transcription factor, transcription regulation, transcription termination; NMR {Escherichia coli} PDB: 2k06_A 2kvq_G
Probab=1.00 E-value=1 Score=148.74 Aligned_cols=131 Identities=15% Similarity=0.200 Sum_probs=108.1
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE-----------------CCCCCEEEEEECCCHHHHHH
Q ss_conf 9939999912723699999999999963048998758899981-----------------79985799995050049998
Q 000247 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEA 286 (1790)
Q Consensus 224 DPkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~I~SVFvp-----------------d~lKGYIYVEA~kq~dV~eA 286 (1790)
+.+||+|+|++|+|+.|+..|.+++..+. ....|+.||+| +.|||||||++.+.++.++.
T Consensus 6 ~~~WYvv~t~sg~E~kv~~~L~~~~~~~~---~~~~~~ev~vP~~~~~~~~~Gk~~~~~~~lfPGYvFV~~~~~~~~~~~ 82 (181)
T 2jvv_A 6 KKRWYVVQAFSGFEGRVATSLREHIKLHN---MEDLFGEVMVPTEEVVEIRGGQRRKSERKFFPGYVLVQMVMNDASWHL 82 (181)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCEEEEEEECCHHHHHHHHHHHHHHHCC---CCCCCEEEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEECCCCHHHH
T ss_conf 89899999979959999999999887679---641432999267999996699999998617897899998867641245
Q ss_pred HCCCCCEEE------CEECCCCHHHHHHHHHCCC-------CCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCE--EEE
Q ss_conf 339997782------1101179989999762043-------6555457988999167689982899999489987--999
Q 000247 287 CKGLSGIYY------SRLAPVPKNEVSHLLSAQI-------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATV 351 (1790)
Q Consensus 287 I~GI~gVy~------sK~vlVPIkEM~dLLkvkk-------ks~dLkvGdwVRIKrGpYKGDLAQVveVDenk~k--V~V 351 (1790)
|+.+++|.. .+|.|||.+||..||.... ....|.+|+.|||+.|||+|..|.|++|+.++.+ |.|
T Consensus 83 vr~t~gV~~fvg~~~~~P~pl~~~ei~~i~~~~~~~~~~~~~~~~~~~Gd~V~V~~GPf~g~~G~v~~v~~~k~r~~V~v 162 (181)
T 2jvv_A 83 VRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSV 162 (181)
T ss_dssp ----------------------------------------CCCCCCCTTEEEEECSSTTTTEEEEEEEEETTTTEEEEEE
T ss_pred HHCCCCCEEECCCCCCEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEE
T ss_conf 21599902975489983768699999999997515355777655689999999954578996899999948999999999
Q ss_pred EEECCC
Q ss_conf 990167
Q 000247 352 KLIPRI 357 (1790)
Q Consensus 352 KLIPRI 357 (1790)
.|+.|-
T Consensus 163 ~ifgr~ 168 (181)
T 2jvv_A 163 SIFGRA 168 (181)
T ss_dssp EETTEE
T ss_pred EECCCC
T ss_conf 977997
No 5
>2e70_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=144.03 Aligned_cols=52 Identities=35% Similarity=0.479 Sum_probs=49.8
Q ss_pred CCCCCCCEEEECCCCCCCCEEEEEEEECCEEEEEECCCCEEEEEECCCCCCC
Q ss_conf 7434798899924889993019998809949999568641999806863212
Q 000247 658 GMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1790)
Q Consensus 658 ~d~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~v 709 (1790)
++.+|||||+|++||||||+|||||+|+++|||||||+||+|+|+|++|.++
T Consensus 16 rd~liGktV~I~kGpyKG~~GiVkd~t~~~~RVELhs~~K~VtV~r~~l~~~ 67 (71)
T 2e70_A 16 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTV 67 (71)
T ss_dssp TTSSTTSEEEECSSTTTTCEEEEEEECSSCEEEEESSSCCEEEECTTTEEEC
T ss_pred CCCCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEEHHHCCCC
T ss_conf 6545897889942688883788997789869999568866999885554136
No 6
>1m1h_A Transcription antitermination protein NUSG; transcription termination, RNP motif, immunoglobulin fold, nucleic acid interaction; 1.95A {Aquifex aeolicus} SCOP: b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A
Probab=1.00 E-value=1 Score=139.34 Aligned_cols=136 Identities=15% Similarity=0.221 Sum_probs=107.3
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCC------CCCC----EE--------------------------------
Q ss_conf 99399999127236999999999999630489------9875----88--------------------------------
Q 000247 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLG------SKMQ----II-------------------------------- 261 (1790)
Q Consensus 224 DPkLWaVKCK~GkEReVV~sLmkKii~lq~~g------~pL~----I~-------------------------------- 261 (1790)
..+||+|+|++|+|+.+...|.+++..+.... .|.. |.
T Consensus 10 ~~~WYvl~t~sg~E~kv~~~L~~~i~~~g~~~~~~~v~vP~e~~~~I~~~G~~~~~~~L~~~~~~i~i~~~~g~n~i~I~ 89 (248)
T 1m1h_A 10 EKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIE 89 (248)
T ss_dssp CCEEEEEEECTTCHHHHHHHHHHHHHHTTCGGGEEEEECSSEEEEEEEETTEEEEEEESSSSCEEEEEECSSSEEEEEEC
T ss_pred CCCEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEECCEEEEEECCCCCCCEEEEECCCCEEEEEEE
T ss_conf 78699999887979999999999897679754035999126999999879999999827777627999468864999997
Q ss_pred --------------------------------------EEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEE-----CEE
Q ss_conf --------------------------------------9998179985799995050049998339997782-----110
Q 000247 262 --------------------------------------SAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY-----SRL 298 (1790)
Q Consensus 262 --------------------------------------SVFvpd~lKGYIYVEA~kq~dV~eAI~GI~gVy~-----sK~ 298 (1790)
-....+.|||||||+|.+.++++++|+.+++|+. .+|
T Consensus 90 dG~irv~es~cPdqCv~~G~I~k~G~~IvCLPnrv~I~I~~~~~lfPGYvfv~~~~~d~~~~~v~~tp~V~~fv~~g~~P 169 (248)
T 1m1h_A 90 NGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKP 169 (248)
T ss_dssp SSCEEEEECSTTCGGGGSCCBCSTTCEEEETTTTEEEEEEEECSSSTTEEEEEECCCHHHHHHHHTSTTEEEECEETTEE
T ss_pred CCEEEEEECCCCHHHHCCCCCCCCCCEEEECCCEEEEEEECCCCCEEEEEEEEEECCHHHHHHHHCCCCEEEEECCCCEE
T ss_conf 99999988999716506564335997898258768999840565020599999961277888886289837997579988
Q ss_pred CCCCHHHHHHHHHCCC-----CCCCCCCCCEEEEECCCCCCCCEEEEEEECCCC--EEEEEEECCCCH
Q ss_conf 1179989999762043-----655545798899916768998289999948998--799999016764
Q 000247 299 APVPKNEVSHLLSAQI-----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATVKLIPRIDL 359 (1790)
Q Consensus 299 vlVPIkEM~dLLkvkk-----ks~dLkvGdwVRIKrGpYKGDLAQVveVDenk~--kV~VKLIPRIDy 359 (1790)
+|||.+||..||+... +...|.+|+.|||+.|||+|+.|.|.+|+.++. .|.|.||.|.-.
T Consensus 170 ~pl~~~ev~~i~~~~~~~~~~~~~~~~~Gd~V~I~~Gpf~g~~G~v~ev~~~k~~~~V~v~ifgr~tp 237 (248)
T 1m1h_A 170 VPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTP 237 (248)
T ss_dssp CEECHHHHHHHHHHTTC---------------------------------------------------
T ss_pred EEECHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEECCCCEE
T ss_conf 17099999999876434667653568999999994168899589999981888999999996798389
No 7
>2oug_A Transcriptional activator RFAH; transcription factor, virulence, transcription pausing, transcription elongation; 2.10A {Escherichia coli}
Probab=1.00 E-value=1 Score=138.06 Aligned_cols=130 Identities=15% Similarity=0.185 Sum_probs=99.9
Q ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCC--------EEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEE-
Q ss_conf 93999991272369999999999996304899875--------889998179985799995050049998339997782-
Q 000247 225 PTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQ--------IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY- 295 (1790)
Q Consensus 225 PkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~--------I~SVFvpd~lKGYIYVEA~kq~dV~eAI~GI~gVy~- 295 (1790)
.+||+|+|++|+|+.|+..|.+..++.- .|.. -......+.|||||||++.+.+..++.|+.+++|..
T Consensus 2 ~~WYvv~t~~g~E~~v~~~L~~~~~e~~---vP~~~~~~~~~gk~~~~~~plfpgYvFV~~~~~~~~~~~v~~~~gv~~f 78 (162)
T 2oug_A 2 QSWYLLYCKRGQLQRAQEHLERQAVNCL---APMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHF 78 (162)
T ss_dssp CEEEEEEECTTTHHHHHHHHHHTTCEEE---CCEEEEEEESSSSEEEEEEESSTTEEEEEECTTTSCHHHHHHSTTEEEE
T ss_pred CEEEEEEECCCHHHHHHHHHHHCCCEEE---CCCEEEEEECCCCEEEEEEECCCCEEEEEEECCCCCEEEEEECCCCCEE
T ss_conf 7299999409779999999986799998---7988999982992899988568998999988266856878717980189
Q ss_pred ----CEECCCCHHHHHHHHHCCC----CCCCCCCCCEEEEECCCCCCCCEEEEEEECCC-CEEEEEEECCC
Q ss_conf ----1101179989999762043----65554579889991676899828999994899-87999990167
Q 000247 296 ----SRLAPVPKNEVSHLLSAQI----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNAR-KRATVKLIPRI 357 (1790)
Q Consensus 296 ----sK~vlVPIkEM~dLLkvkk----ks~dLkvGdwVRIKrGpYKGDLAQVveVDenk-~kV~VKLIPRI 357 (1790)
.+|.|||.+||..++.... ....+.+|+.|||+.|||+|..|.|++|+.++ ..|.|.|+.|-
T Consensus 79 v~~g~~p~pi~~~ei~~i~~~~~~~~~~~~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~kr~~V~v~ifgr~ 149 (162)
T 2oug_A 79 VRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKE 149 (162)
T ss_dssp CCSSSSSCCCCCHHHHHHHHCC--------------CTTHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred ECCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEEECCCCEEEEEEHHHCCC
T ss_conf 79899962759999999986645566566787899889992268889699999988987799997884994
No 8
>3lpe_A Putative transcription antitermination protein NU; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} PDB: 3ewg_A
Probab=1.00 E-value=1 Score=135.73 Aligned_cols=89 Identities=21% Similarity=0.385 Sum_probs=81.7
Q ss_pred CCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEECEE
Q ss_conf 99999993999991272369999999999996304899875889998179985799995050049998339997782110
Q 000247 219 MPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRL 298 (1790)
Q Consensus 219 LPSVkDPkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~I~SVFvpd~lKGYIYVEA~kq~dV~eAI~GI~gVy~sK~ 298 (1790)
-|||+||+||+|+|++|+|+.|+..|++++.. ..++|++||+|..|||||||||++.++++++|+++++|...-.
T Consensus 4 ~~sv~d~~WYvv~~~sG~E~~V~~~L~~~~~~-----~~l~i~~v~vP~~fPGYVfVe~~~~~~~~~~I~~t~gV~gfvg 78 (92)
T 3lpe_A 4 RASVGAHMIFAVRTMVGQEKNIAGLMASRAEK-----EQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVP 78 (92)
T ss_dssp -----CCCEEEEEECTTCHHHHHHHHHHHHHH-----TTCCEEEEEECTTSTTEEEEEESSHHHHHHHHTTCTTEEEECS
T ss_pred CCCCCCCEEEEEEEECCHHHHHHHHHHHHHHH-----CCCCEEEEEEECCCCCEEEEEEECCHHHHHHHHCCCCCEEECC
T ss_conf 67889981999998779599999999998876-----4980899997324697899997646069999977999048278
Q ss_pred CCCCHHHHHHHHHC
Q ss_conf 11799899997620
Q 000247 299 APVPKNEVSHLLSA 312 (1790)
Q Consensus 299 vlVPIkEM~dLLkv 312 (1790)
.||+.+|+..+|.+
T Consensus 79 ~pl~~~Ev~~il~p 92 (92)
T 3lpe_A 79 GTIAIEEIEPLLTP 92 (92)
T ss_dssp SCCCHHHHHHHHCC
T ss_pred CCCCHHHHHHHHCC
T ss_conf 99999999998684
No 9
>2xhc_A Transcription antitermination protein NUSG; 2.45A {Thermotoga maritima}
Probab=1.00 E-value=1 Score=107.26 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=36.3
Q ss_pred CCCCCCEEEECCCCCCCCEEEEEEEECC--EEEEEECCCCEEEEEECC
Q ss_conf 4347988999248899930199988099--499995686419998068
Q 000247 659 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTVKGE 704 (1790)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaTdt--~ARVELHSk~KtITVdKe 704 (1790)
.+.+|++|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|.-+
T Consensus 298 ~f~~Gd~VrV~~GPF~G~~G~V~evd~ek~rv~V~V~ifGR~tpVeL~ 345 (352)
T 2xhc_A 298 GFKVGDMVKIISGPFEDFAGVIKEIDPERQELKVNVTIFGRETPVVLH 345 (352)
T ss_dssp CCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEEEETTEEEEEEEE
T ss_pred CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCCEEEEEC
T ss_conf 479999999950688996899999848889999999987980899984
No 10
>1nz8_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: d.58.42.1
Probab=1.00 E-value=1 Score=96.33 Aligned_cols=87 Identities=22% Similarity=0.370 Sum_probs=71.6
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEC------------------CCCCEEEEEECCCH----
Q ss_conf 99399999127236999999999999630489987588999817------------------99857999950500----
Q 000247 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD------------------HIKGFIFIEADKQC---- 281 (1790)
Q Consensus 224 DPkLWaVKCK~GkEReVV~sLmkKii~lq~~g~pL~I~SVFvpd------------------~lKGYIYVEA~kq~---- 281 (1790)
|++||+|+|++|+|+.|+..|.+++..+.. ...|+.||+|. .|||||||++.+.+
T Consensus 1 ~~~WYvv~t~sg~E~kv~~~L~~~~~~~~~---~~~~~ev~vP~~~v~~~~~g~k~~~~~~~lfPGYVFV~~~~~~~~~~ 77 (119)
T 1nz8_A 1 SIEWYAVHTLVGQEEKAKANLEKRIKAFGL---QDKIFQVLIPTEEVVELREGGKKEVVRKKLFPGYLFIQMDLGDEEEP 77 (119)
T ss_dssp CCEEEEEECCTTTHHHHHHHHHHHHHHHTC---TTTCCEEECSEEEEEEECSSSCEEEEEEESSTTEEEEEECCCSSSSC
T ss_pred CCEEEEEEEECCCHHHHHHHHHHHHHHCCC---CCCCEEEECCEEEEEEECCCCEEEEEEEECCCCEEEEEEECCCCCCC
T ss_conf 974999999788299999999999876787---52412997716999998799999999996789899999643344441
Q ss_pred -HHHHHHCCCCCEEE-----CEECCCCHHHHHHHHHCC
Q ss_conf -49998339997782-----110117998999976204
Q 000247 282 -DINEACKGLSGIYY-----SRLAPVPKNEVSHLLSAQ 313 (1790)
Q Consensus 282 -dV~eAI~GI~gVy~-----sK~vlVPIkEM~dLLkvk 313 (1790)
++++.|+.+++|.. .+|.|||.+||..+|...
T Consensus 78 ~~~~~~vr~t~gV~gfvg~g~~P~pi~~~ev~~i~~~~ 115 (119)
T 1nz8_A 78 NEAWEVVRGTPGITGFVGAGMRPVPLSPDEVRHILEVS 115 (119)
T ss_dssp CHHHHHHHHSTTCCCCCCSSSSSCBCCHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCEEEECCCCEEEECCHHHHHHHHHHH
T ss_conf 45899987599953992779998487999999999888
Done!