Query         gi|254781145|ref|YP_003065558.1| hypothetical protein CLIBASIA_05245 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 350
No_of_seqs    150 out of 629
Neff          8.4 
Searched_HMMs 39220
Date          Mon May 30 05:26:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781145.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam12236 Head-tail_con Bacter  99.8 9.5E-16 2.4E-20  123.8  25.0  280   41-342   132-412 (480)
  2 PHA00670 hypothetical protein   99.6 2.3E-12   6E-17  101.2  25.6  271   43-333   143-420 (540)
  3 pfam05133 Phage_prot_Gp6 Phage  98.8 3.2E-06 8.2E-11   60.4  18.1  167  157-329   192-360 (435)
  4 pfam07360 consensus             97.8  0.0039 9.9E-08   39.8  16.4  181  159-344   178-371 (412)
  5 pfam05126 consensus             97.5  0.0041   1E-07   39.7  12.3  271   30-329   113-397 (473)
  6 TIGR01542 A118_put_portal phag  84.3     2.9 7.4E-05   20.7   8.4  288   24-342   109-421 (489)
  7 pfam09978 consensus             82.8     3.3 8.5E-05   20.3   7.9  141  175-330    71-228 (270)
  8 TIGR01780 SSADH succinic semia  78.4     3.8 9.7E-05   19.9   4.2   15  312-326   277-291 (454)
  9 COG3567 Uncharacterized protei  76.6     5.2 0.00013   19.0   6.1  165  165-348   190-373 (452)
 10 pfam06381 DUF1073 Protein of u  74.1       6 0.00015   18.6  10.2  143  175-332   164-322 (361)
 11 pfam12419 DUF3670 SNF2 Helicas  72.1       2   5E-05   21.8   1.4   17  333-349    96-112 (140)
 12 TIGR01538 portal_SPP1 phage po  67.5     8.4 0.00021   17.7   8.8  152  175-333   243-414 (477)
 13 TIGR01555 phge_rel_HI1409 phag  45.5      19 0.00049   15.2   4.1  225  117-348   126-379 (426)
 14 TIGR01238 D1pyr5carbox3 delta-  39.9      12 0.00032   16.5   0.9   25   31-55    167-191 (525)
 15 pfam00862 Sucrose_synth Sucros  38.6      24 0.00062   14.6   5.5  137  160-302   266-427 (550)
 16 PRK04366 glycine dehydrogenase  36.0      27 0.00068   14.3   3.6   16  302-317   349-364 (490)
 17 TIGR01124 ilvA_2Cterm threonin  35.7      10 0.00026   17.1  -0.0   51  160-210   349-403 (508)
 18 TIGR00601 rad23 UV excision re  31.9      19 0.00048   15.3   0.8   22   71-92    189-213 (453)
 19 cd05131 RasGAP_IQGAP2 IQGAP2 i  29.8      34 0.00086   13.6   4.3   23  183-205   120-142 (339)
 20 TIGR01472 gmd GDP-mannose 4,6-  29.4      27  0.0007   14.2   1.3   10  341-350   312-322 (365)
 21 pfam04860 Phage_portal Phage p  28.9      35 0.00089   13.5  17.3  164  165-348   137-314 (348)
 22 smart00676 DM10 Domains in hyp  26.4      39 0.00098   13.2   2.9   15   11-25     30-44  (104)
 23 PRK07318 dipeptidase PepV; Rev  24.4      42  0.0011   13.0   5.6   68  126-203    69-136 (469)
 24 smart00165 UBA Ubiquitin assoc  22.4      28 0.00071   14.2   0.3   23   77-99      4-26  (37)
 25 cd00194 UBA Ubiquitin Associat  22.2      28 0.00071   14.2   0.2   25   77-101     4-28  (38)
 26 pfam11372 DUF3173 Protein of u  21.9      46  0.0012   12.7   1.3   15   75-89      3-17  (59)

No 1  
>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=99.78  E-value=9.5e-16  Score=123.82  Aligned_cols=280  Identities=13%  Similarity=0.101  Sum_probs=196.9

Q ss_pred             ECCEEEEEEECHHHEEECCCCCCHHHCCEEEEEEEECHHHHHHHCCCCHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCE
Q ss_conf             46836898576587434679988646548999999568999872798044302777876410133202456545567514
Q gi|254781145|r   41 SQGKVCVDAVSPDEFLIHPDSVDIEKSPIVGRKLYLTRSDLISMGYDRESINNLPIISSQNIENTWKFPKNQYSDKALEM  120 (350)
Q Consensus        41 ~~~~v~ie~V~pedf~vdp~A~~l~da~~v~hr~~~t~~eL~~~Gy~~d~v~~~~~~~~~~~~~~~~~~~~~~~d~~~~~  120 (350)
                      .++-++..++|.-+++|.+++.. +..+.|.++..+|..++.++.-+ +.+..       ..  ......   .....++
T Consensus       132 ~~~~~~f~~~pl~~~~v~~d~~G-~~vd~v~R~~~~t~~q~~~~f~~-~~l~~-------~v--~~~~~~---~~~p~~~  197 (480)
T pfam12236       132 RKGVIRFEAVPLGSYVVARDANG-NVVDIVFRRFSLTVRQIVQRFGL-DALSE-------EI--RKALED---GEKPEDK  197 (480)
T ss_pred             CCCCCEEEEEECCEEEEEECCCC-CEEEEEEEEEECCHHHHHHHCCH-HHCCH-------HH--HHHHHC---CCCCCCE
T ss_conf             67762379963153999967999-97899999763249999986171-21897-------78--888752---7897865


Q ss_pred             EEEEEEEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCCCCEEEEEEEECCCCEECCCHHHHHCCHHHHHHHHHHHH
Q ss_conf             99999789986058987410899990787530464046555685689856306873203543543102899998998848
Q gi|254781145|r  121 IEYYELYVTIDYDGDGIAELRRVIMAGGTGKDNILCNEEWNELPFTCLRAMRAPHCFIGESLAASIIEIQKIKTVLLRQT  200 (350)
Q Consensus       121 v~v~E~y~~~D~dgdg~~e~~~v~~~g~~~~~~il~~~~~~~~Pf~~~~~~p~p~~~~G~g~~d~l~~lQ~~~n~~~R~~  200 (350)
                      +++|+|...-. | ++....+..+.........++...+.+..||..+.|...++..||+|+++...+..+.+|.+.+..
T Consensus       198 ~~v~~~V~~~~-d-~~~~~~~~s~~~~~~~~~~~l~e~g~~~~P~~~~Rw~~~~ge~YGrgp~~~~l~d~k~l~~l~~~~  275 (480)
T pfam12236       198 VEIYHAVEPRA-D-DAKNMPFASYQEDAGKDVGVLSESGYDEFPYLVPRWEKIDGEAYGRSPVEDALPDVKSLNKLSEAL  275 (480)
T ss_pred             EEEEEEEEECC-C-CCCCCCEEEEEEECCCCCCEEEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999846-7-778996699999768853034414788786666778737998657086999868999999999999


Q ss_pred             HHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             87876303662253134312100001122574145046665544444456887656799999999999887524666430
Q gi|254781145|r  201 LDNLYWQNQPQTIVQEGSIIDPESVLNPQFGKPIRVAAGMDIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSG  280 (350)
Q Consensus       201 lDn~~l~~~p~~~v~~~~~~~~~d~~~~~~g~~v~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G  280 (350)
                      +.+...++.|.+.+++++..++.++ ...+++.+..... ....+.|++..+..+.+...++.+++.+++...+.-+.+ 
T Consensus       276 ~~~~~~a~~p~~~v~~~~~~~~~~l-~~~~~~~i~~g~~-~~~~~~p~~~~~~~~~~~~~i~~~~~~I~~af~~d~~~~-  352 (480)
T pfam12236       276 LKAAAKASKPPWLVPPSGVTQPRDL-VPGGTGYVVTGVA-GDIGIKPLEKYADFQVAQAVIQDIRQRIREAFMVDLFQM-  352 (480)
T ss_pred             HHHHHHHHCCCEEECCCCCCCCCEE-CCCCCCEEEECCC-CCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf             9999874268578576545474140-3578844742687-776500055678744999999999999999998753147-


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHEEEECCE
Q ss_conf             3544335513899999999999889-9999999999999999999999874885105989682
Q gi|254781145|r  281 FSPEILQNMTATATSLIEQSGVGQV-ELIVRTLAQGLEILFRGLLRLIIQHQDKVRMVRLRDQ  342 (350)
Q Consensus       281 ~~~~~~~~~TAt~is~~~~~a~~r~-~~~~R~~ae~~k~l~~~i~~l~~~~~~~~~~~ri~g~  342 (350)
                        .++ .+.|||+++++++.....+ ..+.|.-.|++.|++.+++.++.+...=|..-+..|.
T Consensus       353 --~~~-~~~TAtEV~~r~~E~~~~LGpv~~rl~~E~l~Pli~r~~~il~r~g~lp~~p~~~g~  412 (480)
T pfam12236       353 --RDA-ERVTATEVRERAEEKEQLLGPVYSRLQEEFLSPLIERTFNILQRAGMLPPPPDELGV  412 (480)
T ss_pred             --CCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCC
T ss_conf             --788-877799999999999987607889999999999999999999977999999246088


No 2  
>PHA00670 hypothetical protein
Probab=99.64  E-value=2.3e-12  Score=101.24  Aligned_cols=271  Identities=11%  Similarity=0.007  Sum_probs=185.7

Q ss_pred             CEEEEEEECHHHEEECCCCCCHHHCCEEEEEEEECHHHHHHHCCCCHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCEEE
Q ss_conf             83689857658743467998864654899999956899987279804430277787641013320245654556751499
Q gi|254781145|r   43 GKVCVDAVSPDEFLIHPDSVDIEKSPIVGRKLYLTRSDLISMGYDRESINNLPIISSQNIENTWKFPKNQYSDKALEMIE  122 (350)
Q Consensus        43 ~~v~ie~V~pedf~vdp~A~~l~da~~v~hr~~~t~~eL~~~Gy~~d~v~~~~~~~~~~~~~~~~~~~~~~~d~~~~~v~  122 (350)
                      +-++-.++|.-++++..++...=|  -|.++..+|..+++.++-+ +.   ++.    ....  ...    .++..+.++
T Consensus       143 ~~irf~~~pl~~~~i~~d~~G~VD--tv~Rkf~mtarqi~~~fg~-~~---l~~----~v~~--~~~----~~p~~~~ve  206 (540)
T PHA00670        143 EVVVFQSSPIGDYYFAEDNRGQVD--TFYRQFRWTVAQMVQEFGD-EN---TSE----SVQS--KAE----EGSNEAWVE  206 (540)
T ss_pred             CCCEEEEEECCCEEEECCCCCCEE--EEEEEEEECHHHHHHHCCC-CC---CCH----HHHH--HHH----CCCCCCEEE
T ss_conf             740268862110898318999812--6899998429999987053-32---998----9998--874----599766058


Q ss_pred             EEEE-EEEEEECC---CCCCCEEEEEEECC-CCCEEEECCCCCCCCCEEEEEEEECCCCEECCCHHHHHCCHHHHHHHHH
Q ss_conf             9997-89986058---98741089999078-7530464046555685689856306873203543543102899998998
Q gi|254781145|r  123 YYEL-YVTIDYDG---DGIAELRRVIMAGG-TGKDNILCNEEWNELPFTCLRAMRAPHCFIGESLAASIIEIQKIKTVLL  197 (350)
Q Consensus       123 v~E~-y~~~D~dg---dg~~e~~~v~~~g~-~~~~~il~~~~~~~~Pf~~~~~~p~p~~~~G~g~~d~l~~lQ~~~n~~~  197 (350)
                      |++| |-+.|.+-   |....++..++... ....+++..--.+..||+.+.|...++..||+|++....+.-+.+|.+.
T Consensus       207 v~h~V~pr~d~d~~~~d~~n~pf~S~y~e~~~d~~~~l~esG~~e~P~~~~R~~~~~~e~YGr~p~~~al~d~k~ln~~~  286 (540)
T PHA00670        207 VVHAVEPRADRDPSKLDPRNMPFKSVYFEKGGDEVRLLRESGYREFPALAPRWRVSGGDVYGFSPAMLALGDVRTLQREQ  286 (540)
T ss_pred             EEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCEEEECCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999866666632123467975799999647762133114766586456777626987667387888706799999999


Q ss_pred             HHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCEEEECCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             848878763036622531343121000011225741450466-6554444445688765679999999999988752466
Q gi|254781145|r  198 RQTLDNLYWQNQPQTIVQEGSIIDPESVLNPQFGKPIRVAAG-MDIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISD  276 (350)
Q Consensus       198 R~~lDn~~l~~~p~~~v~~~~~~~~~d~~~~~~g~~v~~~~~-~~~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~  276 (350)
                      +..+.+...+++|.+.+++++...   ..+..||++.....+ +....+.|++..........+++.+.+.+++..-+--
T Consensus       287 ~~~l~~a~~~v~pp~~vp~dg~~~---~v~l~PGgi~~~~~~~~~~~~~~p~~~~~~~~~~~~~i~~~r~~I~~af~~D~  363 (540)
T PHA00670        287 KRKAQSIDKVINPPLMAPESGKNQ---DISLGPGGLTYVDDMESNGGIRKAFEVNARFDVLLADIQDTRQTINRIYYVDL  363 (540)
T ss_pred             HHHHHHHHHCCCCCEEECCCCCCC---CEEECCCCCEECCCCCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999873047987747533547---31445775001367788867666310589944799999999999999999999


Q ss_pred             HHHHCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             64303544335513899999999999889-9999999999999999999999874885
Q gi|254781145|r  277 ISSGFSPEILQNMTATATSLIEQSGVGQV-ELIVRTLAQGLEILFRGLLRLIIQHQDK  333 (350)
Q Consensus       277 ~~~G~~~~~~~~~TAt~is~~~~~a~~r~-~~~~R~~ae~~k~l~~~i~~l~~~~~~~  333 (350)
                      +..-.+.+. .+.|||++...++--...+ ..+.|..+|++.|++.+++.++.+-.-=
T Consensus       364 f~~l~~~~~-~~mTAtEV~~R~~Ek~~~LGpv~~rl~~ElL~Pli~R~f~il~r~g~l  420 (540)
T PHA00670        364 FQMLANKDS-PAMTATEVQERYEEKLLMLGPVLERLENEFLSPLIQRTFNIMVRANKL  420 (540)
T ss_pred             HHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             985457887-876799999999999987637888776888999999999999977999


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=98.78  E-value=3.2e-06  Score=60.37  Aligned_cols=167  Identities=16%  Similarity=0.101  Sum_probs=116.5

Q ss_pred             CCCCCCCCEEEEEEEECCCCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCC-CCCCCCCCCEEE
Q ss_conf             4655568568985630687320354354310289999899884887876303662253134312100-001122574145
Q gi|254781145|r  157 NEEWNELPFTCLRAMRAPHCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPE-SVLNPQFGKPIR  235 (350)
Q Consensus       157 ~~~~~~~Pf~~~~~~p~p~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~-d~~~~~~g~~v~  235 (350)
                      ..+++.+|++.|..-. .+ .+|.|..+.+.+++++.+.++++..+...-..++. .+..|.....+ .....+..+.+.
T Consensus       192 ~~~~g~vPvv~f~Nn~-~~-~~G~sd~e~v~~liDa~d~~~s~~~n~~~~~~~~~-lv~~g~~~~~~~~~~~~~~~~~~~  268 (435)
T pfam05133       192 PHEFGRVPVVEFNNND-LR-SPGLSDLEPVKSLIDAYDKTLSEFANDFYDFPRAI-LVLKGYGEDDDEFVKDLKDAKLIR  268 (435)
T ss_pred             CCCCCCCCEEEECCCC-CC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEE-EEECCCCCCCCHHHHHHHHCCCEE
T ss_conf             6888852659862585-44-56865177769999999999838778898742003-774177766515678777514301


Q ss_pred             ECCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04666-55444444568876567999999999998875246664303544335513899999999999889999999999
Q gi|254781145|r  236 VAAGM-DIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEILQNMTATATSLIEQSGVGQVELIVRTLAQ  314 (350)
Q Consensus       236 ~~~~~-~~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~ae  314 (350)
                      +..+. .......+.........-+.++.+...+.+.|++++.+.+.-+   ++.++.++........++.+..-|.|.+
T Consensus       269 ~~~~~~~~~d~~~l~~~~~~~~~e~~~~~l~~~i~~~s~~~~~~~~~f~---~n~Sg~Alk~~~~~l~~ka~~~e~~f~~  345 (435)
T pfam05133       269 LLDGAEDDGDAKFLTKQFPVASLENYLDALKQDIYEFAMVPDLPDEYFG---GNASGEALKAKYSLLDLKAERKERKFGE  345 (435)
T ss_pred             CCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1366678997048805688689999999999999998388999946608---8740999999998999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999987
Q gi|254781145|r  315 GLEILFRGLLRLIIQ  329 (350)
Q Consensus       315 ~~k~l~~~i~~l~~~  329 (350)
                      +++.+++.+.+++..
T Consensus       346 ~l~~~~~li~~~~~~  360 (435)
T pfam05133       346 ALRRLLRLALEILGD  360 (435)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             999999999998667


No 4  
>pfam07360 consensus
Probab=97.76  E-value=0.0039  Score=39.84  Aligned_cols=181  Identities=16%  Similarity=0.135  Sum_probs=115.5

Q ss_pred             CCCCCCEEEEEEEECCCCEECCCHHH-HHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCC----CCC----CCCCCCCC
Q ss_conf             55568568985630687320354354-3102899998998848878763036622531343----121----00001122
Q gi|254781145|r  159 EWNELPFTCLRAMRAPHCFIGESLAA-SIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGS----IID----PESVLNPQ  229 (350)
Q Consensus       159 ~~~~~Pf~~~~~~p~p~~~~G~g~~d-~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~----~~~----~~d~~~~~  229 (350)
                      +.+..|.+-|+.-|...+.+|.|-.. -++++|+..+..+--+.-+.-..+.|+-.+- |.    ...    .+..+...
T Consensus       178 ~lG~~pvVp~~n~~~l~rp~G~SeIt~~vm~ltD~a~rtl~~m~vaaef~s~PqR~i~-G~~~~~f~~~~~~~~~~w~a~  256 (412)
T pfam07360       178 GLGVPPVVPIPNRPRLVRPFGTSRITRDLMSLQDAAARTLERMQVTAEFYSFPQRYLL-GADPDELGVDDETGKPMWKAY  256 (412)
T ss_pred             CCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE-CCCHHHCCCCCCCCCCHHHHH
T ss_conf             9998745981367666899885224577899999999999989998886315135674-378776156676665268876


Q ss_pred             CCCEEEECCCCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHHHHHHHHHHHHHHHH
Q ss_conf             5741450466655--4444445688765679999999999988752466643035443355-138999999999998899
Q gi|254781145|r  230 FGKPIRVAAGMDI--RSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEILQN-MTATATSLIEQSGVGQVE  306 (350)
Q Consensus       230 ~g~~v~~~~~~~~--~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~~~-~TAt~is~~~~~a~~r~~  306 (350)
                      .+.++-...+...  ..+.+++..+..+ ...++..+.+.+--.||++....|...+   | .+|-++......-..+.+
T Consensus       257 ~~~i~a~~~~~~g~~p~vgQf~~asl~p-f~d~l~~~a~~~a~~t~lP~~~Lg~~~d---NPaSaeAi~Aae~~L~~~ae  332 (412)
T pfam07360       257 LARILAFPDDEDGDKPDVGQFPAASLAP-FTDALRQLAKLFAGETGLPPDYLGFSSD---NPASAEAIRASEERLIAAAE  332 (412)
T ss_pred             HHHHHCCCCCCCCCCCCEEEECCCCCHH-HHHHHHHHHHHHHHHHCCCHHHHCCCCC---CCCCHHHHHHHHHHHHHHHH
T ss_conf             6666177764458999753326888516-8999999999988634789899622157---85549999998989999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-CCCHHEEEECCEEE
Q ss_conf             999999999999999999999874-88510598968268
Q gi|254781145|r  307 LIVRTLAQGLEILFRGLLRLIIQH-QDKVRMVRLRDQWV  344 (350)
Q Consensus       307 ~~~R~~ae~~k~l~~~i~~l~~~~-~~~~~~~ri~g~~v  344 (350)
                      ...|.|.++++.++++...+.-.. ...++..++.=+|-
T Consensus       333 ~~~~~fG~~~~~v~~la~~~~~~~~~~~~~~~~~~v~Wr  371 (412)
T pfam07360       333 KAQRSFGGALENVARLAVALRDGFGYIPPEFKRIEVKWR  371 (412)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCEEEEC
T ss_conf             999987599999999999985388878655505615776


No 5  
>pfam05126 consensus
Probab=97.54  E-value=0.0041  Score=39.69  Aligned_cols=271  Identities=13%  Similarity=0.087  Sum_probs=144.0

Q ss_pred             EEEEEEEEEEEECCEEEEEEECHHHEEECCCC-CCHHHCCEEEEEEEECHHHHHHHCCCCHHHCCCCCCCCCCHHHHHHC
Q ss_conf             57758999997468368985765874346799-88646548999999568999872798044302777876410133202
Q gi|254781145|r   30 KVHDLRIRRKYSQGKVCVDAVSPDEFLIHPDS-VDIEKSPIVGRKLYLTRSDLISMGYDRESINNLPIISSQNIENTWKF  108 (350)
Q Consensus        30 ~~~~v~~~r~~~~~~v~ie~V~pedf~vdp~A-~~l~da~~v~hr~~~t~~eL~~~Gy~~d~v~~~~~~~~~~~~~~~~~  108 (350)
                      -+..+.++-.++.+++||..|....|++-..- ..+-+|-|+ -++.++...  . +.+.-.++...+.+....--.++.
T Consensus       113 AlGg~a~kpYvd~~~I~v~~v~Ad~f~Pl~~nt~~v~e~~~~-~~~~~~~~~--~-~~yYT~LE~H~~~~~~~Y~I~N~l  188 (473)
T pfam05126       113 ALGGFAMRPYVDGNKVKVAFATADQFYPLQSDTNDVSEAAIA-SRTTETENK--N-TKYYTLLEFHEWQDHDDYVITNEL  188 (473)
T ss_pred             HHCCEEEEEEECCCEEEEEEEECCCEEEEEECCCCCEEEEEE-EEEEEEECC--C-CEEEEEEEEEEECCCCEEEEEEEE
T ss_conf             526658999984993899997137257303458884689999-777885068--8-458999999994268728998888


Q ss_pred             CCCCCCCCCCCEEEEEEEEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCCCC-EEEEEE----EECCCCEECCCHH
Q ss_conf             45654556751499999789986058987410899990787530464046555685-689856----3068732035435
Q gi|254781145|r  109 PKNQYSDKALEMIEYYELYVTIDYDGDGIAELRRVIMAGGTGKDNILCNEEWNELP-FTCLRA----MRAPHCFIGESLA  183 (350)
Q Consensus       109 ~~~~~~d~~~~~v~v~E~y~~~D~dgdg~~e~~~v~~~g~~~~~~il~~~~~~~~P-f~~~~~----~p~p~~~~G~g~~  183 (350)
                      -.....+.-+.+|-+.|.|-.+       .+  .+.+.|             -..| |+.|.+    -....+.+|.|++
T Consensus       189 Y~s~~~~~lG~~v~L~~~~~dL-------~~--~v~i~g-------------~~rPlFaY~K~p~aNnid~~SPlGvSvy  246 (473)
T pfam05126       189 YRSDDPNEVGTKVPLSEVYKDL-------EP--QVKITD-------------LTRPLFAYIKTPGANNKNITSPLGLSVY  246 (473)
T ss_pred             EECCCCHHCCCCCCCCHHHCCC-------CC--CEEECC-------------CCCCCEEEECCCCCCCCCCCCCCCCCHH
T ss_conf             8638931028542363000255-------71--225658-------------8866258874876776778999850437


Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCC---CCCCCCC--CCC-CEEEE-CCCC-CCCCCCCCCCCCCCH
Q ss_conf             43102899998998848878763036622531343121---0000112--257-41450-4666-554444445688765
Q gi|254781145|r  184 ASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIID---PESVLNP--QFG-KPIRV-AAGM-DIRSVLGIHSVPMIE  255 (350)
Q Consensus       184 d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~---~~d~~~~--~~g-~~v~~-~~~~-~~~~i~~~~~~~~~~  255 (350)
                      +...++-+.++.....++.-.-+. .-++.|++..+..   .+.....  .+. .+++. .+.. ....+..+.++--..
T Consensus       247 anA~~~lk~iD~~yd~~~wE~e~g-~~rI~V~~s~lk~~~~~~g~~~p~fd~~~~vy~~~~~~~~~~~~i~d~~~~iR~~  325 (473)
T pfam05126       247 DNAKTTLDTINLTHDQFYWEVKLG-QKRVAVPSSFLKTAVRLDGSHTPYFDSDQNVYFLMQGDDDNGKAIKDITTPIRST  325 (473)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHC-EEEEECCHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEECCCCCHHH
T ss_conf             507989999999989999997645-0789828999603778888847777864111011256787787734656420079


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67999999999998875246664303544335513899999999999889999999999999999999999987
Q gi|254781145|r  256 KSFSMLHYLDQELVDRTGISDISSGFSPEILQNMTATATSLIEQSGVGQVELIVRTLAQGLEILFRGLLRLIIQ  329 (350)
Q Consensus       256 ~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~ae~~k~l~~~i~~l~~~  329 (350)
                      +.+..++.+-..++...|.+--.-..+++  .-+|||++..--+..=+.++.+...+.+++++|...+..|..-
T Consensus       326 ~~~~~in~~L~~ie~~~Gls~Gtfs~d~~--g~KTATEI~S~ns~ty~t~~~~~~~le~aL~~Lv~ai~ela~~  397 (473)
T pfam05126       326 DYIEAINAFLREFEMQIGLSAGTFTFDEN--GLKTATEVVSENSETYQTRNSYSTLVEQGIKELIVSILELAKA  397 (473)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCC--CCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999873836660246887--6322356750530777989999999999999999999999866


No 6  
>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=84.29  E-value=2.9  Score=20.70  Aligned_cols=288  Identities=14%  Similarity=0.093  Sum_probs=164.1

Q ss_pred             CCCCCCEEEEEEEEEEEECCE-EEEEEECHHHEEE-CCCCCCHHHCCEEEEEEEECHHHHHHHCCCCHHHCCCCCCCCCC
Q ss_conf             466761577589999974683-6898576587434-67998864654899999956899987279804430277787641
Q gi|254781145|r   24 REDGGEKVHDLRIRRKYSQGK-VCVDAVSPDEFLI-HPDSVDIEKSPIVGRKLYLTRSDLISMGYDRESINNLPIISSQN  101 (350)
Q Consensus        24 ~~~~~~~~~~v~~~r~~~~~~-v~ie~V~pedf~v-dp~A~~l~da~~v~hr~~~t~~eL~~~Gy~~d~v~~~~~~~~~~  101 (350)
                      .-|.+.-+.+..+|-.++-++ |||-.+-..-||+ ..++.+.++| -|+.|...+.+. ++  .|.-.++-..+.++++
T Consensus       109 ylE~~~AlGg~~~rpYvDg~KnvkvafatAd~~yPL~~dt~~V~e~-aia~~~~~~~n~-~~--~YYTLlEfheWQ~~dd  184 (489)
T TIGR01542       109 YLEEGLALGGLVVRPYVDGDKNVKVAFATADVVYPLQADTEDVDEL-AIASKSVKSINK-KE--VYYTLLEFHEWQDSDD  184 (489)
T ss_pred             HHHHHHHHCCEEEEEEEECCCEEEEEEEECCEECCCCCCCCCCCCE-EEEEEEEEEECC-CE--EEEEEEEECCCCCCCC
T ss_conf             8665542077049877708972899997557205766672121203-455421233207-51--3577521000058997


Q ss_pred             HHHHHHCCCCCCCCCCCCEEEEE--EEEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCCCCEEE-EEE----EECC
Q ss_conf             01332024565455675149999--9789986058987410899990787530464046555685689-856----3068
Q gi|254781145|r  102 IENTWKFPKNQYSDKALEMIEYY--ELYVTIDYDGDGIAELRRVIMAGGTGKDNILCNEEWNELPFTC-LRA----MRAP  174 (350)
Q Consensus       102 ~~~~~~~~~~~~~d~~~~~v~v~--E~y~~~D~dgdg~~e~~~v~~~g~~~~~~il~~~~~~~~Pf~~-~~~----~p~p  174 (350)
                      .--.++.-+-+....-+-+|-+.  |.|-       |+. + .|-+.+             -.+|..+ +.+    -..-
T Consensus       185 YvitnELYrSdd~~~vG~~VpL~sle~y~-------dle-p-~vk~td-------------~~rP~F~y~k~~gaNNKn~  242 (489)
T TIGR01542       185 YVITNELYRSDDKEKVGIKVPLSSLELYE-------DLE-P-EVKVTD-------------LTRPLFIYLKTKGANNKNL  242 (489)
T ss_pred             EEEECCCCCCCCHHHCCCCCCCHHHHHHC-------CCC-C-CCCCCC-------------CCCCEEEEECCCCCCCCCC
T ss_conf             58844431446521078635411455423-------888-8-304788-------------9875377635787887777


Q ss_pred             CCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC---C-CCCCCCCCC-------CCEEEECC--CCC
Q ss_conf             7320354354310289999899884887876303662253134312---1-000011225-------74145046--665
Q gi|254781145|r  175 HCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSII---D-PESVLNPQF-------GKPIRVAA--GMD  241 (350)
Q Consensus       175 ~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~---~-~~d~~~~~~-------g~~v~~~~--~~~  241 (350)
                      .|.-|+|+.+...+.-+.+|....+.++-.-+ ...|+.|+..-+.   + ..+.-...+       ..-+++.|  ...
T Consensus       243 tSPlG~S~~dNa~ttid~in~t~D~f~~EvK~-G~rrv~VP~s~~kt~v~y~~~~d~~~~p~Fdsd~~vy~~m~G~qD~~  321 (489)
T TIGR01542       243 TSPLGLSVYDNALTTIDAINLTYDEFVDEVKL-GQRRVLVPESLVKTAVRYTTDADESTRPRFDSDEEVYILMQGDQDAD  321 (489)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCEEEECCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCC
T ss_conf             77310688986789999873023457899761-87157512456752310135678878988796145653204751554


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             54444445688765679999999999988752466643035443355138999-99999999889999999999999999
Q gi|254781145|r  242 IRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEILQNMTATAT-SLIEQSGVGQVELIVRTLAQGLEILF  320 (350)
Q Consensus       242 ~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~~~~TAt~i-s~~~~~a~~r~~~~~R~~ae~~k~l~  320 (350)
                      ..++.-+..|==+..-...++.+-...+-.+|+|--.=-.++.++  +|||++ +--.+-=|+| ..+...+..++|.|.
T Consensus       322 ~~ai~D~t~pIR~~dyi~~in~~Lr~fe~Q~GlSaGtFtfd~~g~--kTATEvVse~S~TYQtr-nS~~~lvEq~iKel~  398 (489)
T TIGR01542       322 EKAIKDLTVPIRAADYIEAINAFLRLFEMQVGLSAGTFTFDEKGL--KTATEVVSENSETYQTR-NSYVALVEQSIKELV  398 (489)
T ss_pred             CCCEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCC--EEEEEEEECCCCCCHHH-HHHHHHHHHHHHHHH
T ss_conf             566031565434588999999887787644101253133277745--14222450787641235-678998987799999


Q ss_pred             HHHHHHHHHH--CCCHHEEEECCE
Q ss_conf             9999999874--885105989682
Q gi|254781145|r  321 RGLLRLIIQH--QDKVRMVRLRDQ  342 (350)
Q Consensus       321 ~~i~~l~~~~--~~~~~~~ri~g~  342 (350)
                      -.|+++..-+  +.. .+.|-+|.
T Consensus       399 ~sIlE~ak~~~~Y~~-ev~rWtG~  421 (489)
T TIGR01542       399 VSILEVAKVIELYAD-EVARWTGE  421 (489)
T ss_pred             HHHHHHHHHHHHCCC-CCCEEECC
T ss_conf             999988536654058-82135233


No 7  
>pfam09978 consensus
Probab=82.84  E-value=3.3  Score=20.32  Aligned_cols=141  Identities=19%  Similarity=0.133  Sum_probs=69.3

Q ss_pred             CCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECC-CCCCCC---CCCCCCC---------CCEEEECCCCC
Q ss_conf             7320354354310289999899884887876303662253134-312100---0011225---------74145046665
Q gi|254781145|r  175 HCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEG-SIIDPE---SVLNPQF---------GKPIRVAAGMD  241 (350)
Q Consensus       175 ~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~-~~~~~~---d~~~~~~---------g~~v~~~~~~~  241 (350)
                      ..+||.|+.+.+.+.=+.-...+...-+-+.......+.+..- .+.+.+   +.+..+.         .+..-....  
T Consensus        71 ~~~wG~Svlq~~~d~v~~~~~t~~~~~~Ll~~~~~~v~k~~gl~~~~~~~~~~~~l~~r~~~~~~~rs~~g~~~lD~e--  148 (270)
T pfam09978        71 YNFWGDSVLQSLYDRVKAADRTTASAAQLVYEARVDVIKVDGLRELLADGGAAAELLERLDLIARFRSNNGLLVIDAE--  148 (270)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEECCC--
T ss_conf             376780089999999999999998899999862301473143988850865089999999999983732272665375--


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH----HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             544444456887656799999999999887524666----4303544335513899999999999889999999999999
Q gi|254781145|r  242 IRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDI----SSGFSPEILQNMTATATSLIEQSGVGQVELIVRTLAQGLE  317 (350)
Q Consensus       242 ~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~----~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~ae~~k  317 (350)
                       ..+.....+. + .+-   +.+++..+..+|++++    .-|.+|..+   .|||-+-+.+-.    +.+.+....-++
T Consensus       149 -Ee~~~~~~~~-s-Gl~---dvl~~~~~~va~a~~iP~t~L~G~sP~Gl---natGe~d~~~yy----d~i~~~Qe~~l~  215 (270)
T pfam09978       149 -EEYEQKSTSF-S-GLD---DVLDQFAQQLAGASDIPLTRLLGQSPAGL---NSTGESDLRNYY----DRIASIQENELR  215 (270)
T ss_pred             -CEEEEECCCC-C-CHH---HHHHHHHHHHHHHHCCCHHHHCCCCCCCC---CCCCHHHHHHHH----HHHHHHHHHHHH
T ss_conf             -4046605777-8-989---99999999999871786666347899876---776434899999----999999998877


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999874
Q gi|254781145|r  318 ILFRGLLRLIIQH  330 (350)
Q Consensus       318 ~l~~~i~~l~~~~  330 (350)
                      +.+++++.+++..
T Consensus       216 p~l~~l~~~i~~s  228 (270)
T pfam09978       216 PLLERLIDLLVRS  228 (270)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8999999999787


No 8  
>TIGR01780 SSADH succinic semialdehyde dehydrogenase; InterPro: IPR010102   Succinic semialdehyde dehydrogenase is one of three enzymes constituting 4-aminobutyrate (GABA) degradation in both prokaryotes and eukaryotes, catalysing the (NAD(P)+)-dependent catabolism reaction of succinic semialdehyde to succinate for metabolism by the citric acid cycle. In Escherichia coli, succinic semialdehyde dehydrogenase is located in a unidirectionally transcribed gene cluster encoding enzymes for GABA degradation and is suggested to be co-transcribed with succinic semialdehyde transaminase from a common promoter upstream of SSADH . Similar gene arrangements can be found in characterised Ralstonia eutropha  and the genome analysis of Bacillus subtilis.     Prokaryotic succinic semialdehyde dehydrogenases (1.2.1.16 from EC) share high sequence homology to characterised succinic semialdehyde dehydrogenases from rat and human (1.2.1.24 from EC), exhibiting conservation of proposed cofactor binding residues, and putative active sites (G-237 and G-242, C-293 and G-259 respectively of rat SSADH) .    Eukaryotic SSADH enzymes exclusively utilise NAD+ as a cofactor, exhibiting little to no NADP+ activity . While a NADP+ preference has been detected in prokaryotes in addition to both NADP+- and NAD+-dependencies as in Escherichia coli, Pseudomonas, and Klebsiella pneumoniae . The function of this alternative SSADH currently is unknown, but has been suggested to play a possible role in 4-hydroxyphenylacetic degradation .    SSADH enzyme belongs to the aldehyde dehydrogenase family, sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase . Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family. ; GO: 0016620 oxidoreductase activity acting on the aldehyde or oxo group of donors NAD or NADP as acceptor.
Probab=78.45  E-value=3.8  Score=19.94  Aligned_cols=15  Identities=13%  Similarity=0.071  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254781145|r  312 LAQGLEILFRGLLRL  326 (350)
Q Consensus       312 ~ae~~k~l~~~i~~l  326 (350)
                      +++|.+.|-+++-+|
T Consensus       277 ~D~Fa~kL~e~V~kl  291 (454)
T TIGR01780       277 YDEFAKKLAEAVKKL  291 (454)
T ss_pred             CHHHHHHHHHHHHHC
T ss_conf             048899999863313


No 9  
>COG3567 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.65  E-value=5.2  Score=19.03  Aligned_cols=165  Identities=18%  Similarity=0.186  Sum_probs=79.3

Q ss_pred             EEEEEEEECCCC---EECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCEE---EECC
Q ss_conf             689856306873---2035435431028999989988488787630366225313431210000112257414---5046
Q gi|254781145|r  165 FTCLRAMRAPHC---FIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPESVLNPQFGKPI---RVAA  238 (350)
Q Consensus       165 f~~~~~~p~p~~---~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~d~~~~~~g~~v---~~~~  238 (350)
                      .++|.--.-|..   +||.|+.+.+.+.-+......-.+-+-..-+..-.+-+     .+..+.+...-+...   ++.-
T Consensus       190 lii~qgn~~p~e~n~~wg~Svles~~d~lkr~Dta~anvgsl~feakidv~Ki-----~~l~~~lssd~~n~~a~~~f~l  264 (452)
T COG3567         190 LIIFQGNELPWERNGYWGDSVLESMYDALKRYDTATANVGSLFFEAKIDVLKI-----SGLSDTLSSDQGNQEAHKRFQL  264 (452)
T ss_pred             EEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEE-----CCHHHHHCCCCHHHHHHHHHHH
T ss_conf             46650445877546751078999999999985012243787887752015762-----6746442154011689999999


Q ss_pred             CCCCCCCCC--------CCCCCCCHHHHH-HHHHHHHHHHHHHHHHHH----HHHCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             665544444--------456887656799-999999999887524666----4303544335513899999999999889
Q gi|254781145|r  239 GMDIRSVLG--------IHSVPMIEKSFS-MLHYLDQELVDRTGISDI----SSGFSPEILQNMTATATSLIEQSGVGQV  305 (350)
Q Consensus       239 ~~~~~~i~~--------~~~~~~~~~~~~-~l~~~~~~~e~~tGi~~~----~~G~~~~~~~~~TAt~is~~~~~a~~r~  305 (350)
                      .....++..        .....   ..|. +=+.+++.....+|..++    .-|+.|.++   ++ |-+-+++    --
T Consensus       265 ~~~a~ain~llld~eeeytqks---~sfsglkDlLd~f~~~vaGAadmP~T~L~GQs~~gl---~s-gd~Di~N----Yy  333 (452)
T COG3567         265 AAMAKAINMLLLDAEEEYTQKS---NSFSGLKDLLDQFMMDVAGAADMPATRLFGQSPKGL---NS-GDSDIRN----YY  333 (452)
T ss_pred             HHHHHHHHHHHHCHHHHHHHHC---CCCCCHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCC---CC-CHHHHHH----HH
T ss_conf             9999988888623066765520---453457999999999851313474355226676556---65-4477899----99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHEEEECCEEEEECC
Q ss_conf             9999999999999999999999874885105989682685257
Q gi|254781145|r  306 ELIVRTLAQGLEILFRGLLRLIIQHQDKVRMVRLRDQWVSFDP  348 (350)
Q Consensus       306 ~~~~R~~ae~~k~l~~~i~~l~~~~~~~~~~~ri~g~~v~vdp  348 (350)
                      .-+.+....-++|.++.+..+++.-......   ..=|.+++|
T Consensus       334 drisa~QE~rLrP~Le~Ld~lL~~as~g~~P---~Dw~iEfnp  373 (452)
T COG3567         334 DRISAQQEDRLRPVLEVLDALLFRASVGECP---QDWEIEFNP  373 (452)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC---CCCEEECCC
T ss_conf             9988877740054999999999998618999---760576151


No 10 
>pfam06381 DUF1073 Protein of unknown function (DUF1073). This family consists of several hypothetical bacterial proteins. The function of this family is unknown.
Probab=74.07  E-value=6  Score=18.59  Aligned_cols=143  Identities=19%  Similarity=0.139  Sum_probs=67.1

Q ss_pred             CCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCC-CCCCCC--CCCCCC---------CCEEEECCCCCC
Q ss_conf             73203543543102899998998848878763036622531343-121000--011225---------741450466655
Q gi|254781145|r  175 HCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGS-IIDPES--VLNPQF---------GKPIRVAAGMDI  242 (350)
Q Consensus       175 ~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~-~~~~~d--~~~~~~---------g~~v~~~~~~~~  242 (350)
                      ..|||.|+...+.+.=+.....+...-+-+.......+.+..-+ +.+.++  .+.-+.         .+.......   
T Consensus       164 ~~~wG~Svlq~~~d~l~~~~~t~~~~~~ll~~~~~~v~k~~~l~~~~~~~~~~~l~~rl~~~~~~~s~~g~~~lD~e---  240 (361)
T pfam06381       164 YNFWGDSVLQSLYDALKAADRTTNSAAQLVFKARLTVIKVDGLRALLAAGGGDELIERLDLIKRTRSNEGILVIDAE---  240 (361)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEECCC---
T ss_conf             47666628999999999999999999988876410005435489886378679999999999970865372676165---


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH----HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             44444456887656799999999999887524666----43035443355138999999999998899999999999999
Q gi|254781145|r  243 RSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDI----SSGFSPEILQNMTATATSLIEQSGVGQVELIVRTLAQGLEI  318 (350)
Q Consensus       243 ~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~----~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~ae~~k~  318 (350)
                      ..+.....+. + .+-   +.+++..+.++|++++    .-|.+|..+ |  |||=+-+.+-    -..+......-+++
T Consensus       241 e~~e~~~~~l-s-Gl~---dvl~~~~~~iaaas~iP~t~LfG~sp~Gl-n--atGe~d~~nY----yd~i~~~Qe~~l~p  308 (361)
T pfam06381       241 EELEQISYSL-S-GLD---DVLDQFAQQLAGASDIPLTRLFGQSPAGL-N--STGEGDLRNY----YDRIKGIQENELRP  308 (361)
T ss_pred             CEEEEECCCC-C-CHH---HHHHHHHHHHHHHHCCCHHHHCCCCCCCC-C--CCCHHHHHHH----HHHHHHHHHHHHHH
T ss_conf             4146624676-7-889---99999999988750797677538899876-8--7761189999----99999999988768


Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999999987488
Q gi|254781145|r  319 LFRGLLRLIIQHQD  332 (350)
Q Consensus       319 l~~~i~~l~~~~~~  332 (350)
                      .+.+++.+++....
T Consensus       309 ~l~~l~~~i~~s~~  322 (361)
T pfam06381       309 LLERLIELLVLSEL  322 (361)
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             99999999988753


No 11 
>pfam12419 DUF3670 SNF2 Helicase protein. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00271, pfam00176. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=72.12  E-value=2  Score=21.83  Aligned_cols=17  Identities=59%  Similarity=1.081  Sum_probs=14.1

Q ss_pred             CHHEEEECCEEEEECCC
Q ss_conf             51059896826852578
Q gi|254781145|r  333 KVRMVRLRDQWVSFDPR  349 (350)
Q Consensus       333 ~~~~~ri~g~~v~vdpr  349 (350)
                      ....||++|+||.+||+
T Consensus        96 ~~~LV~~rg~WV~vD~~  112 (140)
T pfam12419        96 KRPLVRLRGQWVELDPE  112 (140)
T ss_pred             CCCEEEECCEEEEECHH
T ss_conf             89809998999996899


No 12 
>TIGR01538 portal_SPP1 phage portal protein, SPP1 family; InterPro: IPR006428   This group of sequences represent one of several distantly related families of phage portal protein. 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. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 kDa. .
Probab=67.48  E-value=8.4  Score=17.65  Aligned_cols=152  Identities=13%  Similarity=0.070  Sum_probs=99.3

Q ss_pred             CCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCC-------------------CCCCCCCCEEE
Q ss_conf             73203543543102899998998848878763036622531343121000-------------------01122574145
Q gi|254781145|r  175 HCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPES-------------------VLNPQFGKPIR  235 (350)
Q Consensus       175 ~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~d-------------------~~~~~~g~~v~  235 (350)
                      ..=-++|..+.+.+|-++=|++....++...-=+-..+ +--|....+++                   +++..|  +|.
T Consensus       243 nnee~~sdfe~~~sLid~Yd~~~s~~~~~~~~fsD~~L-~~~G~~~~~~~~~~~~~~R~~~~~~~~~~rllnleP--Pvd  319 (477)
T TIGR01538       243 NNEERMSDFESLISLIDAYDKAQSDTANDVEDFSDALL-VIFGKALEEEDVKEIRANRVEYEKVIREERLLNLEP--PVD  319 (477)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHHHCCCCCCHHHHHHHCCEEECCCCCCCEECCCC--CCC
T ss_conf             37554527888988986555552044003778889999-998410477535788752100110554100010578--867


Q ss_pred             ECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046665544444456887656799999999999887524666430354433-5513899999999999889999999999
Q gi|254781145|r  236 VAAGMDIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEIL-QNMTATATSLIEQSGVGQVELIVRTLAQ  314 (350)
Q Consensus       236 ~~~~~~~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~-~~~TAt~is~~~~~a~~r~~~~~R~~ae  314 (350)
                      -.+......+-.|..+.....+-..++.+...+-..|-+++.+    +... ++.|.-++.=...+..+.....-|.|..
T Consensus       320 qdGreg~~Dv~~L~k~~~~~~~~~~~~ri~~~i~k~~~~~d~~----De~f~G~~sG~AL~~k~~~L~~~~~~~qr~f~~  395 (477)
T TIGR01538       320 QDGREGDVDVKYLEKEFDVDQTEKLLERIEDDIHKITQVPDMS----DEKFGGSASGEALKYKLFGLDNLAVIAQRKFEA  395 (477)
T ss_pred             CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCC----CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4775367630242306886689999875787677640466798----443367772489999999876898998899987


Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999874885
Q gi|254781145|r  315 GLEILFRGLLRLIIQHQDK  333 (350)
Q Consensus       315 ~~k~l~~~i~~l~~~~~~~  333 (350)
                      |+|.-|+++.++...-...
T Consensus       396 sL~~rykL~~~~~~~~~~~  414 (477)
T TIGR01538       396 SLRRRYKLIAEVSRNVGEK  414 (477)
T ss_pred             HHHHHHHHHHHHHHHHCCC
T ss_conf             6778999999999983146


No 13 
>TIGR01555 phge_rel_HI1409 phage-associated protein, HI1409 family; InterPro: IPR006445   This group describes an uncharacterised family of proteins found in prophage regions of a number of bacterial genomes, including Haemophilus influenzae, Xylella fastidiosa, Salmonella typhi, and Enterococcus faecalis. Distantly related proteins can be found in the prophage-bearing plasmids of Borrelia burgdorferi..
Probab=45.49  E-value=19  Score=15.24  Aligned_cols=225  Identities=16%  Similarity=0.124  Sum_probs=113.3

Q ss_pred             CCCEEEEEEEEEE-E----EECCCCCCC----EEEEEEECCCCCEEEECCCCCCCCCEEEEEEEECCCC--------EEC
Q ss_conf             7514999997899-8----605898741----0899990787530464046555685689856306873--------203
Q gi|254781145|r  117 ALEMIEYYELYVT-I----DYDGDGIAE----LRRVIMAGGTGKDNILCNEEWNELPFTCLRAMRAPHC--------FIG  179 (350)
Q Consensus       117 ~~~~v~v~E~y~~-~----D~dgdg~~e----~~~v~~~g~~~~~~il~~~~~~~~Pf~~~~~~p~p~~--------~~G  179 (350)
                      +.+.+.|...|-- .    -+|.|-.++    ...+.++|.+....+-..+.+++-=..++.--..||.        .||
T Consensus       126 s~ksl~~l~~w~~k~~~~g~~D~DvfSpnyGq~~~y~i~g~s~nsrih~~~~v~~SR~~~i~~~~~phq~~~~~~n~~wg  205 (426)
T TIGR01555       126 SLKSLIVLDKWKVKKLSSGQIDEDVFSPNYGQIESYEIAGSSNNSRIHLLERVDYSRLLIISASEVPHQQELLSENELWG  205 (426)
T ss_pred             CEEEEEEECCCCCEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCHHHHHHHCCCCCCC
T ss_conf             42243520143410157873146778888887405786177654123320011034655534330213555413687224


Q ss_pred             CCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCEEEE----CCCC---CCCCCCCCCCCC
Q ss_conf             543543102899998998848878763036622531343121000011225741450----4666---554444445688
Q gi|254781145|r  180 ESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPESVLNPQFGKPIRV----AAGM---DIRSVLGIHSVP  252 (350)
Q Consensus       180 ~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~d~~~~~~g~~v~~----~~~~---~~~~i~~~~~~~  252 (350)
                      .|+.+.|.++-....+..-..-+-.+=+..-.+-...=+-.-..|-.+...-..+.+    +...   ...+--.+....
T Consensus       206 ~S~Le~~yd~L~r~Dta~~~vg~~~fe~~~dv~kiaglsd~~s~dq~~~~v~~~~~~~~~~Ks~~~~lllDae~ey~~k~  285 (426)
T TIGR01555       206 SSLLEKLYDVLKRYDTAVASVGDLLFEAVVDVYKIAGLSDKLSADQLENEVEKEIKLAASIKSAEAILLLDAEEEYDKKE  285 (426)
T ss_pred             CCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCC
T ss_conf             41799999998642201335898998766544300463003666510468999998999888777876411211046301


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             7656799999999999887524666-430354433551389999999999988999999999999999999999998748
Q gi|254781145|r  253 MIEKSFSMLHYLDQELVDRTGISDI-SSGFSPEILQNMTATATSLIEQSGVGQVELIVRTLAQGLEILFRGLLRLIIQHQ  331 (350)
Q Consensus       253 ~~~~~~~~l~~~~~~~e~~tGi~~~-~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~ae~~k~l~~~i~~l~~~~~  331 (350)
                      .  ..-.+=+.++++...++|..++ .+-+-+.+..+.||||-+=+++    --+-|.+....-+||.++.++.+++.-.
T Consensus       286 ~--sf~G~kell~~f~~~~aGAAdmP~T~LfGQs~~g~~~tgd~Di~N----Yy~rI~a~QE~~LRPvLevL~~~L~~a~  359 (426)
T TIGR01555       286 S--SFAGVKELLDEFRDDVAGAADMPKTVLFGQSGKGLAATGDEDIRN----YYERIKALQEDRLRPVLEVLDAVLMRAE  359 (426)
T ss_pred             C--CCCCHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCHHHHH----HHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             0--013368999999987520111663144157886422353034541----7989878404205838899999986652


Q ss_pred             CCHHEEEECCE----EEEECC
Q ss_conf             85105989682----685257
Q gi|254781145|r  332 DKVRMVRLRDQ----WVSFDP  348 (350)
Q Consensus       332 ~~~~~~ri~g~----~v~vdp  348 (350)
                      .... =||.-+    ||+++|
T Consensus       360 ~g~G-Grl~Pdsidw~~eFnp  379 (426)
T TIGR01555       360 VGEG-GRLDPDSIDWEVEFNP  379 (426)
T ss_pred             CCCC-CCCCCCEEEEEEEECC
T ss_conf             4888-7548850346887516


No 14 
>TIGR01238 D1pyr5carbox3 delta-1-pyrroline-5-carboxylate dehydrogenase; InterPro: IPR005933    The delta(1)-pyrroline-5-carboxylate synthetase (1.5.1.12 from EC) a mitochondrial inner membrane, ATP- and NADPH-dependent, bifunctional enzyme, catalyzes the reduction of glutamate to delta1-pyrroline-5-carboxylate, a critical step in the de novo biosynthesis of proline and ornithine. It is the rate-limiting enzyme in proline biosynthesis and is subject to feedback inhibition by proline.  1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH     This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. Members of this branch include the C-terminal domain of the PutA bifunctional proline dehydrogenase / delta-1-pyrroline-5-carboxylate dehydrogenase. ; GO: 0003842 1-pyrroline-5-carboxylate dehydrogenase activity, 0006561 proline biosynthetic process.
Probab=39.92  E-value=12  Score=16.52  Aligned_cols=25  Identities=36%  Similarity=0.335  Sum_probs=10.2

Q ss_pred             EEEEEEEEEEECCEEEEEEECHHHE
Q ss_conf             7758999997468368985765874
Q gi|254781145|r   31 VHDLRIRRKYSQGKVCVDAVSPDEF   55 (350)
Q Consensus        31 ~~~v~~~r~~~~~~v~ie~V~pedf   55 (350)
                      .+|+..||+-.+|.=.+-+|+||||
T Consensus       167 sfdGstrrvsrqG~G~~VcISPWNF  191 (525)
T TIGR01238       167 SFDGSTRRVSRQGLGAVVCISPWNF  191 (525)
T ss_pred             CCCCCCCEEEECCCCCEEEECCCCC
T ss_conf             4476421231057501688678751


No 15 
>pfam00862 Sucrose_synth Sucrose synthase. Sucrose synthases catalyse the synthesis of sucrose from UDP-glucose and fructose. This family includes the bulk of the sucrose synthase protein. However the carboxyl terminal region of the sucrose synthases belongs to the glycosyl transferase family pfam00534.
Probab=38.62  E-value=24  Score=14.55  Aligned_cols=137  Identities=11%  Similarity=0.117  Sum_probs=73.9

Q ss_pred             CCCCCEEEEEEEECCCCEECC----CHHH------HHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             556856898563068732035----4354------310289999899884887876303662253134312100001122
Q gi|254781145|r  160 WNELPFTCLRAMRAPHCFIGE----SLAA------SIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPESVLNPQ  229 (350)
Q Consensus       160 ~~~~Pf~~~~~~p~p~~~~G~----g~~d------~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~d~~~~~  229 (350)
                      ..++|.+--.-+--||.+||.    |.+|      .+.|--+++-..++..+.-..+...|++.+..--+.+-+...-..
T Consensus       266 l~RiPmvF~vvi~SpHGyFgQ~~VLG~PDTGGQVVYILDQvRaLE~em~~rik~qGLdi~P~IlIvTRLIP~a~GT~Cnq  345 (550)
T pfam00862       266 LGRIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRALESEMLVRIKQQGLDITPRILIVTRLLPDAVGTTCNQ  345 (550)
T ss_pred             HHHCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCCCCC
T ss_conf             73265016899965764002357577899897599971777889999999999758887760899974046888983585


Q ss_pred             C-----C----CEEEECCCCCCCCCCCCCCCCCCH-HHHHHHHHHH-----HHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             5-----7----414504666554444445688765-6799999999-----99988752466643035443355138999
Q gi|254781145|r  230 F-----G----KPIRVAAGMDIRSVLGIHSVPMIE-KSFSMLHYLD-----QELVDRTGISDISSGFSPEILQNMTATAT  294 (350)
Q Consensus       230 ~-----g----~~v~~~~~~~~~~i~~~~~~~~~~-~~~~~l~~~~-----~~~e~~tGi~~~~~G~~~~~~~~~TAt~i  294 (350)
                      .     |    -+.|+.=.... .+   -...++. ++++.|+.+-     +...+.-|-+|..-|.-.|.  |--|+=+
T Consensus       346 rlEkv~gT~~~~ILRVPFR~~~-gi---~~~WISRFeiwPYLE~fa~Da~~ei~~el~g~PDLIIGNYSDG--NLVAsLl  419 (550)
T pfam00862       346 RLEKVFGTEHTHILRVPFRTEK-GI---LRKWISRFEVWPYLETFAEDVASEIAAELQAKPDLIIGNYSDG--NLVASLL  419 (550)
T ss_pred             EEEECCCCCCCEEEECCCCCCC-CC---HHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC--HHHHHHH
T ss_conf             3001058765148972246899-81---4435455111187788889999999998489988798417772--2999999


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254781145|r  295 SLIEQSGV  302 (350)
Q Consensus       295 s~~~~~a~  302 (350)
                      +..+..-|
T Consensus       420 a~klgVTQ  427 (550)
T pfam00862       420 AHKLGVTQ  427 (550)
T ss_pred             HHHCCCCE
T ss_conf             86538710


No 16 
>PRK04366 glycine dehydrogenase subunit 2; Validated
Probab=35.97  E-value=27  Score=14.28  Aligned_cols=16  Identities=19%  Similarity=-0.114  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9889999999999999
Q gi|254781145|r  302 VGQVELIVRTLAQGLE  317 (350)
Q Consensus       302 ~~r~~~~~R~~ae~~k  317 (350)
                      -++....+-.=|+.++
T Consensus       349 L~~~s~~AvLNANYl~  364 (490)
T PRK04366        349 LREVSEDAVLNANYLM  364 (490)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             8999999999999999


No 17 
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=35.74  E-value=10  Score=17.07  Aligned_cols=51  Identities=18%  Similarity=0.175  Sum_probs=33.0

Q ss_pred             CCCCCEEEEEE----EECCCCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             55685689856----3068732035435431028999989988488787630366
Q gi|254781145|r  160 WNELPFTCLRA----MRAPHCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQP  210 (350)
Q Consensus       160 ~~~~Pf~~~~~----~p~p~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p  210 (350)
                      .+..-.+-|+|    .+..|=|-|.-+...+.+.|.+++.+.++=.+.+.||.+=
T Consensus       349 lG~r~iTEFnYR~a~~~~A~IFVGv~~~~~l~e~~~l~~~L~~~Gy~~~DLtdde  403 (508)
T TIGR01124       349 LGNRNITEFNYRYADDEDAHIFVGVQLANPLQERQELLARLNEAGYKVVDLTDDE  403 (508)
T ss_pred             CCCCEEEEEECCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCCCEECCCCCC
T ss_conf             1796033443246868975589865248615689999999972889441177453


No 18 
>TIGR00601 rad23 UV excision repair protein Rad23; InterPro: IPR004806   All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. Rad23 contains a ubiquitin-like domain that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains.    In humans, Rad23 complexes with the XPC protein.; GO: 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=31.90  E-value=19  Score=15.33  Aligned_cols=22  Identities=32%  Similarity=0.641  Sum_probs=9.3

Q ss_pred             EEEEEECHHHHHHHC---CCCHHHC
Q ss_conf             999995689998727---9804430
Q gi|254781145|r   71 GRKLYLTRSDLISMG---YDRESIN   92 (350)
Q Consensus        71 ~hr~~~t~~eL~~~G---y~~d~v~   92 (350)
                      +.....+..++.+||   |++..|.
T Consensus       189 G~~~e~~~~~Im~MGGGmYeRe~V~  213 (453)
T TIGR00601       189 GSEREETIEEIMEMGGGMYEREEVE  213 (453)
T ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             0007889999986278835088999


No 19 
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=29.80  E-value=34  Score=13.63  Aligned_cols=23  Identities=17%  Similarity=0.280  Sum_probs=9.8

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             54310289999899884887876
Q gi|254781145|r  183 AASIIEIQKIKTVLLRQTLDNLY  205 (350)
Q Consensus       183 ~d~l~~lQ~~~n~~~R~~lDn~~  205 (350)
                      ...+..+....+..+..+.+++.
T Consensus       120 ~~~l~~Lr~i~~~fl~~I~~s~~  142 (339)
T cd05131         120 ESSIQVLRSVTDKVLGSIMSSLD  142 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999998577


No 20 
>TIGR01472 gmd GDP-mannose 4,6-dehydratase; InterPro: IPR006368   This family represent GDP-mannose 4,6-dehydratase, also known as GDP-D-mannose dehydratase. This enzyme converts GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the first of three steps for the conversion of GDP-mannose to GDP-fucose in animals, plants, and bacteria. In bacteria, GDP-L-fucose acts as a precursor of surface antigens such as the extracellular polysaccharide colanic acid of Escherichia coli. Excluded from this family are members of the clade that are poorly related because of highly dervied (phylogenetically long-branch) sequences, e.g. Aneurinibacillus thermoaerophilus Gmd, described as a bifunctional GDP-mannose 4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase .; GO: 0008446 GDP-mannose 46-dehydratase activity, 0019673 GDP-mannose metabolic process, 0005622 intracellular.
Probab=29.37  E-value=27  Score=14.22  Aligned_cols=10  Identities=50%  Similarity=0.946  Sum_probs=7.3

Q ss_pred             CE-EEEECCCC
Q ss_conf             82-68525789
Q gi|254781145|r  341 DQ-WVSFDPRY  350 (350)
Q Consensus       341 g~-~v~vdpr~  350 (350)
                      |+ +|.|||||
T Consensus       312 Gk~~V~iD~rY  322 (365)
T TIGR01472       312 GKVVVEIDPRY  322 (365)
T ss_pred             CCEEEEECCCC
T ss_conf             70799964865


No 21 
>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=28.89  E-value=35  Score=13.52  Aligned_cols=164  Identities=13%  Similarity=0.120  Sum_probs=77.2

Q ss_pred             EEEEEEEECCCCEECCCHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCC------CCCCCC------CCC
Q ss_conf             68985630687320354354310289999899884887876303662253134312100------001122------574
Q gi|254781145|r  165 FTCLRAMRAPHCFIGESLAASIIEIQKIKTVLLRQTLDNLYWQNQPQTIVQEGSIIDPE------SVLNPQ------FGK  232 (350)
Q Consensus       165 f~~~~~~p~p~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn~~l~~~p~~~v~~~~~~~~~------d~~~~~------~g~  232 (350)
                      ..++........++|.|+.......-....+..+....-..-...|.+.+...+..+.+      +.++..      .|+
T Consensus       137 Vih~k~~~~~~~~~G~sp~~~~~~~i~~~~~~~~~~~~~~~ng~~~~gil~~~~~l~~e~~~~~~~~~~~~~~g~~n~g~  216 (348)
T pfam04860       137 VLHLKNGDSLDGIYGLSPLEAARESIGLALAAEEFARRFFKNGARPSGVLKYPGKLSEEQRERLREALEKQYKGAGNAGR  216 (348)
T ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             79996788887765448899999999999999999999985488755699828979989999999999998558434687


Q ss_pred             EEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             14504666554444445688765679999999999988752466643035443355138999999999998899999999
Q gi|254781145|r  233 PIRVAAGMDIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEILQNMTATATSLIEQSGVGQVELIVRTL  312 (350)
Q Consensus       233 ~v~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~~~~~e~~tGi~~~~~G~~~~~~~~~TAt~is~~~~~a~~r~~~~~R~~  312 (350)
                      ++....+..   +.++...+.-.......++..+.+-...||+....|....+    |.+.+           +...+.|
T Consensus       217 ~~vl~~g~~---~~~l~~~~~d~q~~e~~~~~~~~Ia~~fgVPp~llg~~~~~----t~~n~-----------e~~~~~f  278 (348)
T pfam04860       217 PLVLEGGLD---YTPLSLSPADAQFLESRKFTREDIARAFGVPPHLLGILEKA----TYSNI-----------EQQNLAF  278 (348)
T ss_pred             CEECCCCCC---EEECCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCC----CCCCH-----------HHHHHHH
T ss_conf             210389975---35667882357899999999999999979799993886556----75779-----------9999999


Q ss_pred             HH-HHHHHHHHHHHHH-HHHCCCHHEEEECCEEEEECC
Q ss_conf             99-9999999999999-874885105989682685257
Q gi|254781145|r  313 AQ-GLEILFRGLLRLI-IQHQDKVRMVRLRDQWVSFDP  348 (350)
Q Consensus       313 ae-~~k~l~~~i~~l~-~~~~~~~~~~ri~g~~v~vdp  348 (350)
                      .+ .+.|++..+-.-+ .+-.+..  -+..|.++.+|.
T Consensus       279 ~~~tl~P~~~~ie~el~~kLl~~~--~~~~~~~i~fd~  314 (348)
T pfam04860       279 VTNTLLPLLKRIEQELNRKLLTPE--ERRAGYYFEFNV  314 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCHH--HCCCCEEEEEEC
T ss_conf             996369999999999987535965--605874999925


No 22 
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=26.36  E-value=39  Score=13.23  Aligned_cols=15  Identities=33%  Similarity=0.620  Sum_probs=6.3

Q ss_pred             CCCCCEEEEEEECCC
Q ss_conf             288750464541246
Q gi|254781145|r   11 IKDSDVEVLEHSHRE   25 (350)
Q Consensus        11 ~~~~~ve~~~~~~~~   25 (350)
                      |+|+-|+|.|...++
T Consensus        30 L~DdTi~I~E~~~~N   44 (104)
T smart00676       30 LEDDTIEVFEPDVRN   44 (104)
T ss_pred             ECCCCEEEEECCCCC
T ss_conf             569969999727788


No 23 
>PRK07318 dipeptidase PepV; Reviewed
Probab=24.43  E-value=42  Score=13.00  Aligned_cols=68  Identities=10%  Similarity=0.104  Sum_probs=34.2

Q ss_pred             EEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCCCCEEEEEEEECCCCEECCCHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf             789986058987410899990787530464046555685689856306873203543543102899998998848878
Q gi|254781145|r  126 LYVTIDYDGDGIAELRRVIMAGGTGKDNILCNEEWNELPFTCLRAMRAPHCFIGESLAASIIEIQKIKTVLLRQTLDN  203 (350)
Q Consensus       126 ~y~~~D~dgdg~~e~~~v~~~g~~~~~~il~~~~~~~~Pf~~~~~~p~p~~~~G~g~~d~l~~lQ~~~n~~~R~~lDn  203 (350)
                      +++++++ |+|... .-++-+.|    .+..-+.|..-||..   ....++.||+|..|+=.++=.++=+ ++.+.|.
T Consensus        69 ~~g~~~~-G~g~~~-i~i~gH~D----VVP~gd~W~~dPF~~---~i~dG~lYGRGa~D~KG~~~a~l~A-lk~lkd~  136 (469)
T PRK07318         69 YAGHIEY-GEGEEV-LGILGHLD----VVPAGDGWDTDPYEP---VIKDGKIYARGTSDDKGPTMAAYYA-LKIIKEL  136 (469)
T ss_pred             EEEEEEE-CCCCCE-EEEECCCC----CCCCCCCCCCCCCCE---EEECCEEEEECCCCCCCCHHHHHHH-HHHHHHC
T ss_conf             6999983-699967-99973445----358999987799745---9989999960521266458999999-9999972


No 24 
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=22.42  E-value=28  Score=14.19  Aligned_cols=23  Identities=22%  Similarity=0.341  Sum_probs=15.5

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCCC
Q ss_conf             68999872798044302777876
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIISS   99 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~~   99 (350)
                      +.++|.+|||.++.+.+.-....
T Consensus         4 ~i~~L~~MGF~~~~~~~AL~~~~   26 (37)
T smart00165        4 KIDQLLEMGFSREEALKALRAAN   26 (37)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             89999985999999999999815


No 25 
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.17  E-value=28  Score=14.19  Aligned_cols=25  Identities=24%  Similarity=0.421  Sum_probs=16.1

Q ss_pred             CHHHHHHHCCCCHHHCCCCCCCCCC
Q ss_conf             6899987279804430277787641
Q gi|254781145|r   77 TRSDLISMGYDRESINNLPIISSQN  101 (350)
Q Consensus        77 t~~eL~~~Gy~~d~v~~~~~~~~~~  101 (350)
                      ..++|.+|||.++.+...-..+..+
T Consensus         4 ~v~~L~~MGF~~~~~~~AL~~~~~n   28 (38)
T cd00194           4 KLEQLLEMGFSREEARKALRATNNN   28 (38)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHCCC
T ss_conf             8999998599999999999985899


No 26 
>pfam11372 DUF3173 Protein of unknown function (DUF3173). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=21.86  E-value=46  Score=12.69  Aligned_cols=15  Identities=33%  Similarity=0.722  Sum_probs=11.6

Q ss_pred             EECHHHHHHHCCCCH
Q ss_conf             956899987279804
Q gi|254781145|r   75 YLTRSDLISMGYDRE   89 (350)
Q Consensus        75 ~~t~~eL~~~Gy~~d   89 (350)
                      .+|+.||+++||.+.
T Consensus         3 tvt~~dLi~lGf~~~   17 (59)
T pfam11372         3 TVTKKDLIKLGFKPH   17 (59)
T ss_pred             CCCHHHHHHHCCCHH
T ss_conf             567999999579887


Done!