Query gi|254781213|ref|YP_003065626.1| head-to-tail joining protein, putative [Candidatus Liberibacter asiaticus str. psy62] Match_columns 556 No_of_seqs 167 out of 535 Neff 7.6 Searched_HMMs 39220 Date Mon May 30 08:16:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781213.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PHA00670 hypothetical protein 100.0 0 0 1044.6 55.9 517 6-541 3-537 (540) 2 pfam12236 Head-tail_con Bacter 100.0 0 0 867.4 48.5 465 13-502 1-480 (480) 3 pfam05133 Phage_prot_Gp6 Phage 97.3 0.015 3.8E-07 35.2 26.2 265 113-414 87-358 (435) 4 pfam05126 consensus 95.5 0.19 4.8E-06 28.0 20.4 335 24-420 28-401 (473) 5 PHA00670 hypothetical protein 95.0 0.11 2.9E-06 29.4 6.8 25 503-527 502-526 (540) 6 pfam07360 consensus 80.7 3.8 9.6E-05 19.6 25.6 158 113-306 75-234 (412) 7 TIGR02824 quinone_pig3 putativ 70.8 2.9 7.5E-05 20.3 2.1 14 376-389 276-290 (334) 8 pfam04860 Phage_portal Phage p 68.1 7.8 0.0002 17.6 18.4 101 265-367 145-259 (348) 9 PRK10902 FKBP-type peptidyl-pr 66.3 8.5 0.00022 17.3 8.3 16 93-108 95-110 (270) 10 TIGR00042 TIGR00042 non-canoni 38.2 24 0.00061 14.4 2.9 38 284-321 46-86 (205) 11 KOG1819 consensus 38.0 24 0.00062 14.4 3.4 22 504-525 814-835 (990) 12 KOG0400 consensus 36.1 26 0.00066 14.2 2.3 21 408-428 69-89 (151) 13 pfam07888 CALCOCO1 Calcium bin 35.2 27 0.00068 14.1 3.1 102 149-276 4-108 (546) 14 KOG3982 consensus 35.1 26 0.00066 14.2 2.0 21 151-176 136-156 (475) 15 PRK07079 hypothetical protein; 33.0 29 0.00074 13.9 2.9 10 350-359 343-352 (468) 16 TIGR00088 trmD tRNA (guanine-N 32.0 18 0.00047 15.1 0.8 16 261-276 45-60 (247) 17 PRK09104 hypothetical protein; 31.0 31 0.0008 13.6 2.1 19 8-26 5-23 (465) 18 KOG3861 consensus 30.8 32 0.00081 13.6 4.5 135 111-265 58-204 (438) 19 pfam06381 DUF1073 Protein of u 27.6 36 0.00091 13.3 19.4 257 113-417 50-320 (361) 20 KOG2133 consensus 26.8 37 0.00094 13.2 5.1 19 119-137 780-798 (1229) 21 pfam09978 consensus 26.5 37 0.00095 13.1 15.0 165 245-417 46-228 (270) 22 TIGR00422 valS valyl-tRNA synt 26.5 29 0.00074 13.9 1.0 55 131-189 281-351 (970) 23 KOG2055 consensus 25.7 39 0.00098 13.1 5.9 134 141-275 242-394 (514) 24 COG1139 Uncharacterized conser 25.5 39 0.00099 13.0 2.5 119 150-273 201-334 (459) 25 TIGR01542 A118_put_portal phag 24.4 41 0.001 12.9 9.8 382 10-462 22-451 (489) 26 TIGR01582 FDH-beta formate deh 23.6 24 0.00062 14.4 0.2 15 130-144 221-235 (293) 27 TIGR03549 conserved hypothetic 22.0 45 0.0012 12.6 4.0 24 254-277 399-426 (718) 28 PRK13031 preprotein translocas 21.8 46 0.0012 12.6 4.0 34 390-423 92-125 (149) 29 COG3830 ACT domain-containing 21.3 31 0.0008 13.6 0.3 73 329-402 10-82 (90) 30 TIGR01461 greB transcription e 20.4 49 0.0012 12.4 1.2 19 195-213 121-139 (157) No 1 >PHA00670 hypothetical protein Probab=100.00 E-value=0 Score=1044.56 Aligned_cols=517 Identities=28% Similarity=0.453 Sum_probs=485.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-----------CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEE Q ss_conf 8999999999997235669999999985042289-----------87777525427999999999987641887887601 Q gi|254781213|r 6 AKDIQDRFNYLKNQRGELNYWMEELTGFLYPYKN-----------NAQLRMWDTTGSEACIKLSSLLSSLITPPGQKWHG 74 (556) Q Consensus 6 a~~l~~r~~~l~~~R~~~e~~w~e~~~y~lP~r~-----------~~~~~i~dst~~~a~~~lAs~L~~~ltPp~~~WF~ 74 (556) .++|.+||+.||++|++||+||+|||+|++|+|+ +++.+||||||++|+++|||+|||+||||+++||+ T Consensus 3 ~~~l~kr~~~lk~~R~~we~~WqE~~dy~lP~r~~f~~~~~~~g~~r~~~i~D~Ta~~a~~~lAs~L~s~ltpp~~~WF~ 82 (540) T PHA00670 3 NSKLLKRLGQLKTERQSVESHWDEISDYIMPRRSRFFSDDRNRGENRNRKIFDSTGTDALRTLSSGMMSGITSPARPWFR 82 (540) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHC T ss_conf 78999999999987754899999999986767666777788863323355654379999999999985368999853540 Q ss_pred EEECCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEE Q ss_conf 11081144442023223348999999999999998750231473889999999987541033222167666544466058 Q gi|254781213|r 75 LAESFSAYQAFLYKEDARSKKVREWCDQVTDTLFGFRERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRY 154 (556) Q Consensus 75 l~~~~~~~~~~~~~~~~~~~ev~~~L~~v~~~i~~~~~~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf 154 (556) |...++ ++.+.++|++||++|+++||.+ |++||||.++||+|+||++|||||||+++|. .+++|| T Consensus 83 L~~~d~--------~l~~~~ev~~wL~~v~~~m~~~--~~~SNF~~~ihe~y~dL~~fGta~l~v~~d~-----~~~irf 147 (540) T PHA00670 83 LATRDP--------ELNEDAEVKAWLENVTRDMYSA--FQKSNFYLELNETYISLGGFGTAAMVVEEDE-----DEVVVF 147 (540) T ss_pred CCCCCC--------CCCCCHHHHHHHHHHHHHHHHH--HHHCCCHHHHHHHHHHHHHHCCEEEEEECCC-----CCCCEE T ss_conf 767984--------5353088999999999999999--9966609999999999874135589986478-----874026 Q ss_pred EEEEHHHEEEEECCCCCEEEEEEEECCCHHHHHHHCCCCCCCHHHHHHHCCCCCCC-EEEEEEEEECCCCCC-CCCCCCC Q ss_conf 88655446661089888715320003697786663152235725665410355571-566688853576565-5444532 Q gi|254781213|r 155 ISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSKWGDKVLSSKMKSALARNENER-FTIIHAVYPKSLTDK-KKDKGNK 232 (556) Q Consensus 155 ~~~pl~~~~i~~d~~G~vd~i~r~~~~t~~ql~~~fg~~~l~~~~~~~~~~~~~~~-~~v~~~v~pr~~~~~-~~~~~~~ 232 (556) +++|+++|||++|++|+||+|||+|+||++|++++||++++|+.+++.++++|+++ ++|+|+|+||.++++ +.+.+|| T Consensus 148 ~~~pl~~~~i~~d~~G~VDtv~Rkf~mtarqi~~~fg~~~l~~~v~~~~~~~p~~~~vev~h~V~pr~d~d~~~~d~~n~ 227 (540) T PHA00670 148 QSSPIGDYYFAEDNRGQVDTFYRQFRWTVAQMVQEFGDENTSESVQSKAEEGSNEAWVEVVHAVEPRADRDPSKLDPRNM 227 (540) T ss_pred EEEECCCEEEECCCCCCEEEEEEEEEECHHHHHHHCCCCCCCHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCCCCCCC T ss_conf 88621108983189998126899998429999987053329989998874599766058999998666666321234679 Q ss_pred CEEEEEEECC--CCEECCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCC Q ss_conf 1277654213--76451017866587455511414872102026997588999999999999999997519868932786 Q gi|254781213|r 233 GFHSKFVSVD--ENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSEA 310 (556) Q Consensus 233 ~~~sv~~~~~--~~~vl~e~g~~e~P~~~~Rw~~~~ge~YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~~ 310 (556) ||+|+|++.+ ..++++++||++|||+++||.|.+||+|||||+++||||+|+||++++.++++++++++||++||++| T Consensus 228 pf~S~y~e~~~d~~~~l~esG~~e~P~~~~R~~~~~~e~YGr~p~~~al~d~k~ln~~~~~~l~~a~~~v~pp~~vp~dg 307 (540) T PHA00670 228 PFKSVYFEKGGDEVRLLRESGYREFPALAPRWRVSGGDVYGFSPAMLALGDVRTLQREQKRKAQSIDKVINPPLMAPESG 307 (540) T ss_pred CEEEEEEEECCCCCEEEECCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC T ss_conf 75799999647762133114766586456777626987667387888706799999999999999873047987747533 Q ss_pred CCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHHHHHHCCCC--CCCCCCCHHHHHHHHHHH Q ss_conf 304310024764332458876554220001220269-99999999999997422210132--466677779999999999 Q gi|254781213|r 311 KQRNFDLKPGYMNIGALSREGRSLFQPVQFGNPLPY-HEELNRLKESIRSLFLLDLFQVL--DDKASRSAAESMEKTREK 387 (556) Q Consensus 311 ~~~~~~l~pg~~~~~~~~~~~~~~~~p~~~g~~~~~-~~~i~~~~~~I~~~f~~d~~~~~--~~~~~~TAtEv~~r~~e~ 387 (556) +++++++.||+++++..+.++...+.|++.+.+.++ ...|+++|++|+++||+|+|+++ .++++||||||++|++|| T Consensus 308 ~~~~v~l~PGgi~~~~~~~~~~~~~~p~~~~~~~~~~~~~i~~~r~~I~~af~~D~f~~l~~~~~~~mTAtEV~~R~~Ek 387 (540) T PHA00670 308 KNQDISLGPGGLTYVDDMESNGGIRKAFEVNARFDVLLADIQDTRQTINRIYYVDLFQMLANKDSPAMTATEVQERYEEK 387 (540) T ss_pred CCCCEEECCCCCEECCCCCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH T ss_conf 54731445775001367788867666310589944799999999999999999999985457887876799999999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99977888778878999999999999987399987871113565236888337999985367699999999999987542 Q gi|254781213|r 388 GAFVGPLIGGLQSEFIGAMISRELDILDSQGNLPECEGADNPPVSLLKVEYTSPLFKYQQAESVASALQGVNTVVELGVK 467 (556) Q Consensus 388 ~~~Lg~v~~rl~~E~l~Pli~r~~~il~r~g~lp~~p~~~~~~~~~~~v~y~s~La~aq~~~~~~~~~~~l~~~~~~~~~ 467 (556) +++|||+|+||++|||.|+|+|+|+||+|+|+||++|+.+.+. +++|+|+||||+|||+.+++++.|+++++++++ T Consensus 388 ~~~LGpv~~rl~~ElL~Pli~R~f~il~r~g~lP~~P~~l~g~--~i~i~yvSpLAqaQk~~~~~~i~r~~~~~~~la-- 463 (540) T PHA00670 388 LLMLGPVLERLENEFLSPLIQRTFNIMVRANKLPEPPQELQGA--DLDVEYTSPLAQAQKAIQAASIERWVGSLGQLA-- 463 (540) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCC--CEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHH-- T ss_conf 9876378887768889999999999999779999998577588--315897589999987553889999999999887-- Q ss_pred CCCHHHHHHCCHHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 27878987359899999999970998546199899999999999999999999999999999997578753231 Q gi|254781213|r 468 TGDPSCMDHMDTDRVSRFSLWATNTPAVLIRDTAEVEDIRQQREVQRRVMEEQHLQQQLQQTSQDIGAKAAGRA 541 (556) Q Consensus 468 ~~~p~~~d~~d~d~~~~~~a~~~Gvp~~~~r~~eev~~~rq~r~~~~q~~qq~~~~~~~~~~~~~~~~~~a~~~ 541 (556) +.+|+++|++|+|+++|++|+++|||++++|+++||+++|++|++|||+|||+++++++++.++++|.+-++.. T Consensus 464 q~~P~vld~~d~D~~~~~~a~~~GvP~~~ir~~~ev~~~R~~r~~~qq~~q~~~~~~~~a~~~k~l~~a~~~~~ 537 (540) T PHA00670 464 QIKPEVLDKPDWDRMADMLADMLGVPPTLIVPKEQVQSIRKQRAQQQQAAQQAAIAEAAANAAKALGKAQTSLQ 537 (540) T ss_pred CCCHHHHHHCCHHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 13918876159899999999980989465399999999999999999999999999999999998764110386 No 2 >pfam12236 Head-tail_con Bacteriophage head to tail connecting protein. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 516 and 555 amino acids in length. The head-tail connector, a dodecamer of gp10, is embedded within a unique five-fold vertex of the head. The connector serves as the site of assembly of the transient DNA packaging motor that translocates the dsDNA genome into a precursor head shell, or prohead. Probab=100.00 E-value=0 Score=867.40 Aligned_cols=465 Identities=28% Similarity=0.439 Sum_probs=430.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCC----------CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHH Q ss_conf 999997235669999999985042289----------8777752542799999999998764188788760111081144 Q gi|254781213|r 13 FNYLKNQRGELNYWMEELTGFLYPYKN----------NAQLRMWDTTGSEACIKLSSLLSSLITPPGQKWHGLAESFSAY 82 (556) Q Consensus 13 ~~~l~~~R~~~e~~w~e~~~y~lP~r~----------~~~~~i~dst~~~a~~~lAs~L~~~ltPp~~~WF~l~~~~~~~ 82 (556) |+.|+++|++|++||+||++|++|++. +++.+||||||++|+++||||||++||||++|||+|+++++.. T Consensus 1 y~~l~~~R~~~~~~w~e~a~~~lP~~~~~~~~~~~g~~~~~~i~dst~~~a~~~LAs~L~~~LtPp~~~wFrl~~~d~~~ 80 (480) T pfam12236 1 YEKLKSDRQSWESRWRECADYTLPSLDPFESDSNRGERRNTNIFDSTGARALRNLAAKLMSGLTPPGRPWFRLELRDDED 80 (480) T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCC T ss_conf 96788768779999999999857776787788887443568864028999999999999861589999855700688656 Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHE Q ss_conf 44202322334899999999999999875023147388999999998754103322216766654446605888655446 Q gi|254781213|r 83 QAFLYKEDARSKKVREWCDQVTDTLFGFRERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNV 162 (556) Q Consensus 83 ~~~~~~~~~~~~ev~~~L~~v~~~i~~~~~~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~ 162 (556) . ...+++++||++|+++|+.+ +.+||||.++||+|+||++|||+++|+++|. ++++||+++||++| T Consensus 81 ~-------~~~~ev~~~L~~ve~~~~~~--l~~Snf~~~~~e~~~dL~v~G~a~l~~~~d~-----~~~~~f~~~pl~~~ 146 (480) T pfam12236 81 N-------EAADEVKAWLDAVERRLMSV--LEASNFYVALHEAFKDLLVAGNALLYIEEDR-----KGVIRFEAVPLGSY 146 (480) T ss_pred H-------HHHHHHHHHHHHHHHHHHHH--HHHHCCHHHHHHHHHHHHHHCCEEEEEECCC-----CCCCEEEEEECCEE T ss_conf 0-------13799999999999999999--9870559999999999984185589872356-----77623799631539 Q ss_pred EEEECCCCC-EEEEEEEECCCHHHHHHHCCCCCCCHHHHHHHCC--CCCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEE Q ss_conf 661089888-7153200036977866631522357256654103--5557156668885357656554445321277654 Q gi|254781213|r 163 YMSVNHQNV-VDSVYREFTFTVDQIVSKWGDKVLSSKMKSALAR--NENERFTIIHAVYPKSLTDKKKDKGNKGFHSKFV 239 (556) Q Consensus 163 ~i~~d~~G~-vd~i~r~~~~t~~ql~~~fg~~~l~~~~~~~~~~--~~~~~~~v~~~v~pr~~~~~~~~~~~~~~~sv~~ 239 (556) ||++|++|+ ||+|||+|++|++|+.++||.+++|+.+++.+++ +++++++++|+|+|+.+ +.+|++|.|+|+ T Consensus 147 ~v~~d~~G~~vd~v~R~~~~t~~q~~~~f~~~~l~~~v~~~~~~~~~p~~~~~v~~~V~~~~d-----~~~~~~~~s~~~ 221 (480) T pfam12236 147 VVARDANGNVVDIVFRRFSLTVRQIVQRFGLDALSEEIRKALEDGEKPEDKVEIYHAVEPRAD-----DAKNMPFASYQE 221 (480) T ss_pred EEEECCCCCEEEEEEEEEECCHHHHHHHCCHHHCCHHHHHHHHCCCCCCCEEEEEEEEEECCC-----CCCCCCEEEEEE T ss_conf 999679999789999976324999998617121897788887527897865899999998467-----778996699999 Q ss_pred ECCCCE-ECCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCEEC Q ss_conf 213764-5101786658745551141487210202699758899999999999999999751986893278630431002 Q gi|254781213|r 240 SVDENR-FFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSEAKQRNFDLK 318 (556) Q Consensus 240 ~~~~~~-vl~e~g~~e~P~~~~Rw~~~~ge~YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~~~~~~~~l~ 318 (556) +.+.++ +++++||++|||+++||.+++||+|||||++++|||+|+||+++++++++++++++|||+|+++|++++.++. T Consensus 222 ~~~~~~~~l~e~g~~~~P~~~~Rw~~~~ge~YGrgp~~~~l~d~k~l~~l~~~~~~~~~~a~~p~~~v~~~~~~~~~~l~ 301 (480) T pfam12236 222 DAGKDVGVLSESGYDEFPYLVPRWEKIDGEAYGRSPVEDALPDVKSLNKLSEALLKAAAKASKPPWLVPPSGVTQPRDLV 301 (480) T ss_pred ECCCCCCEEEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCEEC T ss_conf 76885303441478878666677873799865708699986899999999999999998742685785765454741403 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 476433245887655422000122026-9999999999999974222101324666777799999999999997788877 Q gi|254781213|r 319 PGYMNIGALSREGRSLFQPVQFGNPLP-YHEELNRLKESIRSLFLLDLFQVLDDKASRSAAESMEKTREKGAFVGPLIGG 397 (556) Q Consensus 319 pg~~~~~~~~~~~~~~~~p~~~g~~~~-~~~~i~~~~~~I~~~f~~d~~~~~~~~~~~TAtEv~~r~~e~~~~Lg~v~~r 397 (556) ||+.+++..+..+...+.|++++...+ .+..|++++++|+++||+|++.+ +++++||||||++|++|++++|||+|+| T Consensus 302 ~~~~~~i~~g~~~~~~~~p~~~~~~~~~~~~~i~~~~~~I~~af~~d~~~~-~~~~~~TAtEV~~r~~E~~~~LGpv~~r 380 (480) T pfam12236 302 PGGTGYVVTGVAGDIGIKPLEKYADFQVAQAVIQDIRQRIREAFMVDLFQM-RDAERVTATEVRERAEEKEQLLGPVYSR 380 (480) T ss_pred CCCCCEEEECCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 578844742687776500055678744999999999999999998753147-7888777999999999999876078899 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHC Q ss_conf 88789999999999999873999878711135652368883379999853676999999999999875422787898735 Q gi|254781213|r 398 LQSEFIGAMISRELDILDSQGNLPECEGADNPPVSLLKVEYTSPLFKYQQAESVASALQGVNTVVELGVKTGDPSCMDHM 477 (556) Q Consensus 398 l~~E~l~Pli~r~~~il~r~g~lp~~p~~~~~~~~~~~v~y~s~La~aq~~~~~~~~~~~l~~~~~~~~~~~~p~~~d~~ 477 (556) |++|||.|+|+|+|++|+|+|+||++|+++ + .+++|+|+|||+++||+.+++++.++++++++++ +.+|+++|++ T Consensus 381 l~~E~l~Pli~r~~~il~r~g~lp~~p~~~-g--~~v~i~~~s~La~aqr~~~~~~i~~~~~~~~~l~--~~~p~~~d~i 455 (480) T pfam12236 381 LQEEFLSPLIERTFNILQRAGMLPPPPDEL-G--VAVKVEYVTGLAAAQRAIDLASLERFLQAIGQLA--QLKPEVLDKI 455 (480) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCHHH-C--CCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHC T ss_conf 999999999999999999779999992460-8--8532899639999763556999999999999871--7996898736 Q ss_pred CHHHHHHHHHHHCCCCHHHCCCHHH Q ss_conf 9899999999970998546199899 Q gi|254781213|r 478 DTDRVSRFSLWATNTPAVLIRDTAE 502 (556) Q Consensus 478 d~d~~~~~~a~~~Gvp~~~~r~~ee 502 (556) |+|++++++|+++|+|++++|++|| T Consensus 456 d~d~~~~~~a~~~Gvp~~l~rs~ee 480 (480) T pfam12236 456 DWDEAVDRLADALGVPAGLLRSEEE 480 (480) T ss_pred CHHHHHHHHHHHCCCCHHHCCCCCC T ss_conf 9999999999980988423089899 No 3 >pfam05133 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction. This family also includes family Phage_min_cap, pfam05126. Probab=97.28 E-value=0.015 Score=35.17 Aligned_cols=265 Identities=13% Similarity=0.005 Sum_probs=132.7 Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECC--CCCEEEEEEEECCCHHHHHHHC Q ss_conf 23147388999999998754103322216766654446605888655446661089--8887153200036977866631 Q gi|254781213|r 113 RSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNH--QNVVDSVYREFTFTVDQIVSKW 190 (556) Q Consensus 113 ~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~--~G~vd~i~r~~~~t~~ql~~~f 190 (556) +...+|.....++.+++.++|.+.+++..+.+ +.+++..+++.++++--|. .+.+..++|.+...-.. T Consensus 87 ~~~n~~~~~~~~~~~~a~~~G~ay~~~y~d~d-----g~~~~~~~~p~~~~~i~d~~~~~~~~~~vr~~~~~~~~----- 156 (435) T pfam05133 87 LDANDFDDKLSELHKDALIYGRAYELVYIDED-----GEPRIRVVSPEQAFPIYDDTIDRELAAAVRYYTDKDGD----- 156 (435) T ss_pred HHHCCHHHHHHHHHHHHHHCCCEEEEEEECCC-----CCEEEEEECCCEEEEEEECCCCCCEEEEEEEEEEECCC----- T ss_conf 97267877999999999861757999998899-----97899998768489999789887635999999973684----- Q ss_pred CCCCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCC-EECCCCCCCCCCEEEEEEEECCCCC Q ss_conf 522357256654103555715666888535765655444532127765421376-4510178665874555114148721 Q gi|254781213|r 191 GDKVLSSKMKSALARNENERFTIIHAVYPKSLTDKKKDKGNKGFHSKFVSVDEN-RFFEEKQIATFPYIVGRYRVRADEI 269 (556) Q Consensus 191 g~~~l~~~~~~~~~~~~~~~~~v~~~v~pr~~~~~~~~~~~~~~~sv~~~~~~~-~vl~e~g~~e~P~~~~Rw~~~~ge~ 269 (556) ... . ..-+....+++.+.... .+..+.+.. .....-+|...|++.++-. ..+. T Consensus 157 -------~~~-~--~e~y~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~g~vPvv~f~Nn--~~~~ 210 (435) T pfam05133 157 -------KTG-Y--YELYTDDEVYTYVREGG--------------GDLIEVDVIGERIPPHEFGRVPVVEFNNN--DLRS 210 (435) T ss_pred -------EEE-E--EEEEECCEEEEEEECCC--------------CCCCCCCCCCCCCCCCCCCCCCEEEECCC--CCCC T ss_conf -------589-9--99996898999994798--------------64112453345666688885265986258--5445 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCC--C-EECCCCCCCCCCCCCCCCCCCCCC-CCCHHH Q ss_conf 020269975889999999999999999975198689327863043--1-002476433245887655422000-122026 Q gi|254781213|r 270 YGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSEAKQRN--F-DLKPGYMNIGALSREGRSLFQPVQ-FGNPLP 345 (556) Q Consensus 270 YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~~~~~~--~-~l~pg~~~~~~~~~~~~~~~~p~~-~g~~~~ 345 (556) .|.|-.+...+-+..+|.+.-....-.....++.+.+...+.... . .+...+......+.+.......+. ..+... T Consensus 211 ~G~sd~e~v~~liDa~d~~~s~~~n~~~~~~~~~lv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~~~~~~~ 290 (435) T pfam05133 211 PGLSDLEPVKSLIDAYDKTLSEFANDFYDFPRAILVLKGYGEDDDEFVKDLKDAKLIRLLDGAEDDGDAKFLTKQFPVAS 290 (435) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCHHHHHHHHCCCEECCCCCCCCCCEEEEECCCCHHH T ss_conf 68651777699999999998387788987420037741777665156787775143011366678997048805688689 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999997422210132466677779999999999999778887788789999999999999 Q gi|254781213|r 346 YHEELNRLKESIRSLFLLDLFQVLDDKASRSAAESMEKTREKGAFVGPLIGGLQSEFIGAMISRELDIL 414 (556) Q Consensus 346 ~~~~i~~~~~~I~~~f~~d~~~~~~~~~~~TAtEv~~r~~e~~~~Lg~v~~rl~~E~l~Pli~r~~~il 414 (556) ....++.++..|........+..-.-+.+-|+..+......+.+.- ....+.-.+.|.-++.-++.++ T Consensus 291 ~e~~~~~l~~~i~~~s~~~~~~~~~f~~n~Sg~Alk~~~~~l~~ka-~~~e~~f~~~l~~~~~li~~~~ 358 (435) T pfam05133 291 LENYLDALKQDIYEFAMVPDLPDEYFGGNASGEALKAKYSLLDLKA-ERKERKFGEALRRLLRLALEIL 358 (435) T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999983889999466088740999999998999999-9999999999999999999986 No 4 >pfam05126 consensus Probab=95.46 E-value=0.19 Score=28.00 Aligned_cols=335 Identities=11% Similarity=0.072 Sum_probs=161.3 Q ss_pred HHHHHHHHHHCC------CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHCCCCCCCHHHHH Q ss_conf 999999998504------22898777752542799999999998764188788760111081144442023223348999 Q gi|254781213|r 24 NYWMEELTGFLY------PYKNNAQLRMWDTTGSEACIKLSSLLSSLITPPGQKWHGLAESFSAYQAFLYKEDARSKKVR 97 (556) Q Consensus 24 e~~w~e~~~y~l------P~r~~~~~~i~dst~~~a~~~lAs~L~~~ltPp~~~WF~l~~~~~~~~~~~~~~~~~~~ev~ 97 (556) ...|+.+|.=-+ ...+...+|-+.|.+. ..+.|+.|-+.+|.-. ..+.+++ .+.. T Consensus 28 I~~~~~~Y~~~~~~~~y~~~~g~~~~r~~~sl~~--ak~~s~~~A~LvfnE~---~~I~v~d--------------~~~~ 88 (473) T pfam05126 28 IDTDKRYYQDDYAEVHYLNSDGNTKKRRLNSMNL--AKTAAKKIASLVFNEK---AEINVDD--------------KAAN 88 (473) T ss_pred HHHHHHHHCCCCCCEEEEECCCCEEEEHHHCCCH--HHHHHHHHHHHHHHCC---CEEECCC--------------HHHH T ss_conf 9999998527875126763168502300312771--3789999999886401---1476585--------------7899 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECCCCCEEEEEE Q ss_conf 99999999999875023147388999999998754103322216766654446605888655446661089888715320 Q gi|254781213|r 98 EWCDQVTDTLFGFRERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVYR 177 (556) Q Consensus 98 ~~L~~v~~~i~~~~~~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~~G~vd~i~r 177 (556) +||.+ + +..++|+..+.+.+...++.|+.++...-| .+.++..-+.-..|+=.....+.|.++.. T Consensus 89 ~~l~~-------~--l~~n~F~~~~~~~lE~~~AlGg~a~kpYvd------~~~I~v~~v~Ad~f~Pl~~nt~~v~e~~~ 153 (473) T pfam05126 89 EFLLD-------V--LKTNDFTKNFERYLEYGEALGGFAMRPYVD------GNKVKVAFATADQFYPLQSDTNDVSEAAI 153 (473) T ss_pred HHHHH-------H--HHCCCHHHHHHHHHHHHHHHCCEEEEEEEC------CCEEEEEEEECCCEEEEEECCCCCEEEEE T ss_conf 99999-------8--741218899999999987526658999984------99389999713725730345888468999 Q ss_pred EECCCHHHHHHHCCCCCCCHHHHHHHCCCCCCC--------------EEEEEEEEECCCCCCCCCCCCCCEEEEEEECCC Q ss_conf 003697786663152235725665410355571--------------566688853576565544453212776542137 Q gi|254781213|r 178 EFTFTVDQIVSKWGDKVLSSKMKSALARNENER--------------FTIIHAVYPKSLTDKKKDKGNKGFHSKFVSVDE 243 (556) Q Consensus 178 ~~~~t~~ql~~~fg~~~l~~~~~~~~~~~~~~~--------------~~v~~~v~pr~~~~~~~~~~~~~~~sv~~~~~~ 243 (556) ....+ ..+++.+.+ .+|-+-.|.-.+. ......-|...+|.+... T Consensus 154 ~~~~~-------------------~~~~~~~~yYT~LE~H~~~~~~~Y~I~N~lY~s~~~--~~lG~~v~L~~~~~dL~~ 212 (473) T pfam05126 154 ASRTT-------------------ETENKNTKYYTLLEFHEWQDHDDYVITNELYRSDDP--NEVGTKVPLSEVYKDLEP 212 (473) T ss_pred EEEEE-------------------EEECCCCEEEEEEEEEEECCCCEEEEEEEEEECCCC--HHCCCCCCCCHHHCCCCC T ss_conf 97778-------------------850688458999999994268728998888863893--102854236300025571 Q ss_pred CEECCCCCCCCCC-EEEEEEEEC-CCCCCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCCEEECCCCC------- Q ss_conf 6451017866587-455511414-8721020269975889999999999999---999975198689327863------- Q gi|254781213|r 244 NRFFEEKQIATFP-YIVGRYRVR-ADEIYGRSPAMEALPTIRRLNETVNELA---QFGRLSLHPPTIAVSEAK------- 311 (556) Q Consensus 244 ~~vl~e~g~~e~P-~~~~Rw~~~-~ge~YGrgp~~~aL~D~k~Ln~l~~~~l---~~~~~~~~p~~~v~~~~~------- 311 (556) ...+..-.-+-|- |-++.-+.. .++.+|.|....|++.++.||...-... +.+.+.+. ||++.+ T Consensus 213 ~v~i~g~~rPlFaY~K~p~aNnid~~SPlGvSvyanA~~~lk~iD~~yd~~~wE~e~g~~rI~----V~~s~lk~~~~~~ 288 (473) T pfam05126 213 QVKITDLTRPLFAYIKTPGANNKNITSPLGLSVYDNAKTTLDTINLTHDQFYWEVKLGQKRVA----VPSSFLKTAVRLD 288 (473) T ss_pred CEEECCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEE----CCHHHHHCCCCCC T ss_conf 225658886625887487677677899985043750798999999998999999764507898----2899960377888 Q ss_pred --CCCCEECCCCCCCCCCCCCCC--CCCCCCCCC-CHHHHHHHHHHHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHH Q ss_conf --043100247643324588765--542200012-2026999999999999997--422210132466677779999999 Q gi|254781213|r 312 --QRNFDLKPGYMNIGALSREGR--SLFQPVQFG-NPLPYHEELNRLKESIRSL--FLLDLFQVLDDKASRSAAESMEKT 384 (556) Q Consensus 312 --~~~~~l~pg~~~~~~~~~~~~--~~~~p~~~g-~~~~~~~~i~~~~~~I~~~--f~~d~~~~~~~~~~~TAtEv~~r~ 384 (556) ..|. ..+.-.-|....++.. ..++.+.+- ....+...|+.+=..|... |-...|. ..+..-.|||||.--. T Consensus 289 g~~~p~-fd~~~~vy~~~~~~~~~~~~i~d~~~~iR~~~~~~~in~~L~~ie~~~Gls~Gtfs-~d~~g~KTATEI~S~n 366 (473) T pfam05126 289 GSHTPY-FDSDQNVYFLMQGDDDNGKAIKDITTPIRSTDYIEAINAFLREFEMQIGLSAGTFT-FDENGLKTATEVVSEN 366 (473) T ss_pred CCCCCC-CCCCCCCEEECCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCEEEEEEEECC T ss_conf 884777-78641110112567877877346564200799999999999999987383666024-6887632235675053 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 999999778887788789999999999999873999 Q gi|254781213|r 385 REKGAFVGPLIGGLQSEFIGAMISRELDILDSQGNL 420 (556) Q Consensus 385 ~e~~~~Lg~v~~rl~~E~l~Pli~r~~~il~r~g~l 420 (556) ++..+........++. .|.-||-..+.+..--+.+ T Consensus 367 s~ty~t~~~~~~~le~-aL~~Lv~ai~ela~~~~l~ 401 (473) T pfam05126 367 SETYQTRNSYSTLVEQ-GIKELIVSILELAKAIELY 401 (473) T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHC T ss_conf 0777989999999999-9999999999998665432 No 5 >PHA00670 hypothetical protein Probab=95.05 E-value=0.11 Score=29.45 Aligned_cols=25 Identities=8% Similarity=0.065 Sum_probs=8.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999 Q gi|254781213|r 503 VEDIRQQREVQRRVMEEQHLQQQLQ 527 (556) Q Consensus 503 v~~~rq~r~~~~q~~qq~~~~~~~~ 527 (556) +.+.|++.||+||++++++++.+++ T Consensus 502 ~R~~r~~~qq~~q~~~~~~~~a~~~ 526 (540) T PHA00670 502 IRKQRAQQQQAAQQAAIAEAAANAA 526 (540) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999 No 6 >pfam07360 consensus Probab=80.73 E-value=3.8 Score=19.60 Aligned_cols=158 Identities=13% Similarity=0.114 Sum_probs=99.1 Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECCC-CCEEEEEEEECCCHHHHHHHCC Q ss_conf 231473889999999987541033222167666544466058886554466610898-8871532000369778666315 Q gi|254781213|r 113 RSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQ-NVVDSVYREFTFTVDQIVSKWG 191 (556) Q Consensus 113 ~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~~-G~vd~i~r~~~~t~~ql~~~fg 191 (556) +.++|+....+++..+-.++|++-+.|.+..+ ..+.+++++.+..+.+..-|+. |++..-++... T Consensus 75 w~aN~ld~~~~~a~~~Al~~g~sfv~V~~g~d---~~g~p~i~~~sp~~~~a~~Dp~t~~~~~al~~~~----------- 140 (412) T pfam07360 75 WDANNLDIEFDTAITSALIHGCSFVIISKGED---DPDEPLIQVESASQATGEIDPRTRRLTEALRVLE----------- 140 (412) T ss_pred HHHCCCCHHHHHHHHHHHHHCCEEEEECCCCC---CCCCEEEEEECHHHCEEEECCCCCCHHHCEEEEE----------- T ss_conf 87307013407999999985862799816988---9994179986721342646788774412037778----------- Q ss_pred CCCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEECCCCCCCCCCEEEEEEEECCCCCCC Q ss_conf 22357256654103555715666888535765655444532127765421376451017866587455511414872102 Q gi|254781213|r 192 DKVLSSKMKSALARNENERFTIIHAVYPKSLTDKKKDKGNKGFHSKFVSVDENRFFEEKQIATFPYIVGRYRVRADEIYG 271 (556) Q Consensus 192 ~~~l~~~~~~~~~~~~~~~~~v~~~v~pr~~~~~~~~~~~~~~~sv~~~~~~~~vl~e~g~~e~P~~~~Rw~~~~ge~YG 271 (556) .+.+.+.+......|........+.. .+++... ..+-+....|.+++.....-+..+| T Consensus 141 -------------~d~~~~~~~~~ly~p~~t~~~~~~~~-----~~~~~~~----~~~h~lG~~pvVp~~n~~~l~rp~G 198 (412) T pfam07360 141 -------------RDEGNEVTLAALYLPDETVTYPRDEN-----GWQVDVP----YIAHGLGVPPVVPIPNRPRLVRPFG 198 (412) T ss_pred -------------ECCCCCEEEEEEECCCCEEEEEECCC-----CEEEECC----CCCCCCCCCCEEEECCCCCCCCCCC T ss_conf -------------53789578999984895899993598-----3266336----7788999874598136766689988 Q ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 02699-758899999999999999999751986893 Q gi|254781213|r 272 RSPAM-EALPTIRRLNETVNELAQFGRLSLHPPTIA 306 (556) Q Consensus 272 rgp~~-~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v 306 (556) +|--. ..++-+-.++.....+.-+++..+-|-..+ T Consensus 199 ~SeIt~~vm~ltD~a~rtl~~m~vaaef~s~PqR~i 234 (412) T pfam07360 199 TSRITRDLMSLQDAAARTLERMQVTAEFYSFPQRYL 234 (412) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE T ss_conf 522457789999999999998999888631513567 No 7 >TIGR02824 quinone_pig3 putative NAD(P)H quinone oxidoreductase, PIG3 family; InterPro: IPR014189 Members of this family are putative quinone oxidoreductases that belong to the broader superfamily of zinc-dependent alcohol (of medium chain length) dehydrogenases and quinone oxidoreductases. An alignment shows no motif of conserved Cys residues as are found in zinc-binding members of the superfamily, consequently members of this entry are likely to be quinone oxidoreductases. A member of this family in Homo sapiens (Human), PIG3, is induced by p53 but is otherwise uncharacterised.. Probab=70.85 E-value=2.9 Score=20.30 Aligned_cols=14 Identities=21% Similarity=0.105 Sum_probs=5.2 Q ss_pred CH-HHHHHHHHHHHH Q ss_conf 77-999999999999 Q gi|254781213|r 376 SA-AESMEKTREKGA 389 (556) Q Consensus 376 TA-tEv~~r~~e~~~ 389 (556) |. .|=+...+++.+ T Consensus 276 ~~G~~KA~Ia~~l~~ 290 (334) T TIGR02824 276 PVGAEKAAIAAELRE 290 (334) T ss_pred CHHHHHHHHHHHHHH T ss_conf 835899999999888 No 8 >pfam04860 Phage_portal Phage portal protein. Bacteriophage portal proteins form a dodecamer and is located at a five-fold vertex of the viral capsid. The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during infection. The portal protein is though to rotate during DNA packaging. Portal proteins from different phage show little sequence homology, so this family does not represent all portal proteins. Probab=68.13 E-value=7.8 Score=17.55 Aligned_cols=101 Identities=21% Similarity=0.193 Sum_probs=60.7 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCE----------ECCCCCCCC--CCCCCCC Q ss_conf 4872102026997588999999999999999997519868932786304310----------024764332--4588765 Q gi|254781213|r 265 RADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSEAKQRNFD----------LKPGYMNIG--ALSREGR 332 (556) Q Consensus 265 ~~ge~YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~~~~~~~~----------l~pg~~~~~--~~~~~~~ 332 (556) ..+..||.||..-++..+..-+...+.......-...|...+..++.+.+.. ..-|..+.+ ..-.++ T Consensus 145 ~~~~~~G~sp~~~~~~~i~~~~~~~~~~~~~~~ng~~~~gil~~~~~l~~e~~~~~~~~~~~~~~g~~n~g~~~vl~~g- 223 (348) T pfam04860 145 SLDGIYGLSPLEAARESIGLALAAEEFARRFFKNGARPSGVLKYPGKLSEEQRERLREALEKQYKGAGNAGRPLVLEGG- 223 (348) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCEECCCC- T ss_conf 8877654488999999999999999999999854887556998289799899999999999985584346872103899- Q ss_pred CCCCCCCCCCHHHHH--HHHHHHHHHHHHHHHHHHCC Q ss_conf 542200012202699--99999999999974222101 Q gi|254781213|r 333 SLFQPVQFGNPLPYH--EELNRLKESIRSLFLLDLFQ 367 (556) Q Consensus 333 ~~~~p~~~g~~~~~~--~~i~~~~~~I~~~f~~d~~~ 367 (556) -.++|+.. ++.+.+ .........|-++|.+.... T Consensus 224 ~~~~~l~~-~~~d~q~~e~~~~~~~~Ia~~fgVPp~l 259 (348) T pfam04860 224 LDYTPLSL-SPADAQFLESRKFTREDIARAFGVPPHL 259 (348) T ss_pred CCEEECCC-CHHHHHHHHHHHHHHHHHHHHHCCCHHH T ss_conf 75356678-8235789999999999999997979999 No 9 >PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional Probab=66.27 E-value=8.5 Score=17.32 Aligned_cols=16 Identities=0% Similarity=0.046 Sum_probs=7.8 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 4899999999999999 Q gi|254781213|r 93 SKKVREWCDQVTDTLF 108 (556) Q Consensus 93 ~~ev~~~L~~v~~~i~ 108 (556) +.+++..|...+..+. T Consensus 95 deEi~~~l~~~~~~~~ 110 (270) T PRK10902 95 DQEIEQTLQAFEARVK 110 (270) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999999999 No 10 >TIGR00042 TIGR00042 non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family; InterPro: IPR002637 This family contains the Saccharomyces cerevisiae HAM1 protein P47119 from SWISSPROT and other hypothetical archaeal, bacterial and Caenorhabditis elegans proteins. Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine (HAP) which can be a natural product of monooxygenase activity on adenine. HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions .; GO: 0016787 hydrolase activity. Probab=38.23 E-value=24 Score=14.39 Aligned_cols=38 Identities=21% Similarity=0.196 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHHHHHHCC--CCEEECCCCCC-CCCEECCCC Q ss_conf 999999999999997519--86893278630-431002476 Q gi|254781213|r 284 RLNETVNELAQFGRLSLH--PPTIAVSEAKQ-RNFDLKPGY 321 (556) Q Consensus 284 ~Ln~l~~~~l~~~~~~~~--p~~~v~~~~~~-~~~~l~pg~ 321 (556) +|+....+.++.+..+++ -|..|.|+|.. ..++..||. T Consensus 46 Tf~EnA~lkA~~~~~~~~~~~~vi~eDSGL~v~aL~G~PG~ 86 (205) T TIGR00042 46 TFEENALLKAKAAAKILNKGKPVIAEDSGLFVDALNGAPGI 86 (205) T ss_pred CHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEECCCCCCC T ss_conf 68999989799999998179809998452000002799896 No 11 >KOG1819 consensus Probab=38.01 E-value=24 Score=14.36 Aligned_cols=22 Identities=27% Similarity=0.341 Sum_probs=10.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999 Q gi|254781213|r 504 EDIRQQREVQRRVMEEQHLQQQ 525 (556) Q Consensus 504 ~~~rq~r~~~~q~~qq~~~~~~ 525 (556) +++||-.|||||++-|.|++.| T Consensus 814 aqlrqleqqqqqqqlqiqlqrq 835 (990) T KOG1819 814 AQLRQLEQQQQQQQLQIQLQRQ 835 (990) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 8888889988888889999876 No 12 >KOG0400 consensus Probab=36.09 E-value=26 Score=14.17 Aligned_cols=21 Identities=33% Similarity=0.343 Sum_probs=18.1 Q ss_pred HHHHHHHHHCCCCCCCCHHHC Q ss_conf 999999987399987871113 Q gi|254781213|r 408 SRELDILDSQGNLPECEGADN 428 (556) Q Consensus 408 ~r~~~il~r~g~lp~~p~~~~ 428 (556) +..+.||.++|+-|++|+++. T Consensus 69 ~kI~Rilk~~Gl~PeiPeDLy 89 (151) T KOG0400 69 NKILRILKSNGLAPEIPEDLY 89 (151) T ss_pred HHHHHHHHHCCCCCCCCHHHH T ss_conf 699999997699889938899 No 13 >pfam07888 CALCOCO1 Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region. Probab=35.18 E-value=27 Score=14.08 Aligned_cols=102 Identities=13% Similarity=0.185 Sum_probs=47.9 Q ss_pred CCCEEEEEEEHHHEEEEECCCCCEEEEEEEE---CCCHHHHHHHCCCCCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCC Q ss_conf 4660588865544666108988871532000---3697786663152235725665410355571566688853576565 Q gi|254781213|r 149 EEGIRYISVPLSNVYMSVNHQNVVDSVYREF---TFTVDQIVSKWGDKVLSSKMKSALARNENERFTIIHAVYPKSLTDK 225 (556) Q Consensus 149 ~~~~rf~~~pl~~~~i~~d~~G~vd~i~r~~---~~t~~ql~~~fg~~~l~~~~~~~~~~~~~~~~~v~~~v~pr~~~~~ 225 (556) ..++.|.++ +..|+ |+-.|+..|.-- +.+.++=+.-|. + .=....++++++|+..|-.+.++ T Consensus 4 ~~~V~FqNV--aksYl---Pna~vECHYTLt~~i~ph~kDWVGIFK---V-------GWSsvRDY~TFlWa~~PE~y~eG 68 (546) T pfam07888 4 KRGVHFLNV--AVTYF---PNTKVECHYTIPSGHDWSSRDWIGIFK---V-------GWLTVRDYYTFVWALAPEGYQKG 68 (546) T ss_pred CCCCEEEEE--EHHCC---CCCCCEEEEECCCCCCCCCCCCEEEEE---C-------CCCCHHHHHHHHCCCCCCCCCCC T ss_conf 666125632--32117---897404655258878679876157763---2-------54311235541003587555667 Q ss_pred CCCCCCCCEEEEEEECCCCEECCCCCCCCCCEEEEEEEECCCCCCCHHHHH Q ss_conf 544453212776542137645101786658745551141487210202699 Q gi|254781213|r 226 KKDKGNKGFHSKFVSVDENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAM 276 (556) Q Consensus 226 ~~~~~~~~~~sv~~~~~~~~vl~e~g~~e~P~~~~Rw~~~~ge~YGrgp~~ 276 (556) -..+ ++|.+. +--+...+ .-+.-+||...-|++.|+|... T Consensus 69 S~vn-----C~v~FQ--a~YLP~~~----~e~YQF~YV~~kGeV~g~StpF 108 (546) T pfam07888 69 SDAH-----CSVQFQ--ASYLPIPG----VQEYQFRYVDGRGDVCGISSQF 108 (546) T ss_pred CCCC-----EEEEEE--ECCCCCCC----CCCEEEEEECCCCCEECCCCCC T ss_conf 7655-----368741--01158986----2002578862456420456764 No 14 >KOG3982 consensus Probab=35.13 E-value=26 Score=14.18 Aligned_cols=21 Identities=14% Similarity=0.320 Sum_probs=11.6 Q ss_pred CEEEEEEEHHHEEEEECCCCCEEEEE Q ss_conf 60588865544666108988871532 Q gi|254781213|r 151 GIRYISVPLSNVYMSVNHQNVVDSVY 176 (556) Q Consensus 151 ~~rf~~~pl~~~~i~~d~~G~vd~i~ 176 (556) ++-|+++-|+++ ++|.+.+|. T Consensus 136 p~aFkVvaLgdV-----pDgT~Vti~ 156 (475) T KOG3982 136 PVAFKVVALGDV-----PDGTLVTIM 156 (475) T ss_pred CCEEEEEEECCC-----CCCCEEEEE T ss_conf 522699971366-----888679998 No 15 >PRK07079 hypothetical protein; Provisional Probab=33.00 E-value=29 Score=13.85 Aligned_cols=10 Identities=10% Similarity=0.441 Sum_probs=3.6 Q ss_pred HHHHHHHHHH Q ss_conf 9999999999 Q gi|254781213|r 350 LNRLKESIRS 359 (556) Q Consensus 350 i~~~~~~I~~ 359 (556) .+.++.-++. T Consensus 343 ~~~l~~hL~~ 352 (468) T PRK07079 343 IAHLRAHLDA 352 (468) T ss_pred HHHHHHHHHH T ss_conf 9999999985 No 16 >TIGR00088 trmD tRNA (guanine-N1)-methyltransferase; InterPro: IPR002649 In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine-N1-)-methyltransferase 2.1.1.31 from EC is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. It catalyses the reaction:S-adenosyl-L-methionine + tRNA -> S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine methylating guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame . The mechanism of the trmD3-induced frameshift involving mutant tRNA(Pro) and tRNA(Leu) species has been investigated . It has been suggested that the conformation of the anticodon loop may be a major determining element for the formation of m1G37 in vivo . ; GO: 0003723 RNA binding, 0008175 tRNA methyltransferase activity, 0008033 tRNA processing. Probab=32.03 E-value=18 Score=15.14 Aligned_cols=16 Identities=25% Similarity=0.466 Sum_probs=8.2 Q ss_pred EEEECCCCCCCHHHHH Q ss_conf 1141487210202699 Q gi|254781213|r 261 RYRVRADEIYGRSPAM 276 (556) Q Consensus 261 Rw~~~~ge~YGrgp~~ 276 (556) ++.++|...||=|+|| T Consensus 45 KH~tvDD~pYGGG~GM 60 (247) T TIGR00088 45 KHKTVDDRPYGGGAGM 60 (247) T ss_pred CCCCCCCCCCCCCCCC T ss_conf 3452567533789765 No 17 >PRK09104 hypothetical protein; Validated Probab=31.03 E-value=31 Score=13.64 Aligned_cols=19 Identities=5% Similarity=0.001 Sum_probs=7.7 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999723566999 Q gi|254781213|r 8 DIQDRFNYLKNQRGELNYW 26 (556) Q Consensus 8 ~l~~r~~~l~~~R~~~e~~ 26 (556) +|.+-|+.+...++.+... T Consensus 5 ~~~~v~~~i~~~~~~~~~~ 23 (465) T PRK09104 5 DLDPVLDHIDANLDASLER 23 (465) T ss_pred HHHHHHHHHHHCHHHHHHH T ss_conf 8999999999688999999 No 18 >KOG3861 consensus Probab=30.78 E-value=32 Score=13.62 Aligned_cols=135 Identities=15% Similarity=0.158 Sum_probs=75.7 Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECCCCCEEEEEEEECCCHHHHHHHC Q ss_conf 50231473889999999987541033222167666544466058886554466610898887153200036977866631 Q gi|254781213|r 111 RERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSKW 190 (556) Q Consensus 111 ~~~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~~G~vd~i~r~~~~t~~ql~~~f 190 (556) ..-++..|-..=+|++++-+-.|..++.+.-++++++..+-++ +-+.+|=|-.+.+-.|-.+|.++...-+.++. T Consensus 58 ~agP~~~Ft~~Efevlkkyve~GGsl~vllGEGGE~rf~tnvN---f~le~YGI~vN~DtVvR~vy~KyFhPKEalV~-- 132 (438) T KOG3861 58 LAGPQDRFTEDEFEVLKKYVEVGGSLVVLLGEGGEPRFNTNVN---FFLEQYGIYVNGDTVVRPVYYKYFHPKEALVG-- 132 (438) T ss_pred ECCCCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCHH---HHHHHHCEEECCCCEEEHHHHHCCCHHHHHHC-- T ss_conf 5386123543489999999862882899965888743235499---99998476854870563105541686886542-- Q ss_pred CCCCCCHHHHHHHCCCCC--------CCEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEECCCCCCCCC----CEE Q ss_conf 522357256654103555--------71566688853576565544453212776542137645101786658----745 Q gi|254781213|r 191 GDKVLSSKMKSALARNEN--------ERFTIIHAVYPKSLTDKKKDKGNKGFHSKFVSVDENRFFEEKQIATF----PYI 258 (556) Q Consensus 191 g~~~l~~~~~~~~~~~~~--------~~~~v~~~v~pr~~~~~~~~~~~~~~~sv~~~~~~~~vl~e~g~~e~----P~~ 258 (556) ...+...+-.++.+..- +.---+|-+||- .+..-......++-.+|.-.| |.+ T Consensus 133 -~GVvnr~i~raa~K~v~~~v~~~~~~n~qal~F~YPy--------------GaTL~V~~panvvLstGsv~fP~nRP~~ 197 (438) T KOG3861 133 -GGVVNRSIWRAALKLVIEKVYYDFSDNKQALHFQYPY--------------GATLNVSEPANVVLSTGSVVFPFNRPLV 197 (438) T ss_pred -CCEEEHHHHHHHHHHHHHHHHHHCCCCHHEEEEECCC--------------CCEEECCCCCEEEECCCCEECCCCCCCE T ss_conf -5652099999987666888776316651038996466--------------7556526610068534855325787311 Q ss_pred EEEEEEC Q ss_conf 5511414 Q gi|254781213|r 259 VGRYRVR 265 (556) Q Consensus 259 ~~Rw~~~ 265 (556) .+--++. T Consensus 198 af~~~kN 204 (438) T KOG3861 198 AFFTNKN 204 (438) T ss_pred EEEECCC T ss_conf 0011467 No 19 >pfam06381 DUF1073 Protein of unknown function (DUF1073). This family consists of several hypothetical bacterial proteins. The function of this family is unknown. Probab=27.60 E-value=36 Score=13.27 Aligned_cols=257 Identities=13% Similarity=0.094 Sum_probs=119.4 Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECCCCCEEEEEEEECCCHHHHHHHCCC Q ss_conf 23147388999999998754103322216766654446605888655446661089888715320003697786663152 Q gi|254781213|r 113 RSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSKWGD 192 (556) Q Consensus 113 ~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~~G~vd~i~r~~~~t~~ql~~~fg~ 192 (556) ..+-+....+.++++.--.||-|.+++....+......+++...+..+.+-- ..++.+..+++.... -. T Consensus 50 ~~~l~v~~~l~eal~~~RlyGga~i~i~v~~d~~~l~~Pl~~~~i~~g~~~~--------l~v~d~~~i~p~~~~---~~ 118 (361) T pfam06381 50 EERLNVKEALLDAIIWARLYGGAAIVIKVKSDGQDLSQPLNPETVGKGGFKG--------LNVLDRWWVTPGLYI---ES 118 (361) T ss_pred HHHHCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCEEE--------EEEECCEECCCCCCC---CC T ss_conf 9972679999999998403685489998557874313698801258787226--------997333012565322---46 Q ss_pred CCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCEECCCCCCCCCCEEEEEEEECCCCCCCH Q ss_conf 23572566541035557156668885357656554445321277654213764510178665874555114148721020 Q gi|254781213|r 193 KVLSSKMKSALARNENERFTIIHAVYPKSLTDKKKDKGNKGFHSKFVSVDENRFFEEKQIATFPYIVGRYRVRADEIYGR 272 (556) Q Consensus 193 ~~l~~~~~~~~~~~~~~~~~v~~~v~pr~~~~~~~~~~~~~~~sv~~~~~~~~vl~e~g~~e~P~~~~Rw~~~~ge~YGr 272 (556) +..++ ....| +.+ -|.... .. .-+| -.+++...+ ..|+ ++..+....-||. T Consensus 119 dp~sp-----~~g~P----~~y-~i~~~~-------~~----~~iH----~SRli~~~~--~~p~--~~~~~~~~~~wG~ 169 (361) T pfam06381 119 DPFSP-----DFGEP----ETY-RITTAL-------SG----QKIH----KSRLIIFGI--YLPV--EDILKPAYNFWGD 169 (361) T ss_pred CCCCC-----CCCCC----EEE-EEECCC-------CC----EEEE----CCCEEEECC--CCCH--HHHHCCCCCCCCH T ss_conf 87763-----47997----268-884488-------84----6982----472898348--8862--8885424476666 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCC------C----CCCCCEECCC-CCCCCCCCCCCCCCCCCCCCC Q ss_conf 2699758899999999999999999751986893278------6----3043100247-643324588765542200012 Q gi|254781213|r 273 SPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSE------A----KQRNFDLKPG-YMNIGALSREGRSLFQPVQFG 341 (556) Q Consensus 273 gp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~------~----~~~~~~l~pg-~~~~~~~~~~~~~~~~p~~~g 341 (556) |....++..++.-.........-...+.-..+.++.- + +...+.+.-. ..+++...-+..+.+...++ T Consensus 170 Svlq~~~d~l~~~~~t~~~~~~ll~~~~~~v~k~~~l~~~~~~~~~~~l~~rl~~~~~~~s~~g~~~lD~ee~~e~~~~- 248 (361) T pfam06381 170 SVLQSLYDALKAADRTTNSAAQLVFKARLTVIKVDGLRALLAAGGGDELIERLDLIKRTRSNEGILVIDAEEELEQISY- 248 (361) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEECCCCEEEEECC- T ss_conf 2899999999999999999998887641000543548988637867999999999997086537267616541466246- Q ss_pred CHHHHHHHHHHHHHHHHHHHHH---HHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 2026999999999999997422---210132466677779999999999999778887788789999999999999873 Q gi|254781213|r 342 NPLPYHEELNRLKESIRSLFLL---DLFQVLDDKASRSAAESMEKTREKGAFVGPLIGGLQSEFIGAMISRELDILDSQ 417 (556) Q Consensus 342 ~~~~~~~~i~~~~~~I~~~f~~---d~~~~~~~~~~~TAtEv~~r~~e~~~~Lg~v~~rl~~E~l~Pli~r~~~il~r~ 417 (556) ++..+...+....+.|.-+.-. -+|+. .+..+-||.=..+ +.--..+..+|...|.|.++|.+.++++. T Consensus 249 ~lsGl~dvl~~~~~~iaaas~iP~t~LfG~--sp~GlnatGe~d~-----~nYyd~i~~~Qe~~l~p~l~~l~~~i~~s 320 (361) T pfam06381 249 SLSGLDDVLDQFAQQLAGASDIPLTRLFGQ--SPAGLNSTGEGDL-----RNYYDRIKGIQENELRPLLERLIELLVLS 320 (361) T ss_pred CCCCHHHHHHHHHHHHHHHHCCCHHHHCCC--CCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 767889999999999887507976775388--9987687761189-----99999999999988768999999999887 No 20 >KOG2133 consensus Probab=26.79 E-value=37 Score=13.17 Aligned_cols=19 Identities=11% Similarity=0.069 Sum_probs=10.7 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 8899999999875410332 Q gi|254781213|r 119 VGCLQSFYTSVVEFGTGCF 137 (556) Q Consensus 119 ~~~~~e~~~dL~~~Gta~l 137 (556) ..+.-++++||-..-|.|+ T Consensus 780 As~Sa~~~~h~d~~~nS~~ 798 (1229) T KOG2133 780 ASQSARFRKHLDRGTNSCA 798 (1229) T ss_pred HHHHHHHHHHHCCCCCCCC T ss_conf 7888999987515653210 No 21 >pfam09978 consensus Probab=26.55 E-value=37 Score=13.15 Aligned_cols=165 Identities=13% Similarity=0.096 Sum_probs=88.7 Q ss_pred EECCCCCCCCC---CEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECC------CC----- Q ss_conf 45101786658---74555114148721020269975889999999999999999975198689327------86----- Q gi|254781213|r 245 RFFEEKQIATF---PYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVS------EA----- 310 (556) Q Consensus 245 ~vl~e~g~~e~---P~~~~Rw~~~~ge~YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~------~~----- 310 (556) ..++.|..--| |+-++-+.+....-||.|....++..++.-+........-+..+.-..+.++. ++ T Consensus 46 ~~iH~SRli~f~g~~~p~~~~~k~~~~~wG~Svlq~~~d~v~~~~~t~~~~~~Ll~~~~~~v~k~~gl~~~~~~~~~~~~ 125 (270) T pfam09978 46 QKIHRSRLIIFDGVRLPVGDMLKPTYNFWGDSVLQSLYDRVKAADRTTASAAQLVYEARVDVIKVDGLRELLADGGAAAE 125 (270) T ss_pred EEEECCEEEEECCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCHHHHHCCCCCHHH T ss_conf 69872428986598888778861323767800899999999999999988999998623014731439888508650899 Q ss_pred CCCCCEECCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHCCCCCCCCCCCHHHHHHHHHH Q ss_conf 3043100247-643324588765542200012202699999999999999742---221013246667777999999999 Q gi|254781213|r 311 KQRNFDLKPG-YMNIGALSREGRSLFQPVQFGNPLPYHEELNRLKESIRSLFL---LDLFQVLDDKASRSAAESMEKTRE 386 (556) Q Consensus 311 ~~~~~~l~pg-~~~~~~~~~~~~~~~~p~~~g~~~~~~~~i~~~~~~I~~~f~---~d~~~~~~~~~~~TAtEv~~r~~e 386 (556) +...+.+.-- ..+++...-+..+.+...+. ++..+...+.+..+.|.-+.- .-+|+. .+..+.||.=. T Consensus 126 l~~r~~~~~~~rs~~g~~~lD~eEe~~~~~~-~~sGl~dvl~~~~~~va~a~~iP~t~L~G~--sP~GlnatGe~----- 197 (270) T pfam09978 126 LLERLDLIARFRSNNGLLVIDAEEEYEQKST-SFSGLDDVLDQFAQQLAGASDIPLTRLLGQ--SPAGLNSTGES----- 197 (270) T ss_pred HHHHHHHHHHHCCCCCCEEECCCCEEEEECC-CCCCHHHHHHHHHHHHHHHHCCCHHHHCCC--CCCCCCCCCHH----- T ss_conf 9999999998373227266537540466057-778989999999999998717866663478--99876776434----- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999778887788789999999999999873 Q gi|254781213|r 387 KGAFVGPLIGGLQSEFIGAMISRELDILDSQ 417 (556) Q Consensus 387 ~~~~Lg~v~~rl~~E~l~Pli~r~~~il~r~ 417 (556) =.+..-..+..+|..-|.|.++|.+.++++. T Consensus 198 d~~~yyd~i~~~Qe~~l~p~l~~l~~~i~~s 228 (270) T pfam09978 198 DLRNYYDRIASIQENELRPLLERLIDLLVRS 228 (270) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999988778999999999787 No 22 >TIGR00422 valS valyl-tRNA synthetase; InterPro: IPR002303 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=26.50 E-value=29 Score=13.87 Aligned_cols=55 Identities=22% Similarity=0.344 Sum_probs=28.6 Q ss_pred HHHHHHHEECCCCCCCCCCCCEEEEEE-EHHHEEEEECCCCCEEEEE--------------EEEC-CCHHHHHHH Q ss_conf 541033222167666544466058886-5544666108988871532--------------0003-697786663 Q gi|254781213|r 131 EFGTGCFYMEADVDEKGLEEGIRYISV-PLSNVYMSVNHQNVVDSVY--------------REFT-FTVDQIVSK 189 (556) Q Consensus 131 ~~Gta~l~i~~d~~~~~~~~~~rf~~~-pl~~~~i~~d~~G~vd~i~--------------r~~~-~t~~ql~~~ 189 (556) -|||||+.|.|-.|.++-.-+=|+ .+ +.=++ -|.+|.+..-- -+|+ |++-++.++ T Consensus 281 EFGTG~VKvTPAHD~ND~~~g~RH-~LLe~i~~---l~~dG~Lne~a~~~~tG~~~~Y~iP~~y~GL~~~eAR~k 351 (970) T TIGR00422 281 EFGTGAVKVTPAHDFNDYEVGKRH-NLLEFINI---LDEDGLLNENAEVIDTGKEDVYAIPGEYQGLERFEARKK 351 (970) T ss_pred CCCCCEEEEECCCCCCCHHHCCEE-CCCCHHHH---CCCCCCCCCEECEEECCCCCCCCCCHHCCCCCHHHHHHH T ss_conf 417512776087497760013412-11414333---179975011001100777233106522058888999999 No 23 >KOG2055 consensus Probab=25.75 E-value=39 Score=13.05 Aligned_cols=134 Identities=13% Similarity=0.092 Sum_probs=69.1 Q ss_pred CCCCCCCCCCCEEEEEEEHHHEEEEECCCCCEEEEE-EEECCCHHHHHHHCCCCCC----CHHHHHHHCCCCCCCEEEEE Q ss_conf 676665444660588865544666108988871532-0003697786663152235----72566541035557156668 Q gi|254781213|r 141 ADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVY-REFTFTVDQIVSKWGDKVL----SSKMKSALARNENERFTIIH 215 (556) Q Consensus 141 ~d~~~~~~~~~~rf~~~pl~~~~i~~d~~G~vd~i~-r~~~~t~~ql~~~fg~~~l----~~~~~~~~~~~~~~~~~v~~ 215 (556) -|...+..-..++|+-+|+....|..+..-++-+-- |+|.+...-...++-.-.. .+..-...+-.++..+-.+. T Consensus 242 vDGk~N~~lqS~~l~~fPi~~a~f~p~G~~~i~~s~rrky~ysyDle~ak~~k~~~~~g~e~~~~e~FeVShd~~fia~~ 321 (514) T KOG2055 242 VDGKVNPKLQSIHLEKFPIQKAEFAPNGHSVIFTSGRRKYLYSYDLETAKVTKLKPPYGVEEKSMERFEVSHDSNFIAIA 321 (514) T ss_pred ECCCCCHHHEEEEECCCCCCEEEECCCCCEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCHHHEEEECCCCCEEEEC T ss_conf 65735710034552158401046648994689860551378985100011110347877533110026743778769981 Q ss_pred E-------EEECCCCCCCCCCCCCCEEEEEEECCCCEECCCCCCCC-------CCEEEEEEEECCCCCCCHHHH Q ss_conf 8-------85357656554445321277654213764510178665-------874555114148721020269 Q gi|254781213|r 216 A-------VYPKSLTDKKKDKGNKGFHSKFVSVDENRFFEEKQIAT-------FPYIVGRYRVRADEIYGRSPA 275 (556) Q Consensus 216 ~-------v~pr~~~~~~~~~~~~~~~sv~~~~~~~~vl~e~g~~e-------~P~~~~Rw~~~~ge~YGrgp~ 275 (556) . .--...--...-.-+.......|..++++++..+|+.+ .+-+.-||. +.|.+||.+.+ T Consensus 322 G~~G~I~lLhakT~eli~s~KieG~v~~~~fsSdsk~l~~~~~~GeV~v~nl~~~~~~~rf~-D~G~v~gts~~ 394 (514) T KOG2055 322 GNNGHIHLLHAKTKELITSFKIEGVVSDFTFSSDSKELLASGGTGEVYVWNLRQNSCLHRFV-DDGSVHGTSLC 394 (514) T ss_pred CCCCEEEEEHHHHHHHHHEEEECCEEEEEEEECCCCEEEEECCCCEEEEEECCCCCEEEEEE-ECCCCCEEEEE T ss_conf 45764772314444344113455287667980588389998688649999668860578876-45854404552 No 24 >COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion] Probab=25.52 E-value=39 Score=13.03 Aligned_cols=119 Identities=19% Similarity=0.278 Sum_probs=62.7 Q ss_pred CCEEEEEEEHHHEEEEEC-CCCCEEEEEEEECCCH---HHHHHHCCCC-CCCHHHHH-HHCCCCCCCEEEEEEEEECCCC Q ss_conf 660588865544666108-9888715320003697---7866631522-35725665-4103555715666888535765 Q gi|254781213|r 150 EGIRYISVPLSNVYMSVN-HQNVVDSVYREFTFTV---DQIVSKWGDK-VLSSKMKS-ALARNENERFTIIHAVYPKSLT 223 (556) Q Consensus 150 ~~~rf~~~pl~~~~i~~d-~~G~vd~i~r~~~~t~---~ql~~~fg~~-~l~~~~~~-~~~~~~~~~~~v~~~v~pr~~~ 223 (556) +|.+|-.=.-|.+++.+| .+|+.+++.-.-.+.. +-++..|-+. .+-.-+.. ..-..+..+++++.. |+... T Consensus 201 TGaNfa~AetGsv~LVeNEGN~Rm~ttlP~tHIav~GiEKivps~eda~~~~~ll~rsa~G~~ittYin~~tG--P~~t~ 278 (459) T COG1139 201 TGANFAVAETGSVCLVENEGNGRMSTTLPPTHIAVMGIEKIVPTLEDAAVLVSLLQRSATGQRITTYINVITG--PSKTG 278 (459) T ss_pred CCCCEEEECCCCEEEEEECCCCEECCCCCCEEEEEEEHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEECCC--CCCCC T ss_conf 5632256346748999616874001347874589830776347688888999985166507788731564137--87777 Q ss_pred CCCCCCCCCCEEEEEEECCCCEECCCCCCCC---------CCEEEEEEEECCCCCCCHH Q ss_conf 6554445321277654213764510178665---------8745551141487210202 Q gi|254781213|r 224 DKKKDKGNKGFHSKFVSVDENRFFEEKQIAT---------FPYIVGRYRVRADEIYGRS 273 (556) Q Consensus 224 ~~~~~~~~~~~~sv~~~~~~~~vl~e~g~~e---------~P~~~~Rw~~~~ge~YGrg 273 (556) |.. +-+.||.|.++-+-..++....|.+ |=..||-|..++|..||+. T Consensus 279 d~d---Gp~efHlVlvDNGRs~~~~~~~~re~L~CIRCGaC~n~CPvY~~iGgh~y~~~ 334 (459) T COG1139 279 DID---GPKEFHLVLVDNGRSEALADEEFREALRCIRCGACLNHCPVYRHIGGHAYGSI 334 (459) T ss_pred CCC---CCCEEEEEEEECCCHHHCCCHHHHHHHHHHCCHHHHHCCHHHHHCCCEECCCC T ss_conf 678---87348999983880220048689998876000076513815665367202574 No 25 >TIGR01542 A118_put_portal phage portal protein, putative, A118 family; InterPro: IPR006432 These sequences represent a family of phage minor structural proteins. The protein is suggested to be the head-tail connector, or portal protein, on the basis of its position in the phage gene order, its presence in mature phage, its size, and its conservation across a number of complete genomes of tailed phage that lack other candidate portal proteins. Several other known portal protein families lack clear homology to this family and to each other .. Probab=24.40 E-value=41 Score=12.89 Aligned_cols=382 Identities=14% Similarity=0.145 Sum_probs=196.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHHCCCC Q ss_conf 99999999723566999999998504228987777525427999999999987641887887601110811444420232 Q gi|254781213|r 10 QDRFNYLKNQRGELNYWMEELTGFLYPYKNNAQLRMWDTTGSEACIKLSSLLSSLITPPGQKWHGLAESFSAYQAFLYKE 89 (556) Q Consensus 10 ~~r~~~l~~~R~~~e~~w~e~~~y~lP~r~~~~~~i~dst~~~a~~~lAs~L~~~ltPp~~~WF~l~~~~~~~~~~~~~~ 89 (556) ...|+.......-|.++|++...+=+-..+.+..|-.+|... .+.-|.+|-+.+|.-. .++.++| T Consensus 22 ~~ey~rI~~~kryY~~d~~~v~~lNye~~G~t~kr~l~s~n~--~k~aakk~asL~FNE~---~~i~vdD---------- 86 (489) T TIGR01542 22 KEEYERIARDKRYYKDDYKEVLYLNYESDGDTKKRELQSLNV--AKVAAKKLASLVFNEQ---VKIKVDD---------- 86 (489) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCH--HHHHHHHHHHHHCCCE---EEEEECH---------- T ss_conf 223578776534312247888750123587832101104770--6799999876550553---3898535---------- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCEEEEEEEHHHEEEEECCC Q ss_conf 23348999999999999998750231473889999999987541033222167666544466058886554466610898 Q gi|254781213|r 90 DARSKKVREWCDQVTDTLFGFRERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQ 169 (556) Q Consensus 90 ~~~~~ev~~~L~~v~~~i~~~~~~~~snf~~~~~e~~~dL~~~Gta~l~i~~d~~~~~~~~~~rf~~~pl~~~~i~~d~~ 169 (556) +.++++++++ +....|+..+=+.+-...+.|.+|+...-|.+.+ +|..=..-..+|=-.+.- T Consensus 87 ----~aAneF~~~v---------lk~n~F~knfErylE~~~AlGg~~~rpYvDg~Kn-----vkvafatAd~~yPL~~dt 148 (489) T TIGR01542 87 ----EAANEFVDDV---------LKQNDFTKNFERYLEEGLALGGLVVRPYVDGDKN-----VKVAFATADVVYPLQADT 148 (489) T ss_pred ----HHHHHHHHHH---------HHCCCCCCHHHHHHHHHHHHCCEEEEEEEECCCE-----EEEEEEECCEECCCCCCC T ss_conf ----6788899997---------5048864048888665542077049877708972-----899997557205766672 Q ss_pred CCEEEEEEEECCCHHHHHHHCCCCCCCHHHHHHHCCCCCCCEEEEEEE-E-ECCCC----------CCCCCCCCCCEE-- Q ss_conf 887153200036977866631522357256654103555715666888-5-35765----------655444532127-- Q gi|254781213|r 170 NVVDSVYREFTFTVDQIVSKWGDKVLSSKMKSALARNENERFTIIHAV-Y-PKSLT----------DKKKDKGNKGFH-- 235 (556) Q Consensus 170 G~vd~i~r~~~~t~~ql~~~fg~~~l~~~~~~~~~~~~~~~~~v~~~v-~-pr~~~----------~~~~~~~~~~~~-- 235 (556) ..|+.+..-- ..++. .++.+.++|.++-- | ..+++ +......+-|.. T Consensus 149 ~~V~e~aia~-----------------~~~~~--~n~~~~YYTLlEfheWQ~~ddYvitnELYrSdd~~~vG~~VpL~sl 209 (489) T TIGR01542 149 EDVDELAIAS-----------------KSVKS--INKKEVYYTLLEFHEWQDSDDYVITNELYRSDDKEKVGIKVPLSSL 209 (489) T ss_pred CCCCCEEEEE-----------------EEEEE--ECCCEEEEEEEEECCCCCCCCEEEECCCCCCCCHHHCCCCCCCHHH T ss_conf 1212034554-----------------21233--2075135775210000589975884443144652107863541145 Q ss_pred EEEEECCCCEECCCCCCCCCCEEEEEE-----EECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCC Q ss_conf 765421376451017866587455511-----414872102026997588999999999999999997519868932786 Q gi|254781213|r 236 SKFVSVDENRFFEEKQIATFPYIVGRY-----RVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSLHPPTIAVSEA 310 (556) Q Consensus 236 sv~~~~~~~~vl~e~g~~e~P~~~~Rw-----~~~~ge~YGrgp~~~aL~D~k~Ln~l~~~~l~~~~~~~~p~~~v~~~~ 310 (556) -+|.+.+... ...++. -|.+++-= +|.=.+.-|.|.-.+++--|+.||.+-=.-+.-.-+.=+ -++||.+- T Consensus 210 e~y~dlep~v--k~td~~-rP~F~y~k~~gaNNKn~tSPlG~S~~dNa~ttid~in~t~D~f~~EvK~G~r-rv~VP~s~ 285 (489) T TIGR01542 210 ELYEDLEPEV--KVTDLT-RPLFIYLKTKGANNKNLTSPLGLSVYDNALTTIDAINLTYDEFVDEVKLGQR-RVLVPESL 285 (489) T ss_pred HHHCCCCCCC--CCCCCC-CCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE-EEECCHHH T ss_conf 5423888830--478898-7537763578788777777310688986789999873023457899761871-57512456 Q ss_pred CCCCCEECCCCCCCCCC-CCCCCCCCCC------CCCCCHHHHHHHHH---------HHHHHHHHHHHHHHCCCC----- Q ss_conf 30431002476433245-8876554220------00122026999999---------999999997422210132----- Q gi|254781213|r 311 KQRNFDLKPGYMNIGAL-SREGRSLFQP------VQFGNPLPYHEELN---------RLKESIRSLFLLDLFQVL----- 369 (556) Q Consensus 311 ~~~~~~l~pg~~~~~~~-~~~~~~~~~p------~~~g~~~~~~~~i~---------~~~~~I~~~f~~d~~~~~----- 369 (556) +.-.++ |+.. ....++.+-| ...|..+.-...|+ +....|...+ ..|.|+ T Consensus 286 ~kt~v~-------y~~~~d~~~~p~Fdsd~~vy~~m~G~qD~~~~ai~D~t~pIR~~dyi~~in~~L--r~fe~Q~GlSa 356 (489) T TIGR01542 286 VKTAVR-------YTTDADESTRPRFDSDEEVYILMQGDQDADEKAIKDLTVPIRAADYIEAINAFL--RLFEMQVGLSA 356 (489) T ss_pred HHHHHC-------CCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCEECCCCCCCHHHHHHHHHHHH--HHHHHHHHHCC T ss_conf 752310-------135678878988796145653204751554566031565434588999999887--78764410125 Q ss_pred -----CCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCEEEEEECCH Q ss_conf -----46667777999999999999---9778887788789999999999999873999878711135652368883379 Q gi|254781213|r 370 -----DDKASRSAAESMEKTREKGA---FVGPLIGGLQSEFIGAMISRELDILDSQGNLPECEGADNPPVSLLKVEYTSP 441 (556) Q Consensus 370 -----~~~~~~TAtEv~~r~~e~~~---~Lg~v~~rl~~E~l~Pli~r~~~il~r~g~lp~~p~~~~~~~~~~~v~y~s~ 441 (556) ++..=.|||||---.++=-+ ..-..++.---|+..-+++-.-.+-.-.+..|..-.++- ..++.|.+-=. T Consensus 357 GtFtfd~~g~kTATEvVse~S~TYQtrnS~~~lvEq~iKel~~sIlE~ak~~~~Y~~ev~rWtG~~D--~ldIti~fdDg 434 (489) T TIGR01542 357 GTFTFDEKGLKTATEVVSENSETYQTRNSYVALVEQSIKELVVSILEVAKVIELYADEVARWTGELD--SLDITIDFDDG 434 (489) T ss_pred CEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCC--CEEEEEEECCC T ss_conf 3133277745142224507876412356789989877999999999885366540588213523325--33578860786 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999853676999999999999 Q gi|254781213|r 442 LFKYQQAESVASALQGVNTVV 462 (556) Q Consensus 442 La~aq~~~~~~~~~~~l~~~~ 462 (556) ++.-+. +.+.++++.+. T Consensus 435 vf~D~d----~~~~~~~~avn 451 (489) T TIGR01542 435 VFVDRD----AKLDAYLKAVN 451 (489) T ss_pred EECCCH----HHHHHHHHHHH T ss_conf 211633----45788989986 No 26 >TIGR01582 FDH-beta formate dehydrogenase, beta subunit; InterPro: IPR006470 The sequences in this group represent the beta subunit of the gamma-proteobacterial formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (IPR006443 from INTERPRO) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane . In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within this group. This appears to be the case for the alpha, gamma and epsilon (accessory protein IPR006452 from INTERPRO) chains as well. ; GO: 0008863 formate dehydrogenase activity, 0045333 cellular respiration, 0016021 integral to membrane. Probab=23.60 E-value=24 Score=14.35 Aligned_cols=15 Identities=27% Similarity=0.147 Sum_probs=7.4 Q ss_pred HHHHHHHHEECCCCC Q ss_conf 754103322216766 Q gi|254781213|r 130 VEFGTGCFYMEADVD 144 (556) Q Consensus 130 ~~~Gta~l~i~~d~~ 144 (556) +|.||+.|||.+..| T Consensus 221 GVGGThv~YVLhH~D 235 (293) T TIGR01582 221 GVGGTHVMYVLHHGD 235 (293) T ss_pred CCCCCCEEEEECCCC T ss_conf 978741188805888 No 27 >TIGR03549 conserved hypothetical protein TIGR03549. This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. This family has an OsmC-like N-terminal domain. It shares a central domain, modeled by pfam02624 and TIGR00702, with other families of smaller proteins. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may be fortuitous. Probab=22.02 E-value=45 Score=12.60 Aligned_cols=24 Identities=25% Similarity=0.577 Sum_probs=11.5 Q ss_pred CCCEEEEEEE-ECCCCCC---CHHHHHH Q ss_conf 5874555114-1487210---2026997 Q gi|254781213|r 254 TFPYIVGRYR-VRADEIY---GRSPAME 277 (556) Q Consensus 254 e~P~~~~Rw~-~~~ge~Y---Grgp~~~ 277 (556) .||.++.... ...|.+. |--|-.+ T Consensus 399 ~fPVmcVtL~NP~ng~~FASFGAHP~fe 426 (718) T TIGR03549 399 QFPVMCVTLMNPRTGGVFASFGAHPSFE 426 (718) T ss_pred CCCEEEEEEECCCCCCEEEEECCCCCHH T ss_conf 7755899977179995798715786257 No 28 >PRK13031 preprotein translocase subunit SecB; Provisional Probab=21.77 E-value=46 Score=12.56 Aligned_cols=34 Identities=9% Similarity=0.096 Sum_probs=26.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 9778887788789999999999999873999878 Q gi|254781213|r 390 FVGPLIGGLQSEFIGAMISRELDILDSQGNLPEC 423 (556) Q Consensus 390 ~Lg~v~~rl~~E~l~Pli~r~~~il~r~g~lp~~ 423 (556) .+.+++...-..+|=|+.+++..-+.+.|.+||+ T Consensus 92 ~~~~~L~v~cP~iLFPyaR~iIsd~~~~gGFPpL 125 (149) T PRK13031 92 QIEHAKKAFCPNILYHYAREAISDLVISGGFPQL 125 (149) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 9888885043365678799999988743799863 No 29 >COG3830 ACT domain-containing protein [Signal transduction mechanisms] Probab=21.30 E-value=31 Score=13.65 Aligned_cols=73 Identities=12% Similarity=0.008 Sum_probs=46.3 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 87655422000122026999999999999997422210132466677779999999999999778887788789 Q gi|254781213|r 329 REGRSLFQPVQFGNPLPYHEELNRLKESIRSLFLLDLFQVLDDKASRSAAESMEKTREKGAFVGPLIGGLQSEF 402 (556) Q Consensus 329 ~~~~~~~~p~~~g~~~~~~~~i~~~~~~I~~~f~~d~~~~~~~~~~~TAtEv~~r~~e~~~~Lg~v~~rl~~E~ 402 (556) +.++..+...-++....++.+|.++.|.+-+.++.-.+..--..+....++++.+..+....||=-+ +.|.|= T Consensus 10 GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~lgv~V-~vq~ed 82 (90) T COG3830 10 GKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVDISKEVVDFAALRDELAAEGKKLGVDV-RVQRED 82 (90) T ss_pred CCCCCCHHHHHHHHHHHCCCCEEEHHHHHHHHHCEEEEEECCCHHHCCHHHHHHHHHHHHHHCCCEE-EEEEHH T ss_conf 5887733499999999769818877799996231166577277676129999999999998609679-995589 No 30 >TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358 Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue preexisting arrested complexes . A 15 Å resolution helical reconstruction of the Escherichia coli core RNA polymerase (RNAP)/GreB complex that allows fitting of high-resolution RNAP and GreB structures. The model of the complex reveals a remarkable binding mode for GreB; the globular C-terminal domain binds RNAP at the edge of the active site channel, while the N-terminal coiled-coil domain extends 45 Å into a channel directly to the RNAP active site. The results point to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNAP active site to catalyse the transcript cleavage reaction, and mutational studies confirm that these positions are critical for Gre factor function. Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=20.44 E-value=49 Score=12.40 Aligned_cols=19 Identities=5% Similarity=0.163 Sum_probs=10.6 Q ss_pred CCHHHHHHHCCCCCCCEEE Q ss_conf 5725665410355571566 Q gi|254781213|r 195 LSSKMKSALARNENERFTI 213 (556) Q Consensus 195 l~~~~~~~~~~~~~~~~~v 213 (556) -|+-.|.+.++.-++.+-+ T Consensus 121 dSPlARaL~kke~gdevvv 139 (157) T TIGR01461 121 DSPLARALIKKEVGDEVVV 139 (157) T ss_pred ECHHHHHHHCCCCCCEEEE T ss_conf 2667888630125877787 Done!