Query 001639
Match_columns 1039
No_of_seqs 388 out of 576
Neff 5.6
Searched_HMMs 29240
Date Tue Mar 26 15:50:24 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001639.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_938-942//hhsearch_pdb/001639hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h7h_B Transcription elongatio 1.0 1 1 207.2 10.3 100 178-277 2-106 (106)
2 2exu_A Transcription initiatio 1.0 1 1 206.7 10.9 103 166-268 78-193 (200)
3 2ckk_A KIN17; beta barrel, rib 1.0 1 1 181.3 12.1 105 931-1037 11-127 (127)
4 3p8b_B Transcription antitermi 1.0 1 1 171.4 14.8 129 182-312 3-131 (152)
5 2do3_A Transcription elongatio 1.0 1 1 165.4 6.2 66 463-528 4-69 (69)
6 2e70_A Transcription elongatio 1.0 1 1 148.7 8.0 62 695-756 7-68 (71)
7 3lpe_A Putative transcription 1.0 1 1 119.1 10.0 89 176-266 4-92 (92)
8 2jvv_A Transcription antitermi 1.0 1 1 115.8 5.7 130 181-310 6-167 (181)
9 1m1h_A Transcription antitermi 1.0 1 1 106.9 8.8 131 181-311 10-235 (248)
10 2oug_A Transcriptional activat 1.0 1 1 99.0 -4.3 119 182-300 2-137 (162)
No 1
>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=207.17 Aligned_cols=100 Identities=48% Similarity=0.761 Sum_probs=94.8
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHHHHHHH---CCCCCEEEEEEECCCCCEEEEEECCHHHHHHHHHCCCCCCE--EEE
Q ss_conf 9999927999903714799999999999850---89853589983169743799992666899999814865010--123
Q 001639 178 SVRDPKLWMVKCAIGREREAAVCLMQKCIDK---GSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS--QKV 252 (1039)
Q Consensus 178 sv~DP~lw~Vkc~~G~Er~vv~~Lm~K~~~~---~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gi~~i~~--~~~ 252 (1039)
|++||+||+|||++|+||++|++||+|+.++ +++++|+|||+++++||||||||+++.+|.+||+|++|+|+ +++
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 EEECHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 6408465641012333322478996
Q 001639 253 MLVPIREMTDVLAVESKAIDLSRDT 277 (1039)
Q Consensus 253 ~lVpi~Em~~vL~~~~~~~~l~~G~ 277 (1039)
.|||++||+++|+++++...|++|+
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 2
>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta sheet; 2.23A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=206.71 Aligned_cols=103 Identities=28% Similarity=0.542 Sum_probs=95.2
Q ss_pred CCCCHHHHH--CCCCC------CCCCEEEEECCCCHHHHHHHHHHHHHHHH-----CCCCCEEEEEEECCCCCEEEEEEC
Q ss_conf 210044341--19999------99927999903714799999999999850-----898535899831697437999926
Q 001639 166 ETTDVEQQA--LLPSV------RDPKLWMVKCAIGREREAAVCLMQKCIDK-----GSELQIRSVIALDHLKNYIYIEAD 232 (1039)
Q Consensus 166 ~~~~v~q~~--LlPsv------~DP~lw~Vkc~~G~Er~vv~~Lm~K~~~~-----~~~l~I~Svf~~~~lkGYIYIEA~ 232 (1039)
..+.+||+. +||+. +||+||+|||++|+||++|++||+|++++ +++|+|+|||++++|||||||||+
T Consensus 78 V~G~LPq~i~~lLp~y~~r~~S~DP~iw~Vkc~~G~Er~va~~l~~K~~~~~~~~~~~~l~I~Si~~~d~lkGYIyVEA~ 157 (200)
T 2exu_A 78 VDGRLPAEVVELLPHYKPRDGSGSATIWGVRCRPGKEKELIRKLLKKKFNLDRAMGKKKLKILSIFQRDNYTGRIYIEAP 157 (200)
T ss_dssp ECSCCCHHHHTTCTTCCCTTSCSCCCEEEEEECTTCHHHHHHHHHHHHHHHHHHSCSSCCCCCEEECCTTSTTEEEEECS
T ss_pred CCCCCCHHHHHHCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEC
T ss_conf 15768688996387766777678887799965798699999999999998650157998637999954898579999979
Q ss_pred CHHHHHHHHHCCCCCCEEEEEEECHHHHHHCCCCCC
Q ss_conf 668999998148650101236408465641012333
Q 001639 233 KEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVES 268 (1039)
Q Consensus 233 ~~~~V~~ai~Gi~~i~~~~~~lVpi~Em~~vL~~~~ 268 (1039)
++.+|.+||+|+++||.+++.|||++||+++|++.-
T Consensus 158 ~~~~V~~ai~Gi~~vy~~~~~lVPi~Em~dll~v~~ 193 (200)
T 2exu_A 158 KQSVIEKFCNGVPDIYISQKLLIPVQELPLLLKPNL 193 (200)
T ss_dssp CHHHHHHHHTTCTTEEEEEEEECCGGGHHHHHCSSC
T ss_pred CHHHHHHHHHHHHHHHCCCCEEECHHHHHHHHHHHH
T ss_conf 889999999604444237845764899676754455
No 3
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens}
Probab=1.00 E-value=1 Score=181.27 Aligned_cols=105 Identities=22% Similarity=0.391 Sum_probs=94.6
Q ss_pred CCCCCCCCEEE-E--C---CCCCCCEEEEEEECCCCEEEEEECCCCCCCEEEECCCCEEECCCCCCCCEEEECCCCCCCE
Q ss_conf 99963283999-7--0---7986207999996789839999255899946984499705549999992999808899843
Q 001639 931 EGPWFMPDILV-R--R---SGEESVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGAT 1004 (1039)
Q Consensus 931 ~~~W~~~~I~V-~--~---~g~~~~~gvV~~V~~~g~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~t 1004 (1039)
.++|+++||+| + + .|+++|+|||++|.++++|+|+|+++ |++++++|+|||||+|++|++|+||+|+|||++
T Consensus 11 ~~~Wl~~~I~Vrii~k~~~~g~y~~KgvV~~V~~~~~c~V~l~~~--g~~v~v~q~~LETViP~~g~~V~Iv~G~~rG~~ 88 (127)
T 2ckk_A 11 TDYWLQPEIIVKIITKKLGEKYHKKKAIVKEVIDKYTAVVKMIDS--GDKLKLDQTHLETVIPAPGKRILVLNGGYRGNE 88 (127)
T ss_dssp CSCCCCTTBEEEECCSTTCGGGTTCEEEEEEEETTTEEEEEETTT--CCEEEEEGGGEEECCCCTTCEEEECSSTTTTCE
T ss_pred CCCCCCCCEEEEEEECCCCCCCCCCEEEEEEECCCCEEEEEECCC--CCEEEECHHHCEEECCCCCCEEEEEECCCCCCE
T ss_conf 888530986999997667875137408999966898199997799--979987369928843789998999844657848
Q ss_pred EEEEEEECC--CCEEEECC----CCCEEEEECCCCCCCC
Q ss_conf 899977489--81999427----9946998331201026
Q 001639 1005 GKLIGVDGT--DGIVKVDV----SLDVKILDMAILAKLA 1037 (1039)
Q Consensus 1005 G~LisiD~~--dgiVk~d~----~~~~kil~~~~L~Kl~ 1037 (1039)
|+|+++|.+ .|+|+|++ +..+++|+|.++||++
T Consensus 89 g~L~~id~~~~~~~V~l~~~~~~~~~v~~l~~ddi~k~~ 127 (127)
T 2ckk_A 89 GTLESINEKTFSATIVIETGPLKGRRVEGIQYEDISKLA 127 (127)
T ss_dssp EEEEEEEGGGTEEEEEECSSTTTTCEEEEEEGGGEEEBC
T ss_pred EEEEEEECCCCEEEEEECCCCCCCCEEEEECHHHHHCCC
T ss_conf 999999687768999986688788799754899940429
No 4
>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=171.40 Aligned_cols=129 Identities=29% Similarity=0.442 Sum_probs=118.5
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECCHHHHHHHHHCCCCCCEEEEEEECHHHHH
Q ss_conf 92799990371479999999999985089853589983169743799992666899999814865010123640846564
Q 001639 182 PKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMT 261 (1039)
Q Consensus 182 P~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gi~~i~~~~~~lVpi~Em~ 261 (1039)
-+||+|+|++|+|+.++..|++++.. .++.|+++++|..++||||||+....+++.+|+++++|++....+||.+||.
T Consensus 3 ~~WYvv~~~~g~E~~v~~~L~~~~~~--~~l~i~~v~vp~~fPGYVfVe~~~~~~~~~~v~~t~gV~~fvg~~v~~~Ei~ 80 (152)
T 3p8b_B 3 GKIFAVRVTHGQEETTAKLIYSKVRT--YNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIE 80 (152)
T ss_dssp CEEEEEEECTTCHHHHHHHHHHHHHH--HTCCCCEEEECTTCCSEEEEEESSHHHHHHHHTTCTTEEEECSSCBCGGGTG
T ss_pred CEEEEEEEECCHHHHHHHHHHHHHHH--CCCCEEEEEEECCCCCEEEEEEECHHHHHHHHHCCCCEEEECCCCCCHHHHH
T ss_conf 54999999789799999999998743--6983899996658991999999853999999868998787478888999999
Q ss_pred HCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEECCC
Q ss_conf 101233332247899699973587899705999961789789999930565
Q 001639 262 DVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRID 312 (1039)
Q Consensus 262 ~vL~~~~~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~VkLiPRiD 312 (1039)
++|...+....+++|+||||+.|||+|+.|+|.+++..+.+++|.+.+.-.
T Consensus 81 ~il~~~~~~~~~~~Gd~VrI~~Gpf~g~~g~V~~vd~~k~~v~V~v~~~gr 131 (152)
T 3p8b_B 81 HFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIV 131 (152)
T ss_dssp GGCCCSCTTTTCCTTCEEEECSSTTTTCEEEEEEEETTTTEEEEEESSCSS
T ss_pred HHHCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCEEEEEEEECCE
T ss_conf 986727765567789999994405899789999992898899999993363
No 5
>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5
Probab=1.00 E-value=1 Score=165.43 Aligned_cols=66 Identities=36% Similarity=0.645 Sum_probs=63.6
Q ss_pred CCCEEECCCCCEEECCCCCCEEEECCCCCCCEEEEEEEECCEEEEEECCCCCEEEEECCCCCCCCC
Q ss_conf 950355142321320278816992363158357999995748999838997548993243111223
Q 001639 463 PKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSE 528 (1039)
Q Consensus 463 ~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVv~Ve~~~v~ilSD~t~~ei~V~~~dL~~~se 528 (1039)
+-+|+||+++|||||++|||||||+|+|+|+|||||+|+++.|+||||+||+||+||++||++|+|
T Consensus 4 ~~~i~~p~~~LrK~F~~GDHVkVi~G~~~getGlVV~v~~d~v~v~SD~t~~Ei~V~~~dL~~~~d 69 (69)
T 2do3_A 4 GSSGEFPAQELRKYFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLCSE 69 (69)
T ss_dssp CSCCCCCCCCCCSSCCTTCEEEESSSTTTTCEEEEEEECSSCEEEEESSSCSEEEECTTSEEESCC
T ss_pred CCEEEECHHHCEEECCCCCEEEEECCEECCCEEEEEEEECCEEEEEECCCCCEEEEEHHHHHHHCC
T ss_conf 747997179904412599869990667859618899993999999968998789997689465339
No 6
>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=148.69 Aligned_cols=62 Identities=39% Similarity=0.658 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCEEEEEECCCCEEEEEECCCCCCCC
Q ss_conf 99999999876456847999335888721499951397699994478649998257633563
Q 001639 695 GRNRGGRGGHDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDNV 756 (1039)
Q Consensus 695 g~~~~~~~~~d~liGktV~I~~GpyKG~~G~Vkd~t~~~~rVELhs~~k~i~V~r~~l~~~~ 756 (1039)
|+++++..+||.+|||||+|++||||||+|||||+|+++|||||||+||+|+|+|++|..++
T Consensus 7 G~~~gr~~grd~liGktV~I~kGpyKG~~GiVkd~t~~~~RVELhs~~K~VtV~r~~l~~~~ 68 (71)
T 2e70_A 7 GMSRGRGRRDNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLTTVG 68 (71)
T ss_dssp CCCCCSSCCTTSSTTSEEEECSSTTTTCEEEEEEECSSCEEEEESSSCCEEEECTTTEEECC
T ss_pred CCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEEHHHCCCCC
T ss_conf 76788886765458978899426888837889977898699995688669998855541368
No 7
>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=119.11 Aligned_cols=89 Identities=24% Similarity=0.404 Sum_probs=81.6
Q ss_pred CCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECCHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf 99999992799990371479999999999985089853589983169743799992666899999814865010123640
Q 001639 176 LPSVRDPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLV 255 (1039)
Q Consensus 176 lPsv~DP~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gi~~i~~~~~~lV 255 (1039)
-||++|++||+|+|++|+|+.++..|++++.. ..+.|++++++..++||||||+....+++.+|+++++|.+..-.++
T Consensus 4 ~~sv~d~~WYvv~~~sG~E~~V~~~L~~~~~~--~~l~i~~v~vP~~fPGYVfVe~~~~~~~~~~I~~t~gV~gfvg~pl 81 (92)
T 3lpe_A 4 RASVGAHMIFAVRTMVGQEKNIAGLMASRAEK--EQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTI 81 (92)
T ss_dssp -----CCCEEEEEECTTCHHHHHHHHHHHHHH--TTCCEEEEEECTTSTTEEEEEESSHHHHHHHHTTCTTEEEECSSCC
T ss_pred CCCCCCCEEEEEEEECCHHHHHHHHHHHHHHH--CCCCEEEEEEECCCCCEEEEEEECCHHHHHHHHCCCCCEEECCCCC
T ss_conf 67889981999998779599999999998876--4980899997324697899997646069999977999048278999
Q ss_pred CHHHHHHCCCC
Q ss_conf 84656410123
Q 001639 256 PIREMTDVLAV 266 (1039)
Q Consensus 256 pi~Em~~vL~~ 266 (1039)
+.+|+..+|++
T Consensus 82 ~~~Ev~~il~p 92 (92)
T 3lpe_A 82 AIEEIEPLLTP 92 (92)
T ss_dssp CHHHHHHHHCC
T ss_pred CHHHHHHHHCC
T ss_conf 99999998684
No 8
>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=115.76 Aligned_cols=130 Identities=14% Similarity=0.184 Sum_probs=101.1
Q ss_pred CCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE-----------------CCCCCEEEEEECCHHHHHHHHHC
Q ss_conf 9927999903714799999999999850898535899831-----------------69743799992666899999814
Q 001639 181 DPKLWMVKCAIGREREAAVCLMQKCIDKGSELQIRSVIAL-----------------DHLKNYIYIEADKEAHVKEACKG 243 (1039)
Q Consensus 181 DP~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~l~I~Svf~~-----------------~~lkGYIYIEA~~~~~V~~ai~G 243 (1039)
+.+||+|+|++|+|+.+...|.+++...+-.-.++.+|+| +.++|||||++......+..|+.
T Consensus 6 ~~~WYvv~t~sg~E~kv~~~L~~~~~~~~~~~~~~ev~vP~~~~~~~~~Gk~~~~~~~lfPGYvFV~~~~~~~~~~~vr~ 85 (181)
T 2jvv_A 6 KKRWYVVQAFSGFEGRVATSLREHIKLHNMEDLFGEVMVPTEEVVEIRGGQRRKSERKFFPGYVLVQMVMNDASWHLVRS 85 (181)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEECCCCHHHHHHC
T ss_conf 89899999979959999999999887679641432999267999996699999998617897899998867641245215
Q ss_pred CCCCCE------EEEEEECHHHHHHCCCCCC-------CCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEE--EEEE
Q ss_conf 865010------1236408465641012333-------322478996999735878997059999617897899--9993
Q 001639 244 LRNIYS------QKVMLVPIREMTDVLAVES-------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVT--VKLI 308 (1039)
Q Consensus 244 i~~i~~------~~~~lVpi~Em~~vL~~~~-------~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~--VkLi 308 (1039)
++++.+ .++.+||-+||..++.... ....+++|+.|||+.|||+|..|.|.+++..+.++. |.+.
T Consensus 86 t~gV~~fvg~~~~~P~pl~~~ei~~i~~~~~~~~~~~~~~~~~~~Gd~V~V~~GPf~g~~G~v~~v~~~k~r~~V~v~if 165 (181)
T 2jvv_A 86 VPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIF 165 (181)
T ss_dssp -------------------------------------CCCCCCCTTEEEEECSSTTTTEEEEEEEEETTTTEEEEEEEET
T ss_pred CCCCEEECCCCCCEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEEC
T ss_conf 99902975489983768699999999997515355777655689999999954578996899999948999999999977
Q ss_pred EC
Q ss_conf 05
Q 001639 309 PR 310 (1039)
Q Consensus 309 PR 310 (1039)
-|
T Consensus 166 gr 167 (181)
T 2jvv_A 166 GR 167 (181)
T ss_dssp TE
T ss_pred CC
T ss_conf 99
No 9
>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=106.91 Aligned_cols=131 Identities=20% Similarity=0.300 Sum_probs=95.4
Q ss_pred CCCEEEEECCCCHHHHHHHHHHHHHHHHCC---------CCC----EE--------------------------------
Q ss_conf 992799990371479999999999985089---------853----58--------------------------------
Q 001639 181 DPKLWMVKCAIGREREAAVCLMQKCIDKGS---------ELQ----IR-------------------------------- 215 (1039)
Q Consensus 181 DP~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~---------~l~----I~-------------------------------- 215 (1039)
..+||+++|++|+|+.+...|.+++...+- |.. |.
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 --------------------------------------EEEEECCCCCEEEEEECCHHHHHHHHHCCCCCCE-----EEE
Q ss_conf --------------------------------------9983169743799992666899999814865010-----123
Q 001639 216 --------------------------------------SVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS-----QKV 252 (1039)
Q Consensus 216 --------------------------------------Svf~~~~lkGYIYIEA~~~~~V~~ai~Gi~~i~~-----~~~ 252 (1039)
-......++|||||++....+.|.+++.+++|.+ .++
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 EEECHHHHHHCCCCCC-----CCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEE--EEECC
Q ss_conf 6408465641012333-----32247899699973587899705999961789789999--93056
Q 001639 253 MLVPIREMTDVLAVES-----KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK--LIPRI 311 (1039)
Q Consensus 253 ~lVpi~Em~~vL~~~~-----~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~~~V~Vk--LiPRi 311 (1039)
.++|-+||..+|+... +...+++|+.|||+.|||+|.-|.|.+++..+.++.|. +.-|.
T Consensus 170 ~pl~~~ev~~i~~~~~~~~~~~~~~~~~Gd~V~I~~Gpf~g~~G~v~ev~~~k~~~~V~v~ifgr~ 235 (248)
T 1m1h_A 170 VPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRM 235 (248)
T ss_dssp CEECHHHHHHHHHHTTC-------------------------------------------------
T ss_pred EEECHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEECCCC
T ss_conf 170999999998764346676535689999999941688995899999818889999999967983
No 10
>2oug_A Transcriptional activator RFAH; transcription factor, virulence, transcription pausing, transcription elongation; 2.10A {Escherichia coli}
Probab=1.00 E-value=1 Score=99.02 Aligned_cols=119 Identities=15% Similarity=0.223 Sum_probs=92.6
Q ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHCCC--------CCEEEEEEECCCCCEEEEEECCHHHHHHHHHCCCCCCE----
Q ss_conf 927999903714799999999999850898--------53589983169743799992666899999814865010----
Q 001639 182 PKLWMVKCAIGREREAAVCLMQKCIDKGSE--------LQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS---- 249 (1039)
Q Consensus 182 P~lw~Vkc~~G~Er~vv~~Lm~K~~~~~~~--------l~I~Svf~~~~lkGYIYIEA~~~~~V~~ai~Gi~~i~~---- 249 (1039)
.+||+|+|++|+|+.+...|.++.+.---| -+-......+.++|||||++......+..|+.++++.+
T Consensus 2 ~~WYvv~t~~g~E~~v~~~L~~~~~e~~vP~~~~~~~~~gk~~~~~~plfpgYvFV~~~~~~~~~~~v~~~~gv~~fv~~ 81 (162)
T 2oug_A 2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRF 81 (162)
T ss_dssp CEEEEEEECTTTHHHHHHHHHHTTCEEECCEEEEEEESSSSEEEEEEESSTTEEEEEECTTTSCHHHHHHSTTEEEECCS
T ss_pred CEEEEEEECCCHHHHHHHHHHHCCCEEECCCEEEEEECCCCEEEEEEECCCCEEEEEEECCCCCEEEEEECCCCCEEECC
T ss_conf 72999994097799999999867999987988999982992899988568998999988266856878717980189798
Q ss_pred -EEEEEECHHHHHHCCCCCC----CCCCCCCCCEEEEECCCCCCCEEEEEEEECCC
Q ss_conf -1236408465641012333----32247899699973587899705999961789
Q 001639 250 -QKVMLVPIREMTDVLAVES----KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVR 300 (1039)
Q Consensus 250 -~~~~lVpi~Em~~vL~~~~----~~~~l~~G~wVRIk~G~YkGDlAqV~~Vd~~~ 300 (1039)
.++.++|-+||..++.... ....+++|+.|||+.|||+|..|.|.+++..+
T Consensus 82 g~~p~pi~~~ei~~i~~~~~~~~~~~~~~~~Gd~V~V~~Gpf~g~~g~v~~v~~~k 137 (162)
T 2oug_A 82 GASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEA 137 (162)
T ss_dssp SSSSCCCCCHHHHHHHHCC--------------CTTHHHHHHHHHHHHTTCSSHHH
T ss_pred CCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEEECCCC
T ss_conf 99962759999999986645566566787899889992268889699999988987
Done!