Query 000294
Match_columns 1711
No_of_seqs 390 out of 941
Neff 3.9
Searched_HMMs 29240
Date Tue Mar 26 18:36:50 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000294.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_70-74//hhsearch_pdb/000294hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2exu_A Transcription initiatio 1.0 1 1 217.5 7.3 104 211-314 80-193 (200)
2 3h7h_B Transcription elongatio 1.0 1 1 212.1 6.9 103 221-323 2-106 (106)
3 3p8b_B Transcription antitermi 1.0 1 1 190.6 13.4 128 225-357 3-130 (152)
4 2jvv_A Transcription antitermi 1.0 1 1 149.1 5.3 131 224-357 6-168 (181)
5 2e70_A Transcription elongatio 1.0 1 1 143.8 8.3 52 658-709 16-67 (71)
6 1m1h_A Transcription antitermi 1.0 1 1 140.0 10.0 136 224-359 10-237 (248)
7 2oug_A Transcriptional activat 1.0 1 1 137.7 -10.2 129 225-357 2-149 (162)
8 3lpe_A Putative transcription 1.0 1 1 134.5 11.6 89 219-312 4-92 (92)
9 2xhc_A Transcription antitermi 1.0 1 1 106.3 11.1 46 659-704 298-345 (352)
10 1nz8_A Transcription antitermi 1.0 1 1 95.2 8.5 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=217.46 Aligned_cols=104 Identities=34% Similarity=0.559 Sum_probs=97.3
Q ss_pred HHCCCCC--CCCCC------CCCCEEEEEECCCHHHHHHHHHHHHHHHHCCC--CCCCCEEEEEEECCCCCEEEEEECCC
Q ss_conf 2000112--79999------99939999921623799999999999963058--99875889998179985799995050
Q 000294 211 KMLEREY--HMPCP------EDPTIWKVKCMAGRERQSAFCLMQKFVDLQSL--GSKMQIISAFAVDHIKGFIFIEADKQ 280 (1711)
Q Consensus 211 ~~VpQq~--LLPSV------~DPkLWvVKCK~GkEReVV~~LmkKii~lq~~--g~~L~I~SVFvpd~lKGYIYIEA~kq 280 (1711)
+.+||+. |||+. +||+||+|||++|+||+||++||+|++++++. +.+|+|+|||+|++|||||||||+++
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 HHHHHHHCCCCCEEECCCCCCCHHHHHHHHHCCC
Q ss_conf 1499985189986721001269989999752043
Q 000294 281 CDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQI 314 (1711)
Q Consensus 281 ~dV~eAI~GI~gVy~~k~~lVPikEM~dLLkvkk 314 (1711)
.+|.+||+||++||..++.|||++||++||++.-
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=212.10 Aligned_cols=103 Identities=33% Similarity=0.602 Sum_probs=97.9
Q ss_pred CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEEC--CC
Q ss_conf 9999939999921623799999999999963058998758899981799857999950501499985189986721--00
Q 000294 221 CPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYS--RL 298 (1711)
Q Consensus 221 SV~DPkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dV~eAI~GI~gVy~~--k~ 298 (1711)
||+||+||+|||++|+|++||++||+|+++++....+|+|+|||+|+++||||||||+++.+|.+||+||++||.. ++
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 1269989999752043665546798
Q 000294 299 APVPKNEVSHLLSAQIKRNEVSEGT 323 (1711)
Q Consensus 299 ~lVPikEM~dLLkvkkk~~~LkvGd 323 (1711)
.+||++||++||+++++...|++|+
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=190.59 Aligned_cols=128 Identities=26% Similarity=0.425 Sum_probs=116.8
Q ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEECCCCCCCHH
Q ss_conf 93999992162379999999999996305899875889998179985799995050149998518998672100126998
Q 000294 225 PTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKN 304 (1711)
Q Consensus 225 PkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dV~eAI~GI~gVy~~k~~lVPik 304 (1711)
-+||+|+|++|+|+.|+.+|++++... ++.|++||+|..|||||||||.+.++++++|+++++|+.....|||.+
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 99997520436655467988999167689982899999589987999991167
Q 000294 305 EVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1711)
Q Consensus 305 EM~dLLkvkkk~~~LkvGdwVRIKrGpYKGDLAQVveVdenk~kV~VKLIPRI 357 (1711)
||.+||...+....|++|++|||++|||+|++|+|++|+.++.+|+|.|.+.-
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=149.12 Aligned_cols=131 Identities=14% Similarity=0.195 Sum_probs=107.9
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEE-----------------CCCCCEEEEEECCCHHHHHH
Q ss_conf 9939999921623799999999999963058998758899981-----------------79985799995050149998
Q 000294 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEA 286 (1711)
Q Consensus 224 DPkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYIEA~kq~dV~eA 286 (1711)
+.+||+|+|++|+|+.|+..|.+++..+. ....|+.||+| +.|||||||++...++.++.
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 HCCCCCEE---E---CCCCCCCHHHHHHHHHCCC-------CCCCCCCCCEEEEECCCCCCCCEEEEEEECCCC--EEEE
Q ss_conf 51899867---2---1001269989999752043-------665546798899916768998289999958998--7999
Q 000294 287 CKGLSGIY---Y---SRLAPVPKNEVSHLLSAQI-------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATV 351 (1711)
Q Consensus 287 I~GI~gVy---~---~k~~lVPikEM~dLLkvkk-------k~~~LkvGdwVRIKrGpYKGDLAQVveVdenk~--kV~V 351 (1711)
|+.+++|. . .+|.|||.+||..||.... ....|++|+.|||+.|||+|+.|.|++|+.++. .|.|
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 991167
Q 000294 352 KLIPRI 357 (1711)
Q Consensus 352 KLIPRI 357 (1711)
.|+.|-
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=143.83 Aligned_cols=52 Identities=35% Similarity=0.479 Sum_probs=49.8
Q ss_pred CCCCCCCEEEECCCCCCCCEEEEEEEECCEEEEEECCCCEEEEEECCCCCCC
Q ss_conf 7434698899924889994019998809948999568741999807862112
Q 000294 658 GMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1711)
Q Consensus 658 ~d~lIGKTVkIrkGPYKGylGiVKDaTds~ARVELHSk~KvITVdK~~Ls~v 709 (1711)
++.||||||+|++||||||+|||||+|+++|||||||+||+|+|+|++|.++
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=139.96 Aligned_cols=136 Identities=15% Similarity=0.214 Sum_probs=106.9
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCC------CCC----CEE--------------------------------
Q ss_conf 99399999216237999999999999630589------987----588--------------------------------
Q 000294 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLG------SKM----QII-------------------------------- 261 (1711)
Q Consensus 224 DPkLWvVKCK~GkEReVV~~LmkKii~lq~~g------~~L----~I~-------------------------------- 261 (1711)
..+||+|+|++|+|+.|+..|.+++..+.... .|. .|.
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-----CCC
Q ss_conf --------------------------------------9998179985799995050149998518998672-----100
Q 000294 262 --------------------------------------SAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY-----SRL 298 (1711)
Q Consensus 262 --------------------------------------SVFvpd~lKGYIYIEA~kq~dV~eAI~GI~gVy~-----~k~ 298 (1711)
=+...+.|||||||+|.+.++++++++.+++|.. .+|
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 1269989999752043-----665546798899916768998289999958998--799999116765
Q 000294 299 APVPKNEVSHLLSAQI-----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATVKLIPRIDL 359 (1711)
Q Consensus 299 ~lVPikEM~dLLkvkk-----k~~~LkvGdwVRIKrGpYKGDLAQVveVdenk~--kV~VKLIPRIDy 359 (1711)
.|||.+||..||.... +...|++|+.|||+.|||+|+.|.|.+|+.++. .|.|.||.|.-.
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=137.70 Aligned_cols=129 Identities=16% Similarity=0.201 Sum_probs=99.7
Q ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCC---------CEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEE
Q ss_conf 9399999216237999999999999630589987---------5889998179985799995050149998518998672
Q 000294 225 PTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKM---------QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY 295 (1711)
Q Consensus 225 PkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L---------~I~SVFvpd~lKGYIYIEA~kq~dV~eAI~GI~gVy~ 295 (1711)
.+||+|+|++|+|+.|+..|.+..++.- .|. .. .....+.|||||||++...+..+..|+.+++|..
T Consensus 2 ~~WYvv~t~~g~E~~v~~~L~~~~~e~~---vP~~~~~~~~~gk~-~~~~~plfpgYvFV~~~~~~~~~~~v~~~~gv~~ 77 (162)
T 2oug_A 2 QSWYLLYCKRGQLQRAQEHLERQAVNCL---APMITLEKIVRGKR-TAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSH 77 (162)
T ss_dssp CEEEEEEECTTTHHHHHHHHHHTTCEEE---CCEEEEEEESSSSE-EEEEEESSTTEEEEEECTTTSCHHHHHHSTTEEE
T ss_pred CEEEEEEECCCHHHHHHHHHHHCCCEEE---CCCEEEEEECCCCE-EEEEEECCCCEEEEEEECCCCCEEEEEECCCCCE
T ss_conf 7299999409779999999986799998---79889999829928-9998856899899998826685687871798018
Q ss_pred -----CCCCCCCHHHHHHHHHCCC----CCCCCCCCCEEEEECCCCCCCCEEEEEEECCC-CEEEEEEECCC
Q ss_conf -----1001269989999752043----66554679889991676899828999995899-87999991167
Q 000294 296 -----SRLAPVPKNEVSHLLSAQI----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNAR-KRATVKLIPRI 357 (1711)
Q Consensus 296 -----~k~~lVPikEM~dLLkvkk----k~~~LkvGdwVRIKrGpYKGDLAQVveVdenk-~kV~VKLIPRI 357 (1711)
.+|.|||.+||..++.... ....+.+|+.|||+.|||+|..|.|.+|+.++ ..|.|.|+.|-
T Consensus 78 fv~~g~~p~pi~~~ei~~i~~~~~~~~~~~~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~kr~~V~v~ifgr~ 149 (162)
T 2oug_A 78 FVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKE 149 (162)
T ss_dssp ECCSSSSSCCCCCHHHHHHHHCC--------------CTTHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred EECCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEEECCCCEEEEEEHHHCCC
T ss_conf 979899962759999999986645566566787899889992268889699999988987799997884994
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=134.47 Aligned_cols=89 Identities=21% Similarity=0.374 Sum_probs=81.6
Q ss_pred CCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEECCCHHHHHHHCCCCCEEECCC
Q ss_conf 99999993999992162379999999999996305899875889998179985799995050149998518998672100
Q 000294 219 MPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRL 298 (1711)
Q Consensus 219 LPSV~DPkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dV~eAI~GI~gVy~~k~ 298 (1711)
-|||+||+||+|+|++|+|+.|+..|++++... .++|++||+|..|||||||||++.++++++|+++++|.....
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 RASVGAHMIFAVRTMVGQEKNIAGLMASRAEKE-----QLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVP 78 (92)
T ss_dssp -----CCCEEEEEECTTCHHHHHHHHHHHHHHT-----TCCEEEEEECTTSTTEEEEEESSHHHHHHHHTTCTTEEEECS
T ss_pred CCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHC-----CCCEEEEEEECCCCCEEEEEEECCHHHHHHHHCCCCCEEECC
T ss_conf 678899819999987795999999999988764-----980899997324697899997646069999977999048278
Q ss_pred CCCCHHHHHHHHHC
Q ss_conf 12699899997520
Q 000294 299 APVPKNEVSHLLSA 312 (1711)
Q Consensus 299 ~lVPikEM~dLLkv 312 (1711)
.||+.+|+..+|.+
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=106.34 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=37.0
Q ss_pred CCCCCCEEEECCCCCCCCEEEEEEEECC--EEEEEECCCCEEEEEECC
Q ss_conf 4346988999248899940199988099--489995687419998078
Q 000294 659 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTVKGE 704 (1711)
Q Consensus 659 d~lIGKTVkIrkGPYKGylGiVKDaTds--~ARVELHSk~KvITVdK~ 704 (1711)
.+.+|..|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|.-+
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=95.19 Aligned_cols=87 Identities=22% Similarity=0.372 Sum_probs=71.8
Q ss_pred CCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEC--------C----------CCCEEEEEECCCH----
Q ss_conf 99399999216237999999999999630589987588999817--------9----------9857999950501----
Q 000294 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD--------H----------IKGFIFIEADKQC---- 281 (1711)
Q Consensus 224 DPkLWvVKCK~GkEReVV~~LmkKii~lq~~g~~L~I~SVFvpd--------~----------lKGYIYIEA~kq~---- 281 (1711)
|.+||+|+|++|+|+.|+..|.+++..+. ....|+.||+|. . |||||||++...+
T Consensus 1 ~~~WYvv~t~sg~E~kv~~~L~~~~~~~~---~~~~~~ev~vP~~~v~~~~~g~k~~~~~~~lfPGYVFV~~~~~~~~~~ 77 (119)
T 1nz8_A 1 SIEWYAVHTLVGQEEKAKANLEKRIKAFG---LQDKIFQVLIPTEEVVELREGGKKEVVRKKLFPGYLFIQMDLGDEEEP 77 (119)
T ss_dssp CCEEEEEECCTTTHHHHHHHHHHHHHHHT---CTTTCCEEECSEEEEEEECSSSCEEEEEEESSTTEEEEEECCCSSSSC
T ss_pred CCEEEEEEEECCCHHHHHHHHHHHHHHCC---CCCCCEEEECCEEEEEEECCCCEEEEEEEECCCCEEEEEEECCCCCCC
T ss_conf 97499999978829999999999987678---752412997716999998799999999996789899999643344441
Q ss_pred -HHHHHHCCCCCEEE-----CCCCCCCHHHHHHHHHCC
Q ss_conf -49998518998672-----100126998999975204
Q 000294 282 -DINEACKGLSGIYY-----SRLAPVPKNEVSHLLSAQ 313 (1711)
Q Consensus 282 -dV~eAI~GI~gVy~-----~k~~lVPikEM~dLLkvk 313 (1711)
++++.|+.+++|.. .+|.|||.+||..+|...
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!