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  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  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!