Query         gi|254780528|ref|YP_003064941.1| chemotaxis protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 396
No_of_seqs    40 out of 42
Neff          4.5 
Searched_HMMs 39220
Date          Sun May 29 22:50:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780528.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12798 chemotaxis protein; R 100.0       0       0  870.7  42.6  367   29-396    31-415 (416)
  2 pfam07219 HemY_N HemY protein   81.6     2.1 5.3E-05   21.6   3.7   65   92-157    67-131 (134)
  3 TIGR02795 tol_pal_ybgF tol-pal  76.8     5.3 0.00013   19.2   9.5  103  184-287     3-109 (119)
  4 COG1729 Uncharacterized protei  73.7     6.4 0.00016   18.7   9.6   97  191-288   150-249 (262)
  5 PHA00368 internal virion prote  72.5     4.1 0.00011   19.8   3.1   17   30-46     23-39  (1316)
  6 PRK10803 hypothetical protein;  63.7      10 0.00026   17.4  10.6  104  182-286   141-248 (262)
  7 PRK10747 putative protoheme IX  57.8      13 0.00034   16.8  10.5  230   89-342    94-341 (398)
  8 pfam10602 RPN7 26S proteasome   57.5      13 0.00034   16.8   7.4   86  249-334    68-159 (174)
  9 TIGR03345 VI_ClpV1 type VI sec  52.9      11 0.00029   17.2   2.4   49  304-352   529-592 (852)
 10 TIGR03302 OM_YfiO outer membra  46.2      20 0.00052   15.7  16.8  186  110-318    33-228 (235)
 11 TIGR03346 chaperone_ClpB ATP-d  44.8      21 0.00055   15.5   3.5   49  304-352   528-591 (852)
 12 pfam02530 Porin_2 Porin subfam  44.4     9.6 0.00025   17.6   0.9   36    1-37      1-38  (378)
 13 PRK10716 long-chain fatty acid  42.0      20 0.00051   15.7   2.3   25    1-25      3-27  (437)
 14 pfam11768 DUF3312 Protein of u  41.1      24 0.00062   15.2   4.2  152   83-275   381-543 (544)
 15 PRK10865 protein disaggregatio  38.8      27 0.00068   15.0   3.1   49  304-352   531-594 (857)
 16 PRK00430 fis DNA-binding prote  33.0      33 0.00084   14.4   2.7   47   90-141    42-88  (98)
 17 KOG3928 consensus               29.7      38 0.00096   14.1   2.1  187  137-340   137-357 (461)
 18 COG3573 Predicted oxidoreducta  28.8      26 0.00065   15.1   1.1  152   91-249   227-409 (552)
 19 TIGR01163 rpe ribulose-phospha  28.4      39   0.001   13.9   2.2   26  368-393   137-162 (216)
 20 pfam10236 DAP3 Mitochondrial r  27.3      27 0.00068   15.0   0.9   19  320-338   178-196 (274)
 21 PRK10866 outer membrane protei  25.4      45  0.0011   13.6  10.7  116  111-226    33-168 (243)
 22 pfam08012 DUF1702 Protein of u  25.2      45  0.0012   13.6   6.2  139  192-346   141-296 (318)
 23 TIGR01818 ntrC nitrogen regula  24.2      47  0.0012   13.5   1.8   59   73-134   399-458 (471)
 24 PRK01905 DNA-binding protein F  24.0      48  0.0012   13.4   2.8   48   89-141    20-67  (77)
 25 TIGR00207 fliG flagellar motor  22.3      51  0.0013   13.2   2.3  167  114-305    33-216 (346)
 26 PRK11447 cellulose synthase su  21.4      54  0.0014   13.1  22.8   79  255-333   463-570 (1158)
 27 pfam10037 MRP-S27 Mitochondria  21.3      47  0.0012   13.5   1.3   25   77-101    99-123 (417)
 28 pfam07624 PSD2 Protein of unkn  20.8      55  0.0014   13.1   2.3   34   93-127     7-40  (76)

No 1  
>PRK12798 chemotaxis protein; Reviewed
Probab=100.00  E-value=0  Score=870.68  Aligned_cols=367  Identities=26%  Similarity=0.346  Sum_probs=346.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCC
Q ss_conf             77668999999999999965988999999999999989986169676056233799999897489889999998618898
Q gi|254780528|r   29 TIVPYQCVRSLQRALDEAMRGDISLQKKIPDIVKETGVQLRATHMDVFVDNRNIDAVWIYTIISQDLSVVDDLIAKDTKG  108 (396)
Q Consensus        29 ~l~Py~lvRSLq~lQD~Va~Gd~sA~~~q~~Ll~~i~~~l~~a~~~vw~d~rNv~Aa~iY~lSGG~P~~lr~l~~~d~~~  108 (396)
                      ..+|||||||||++||+||+|||+|++|||+||++|+++|++++|+||+||||+||+|||+||||||+|||+|+++|+.|
T Consensus        31 ~~~Py~lvRSLQ~lQD~ia~Gd~~A~~~qr~LL~~i~~~l~~a~~~vw~dprNv~Aaviy~lsGG~P~~l~~l~~~~~~~  110 (416)
T PRK12798         31 AREPYKLVRSLQLLQDRVAAGDHSAHEMQRFLLGTIDERLRAADPEVWDDPRNVRAALIYLLSGGNPATLRKLLARDKLG  110 (416)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCHHHHHHHHHCCCCHHHHHHHHHCCCCC
T ss_conf             33819999999999999974888899999999999869987189877278641248887785189869999999726787


Q ss_pred             CCCHHHHHHHHHHHCCCHHHHHHHHCCCCHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             43269999999972698799999831267100361000138887666643219899999999999967852999998776
Q gi|254780528|r  109 YFDIAIVYALKKYFSGQLEESSKELSKIKDKDNTRGIVPYLHLLIGRAMMPFSSQQAVHFFDYVRLTSPGTFLEEIALRN  188 (396)
Q Consensus       109 ~~d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a~l~~~~dp~~Al~llD~aRLlaPGTLvEEAALRR  188 (396)
                      ++|++|++|++||+|||++++++.|++|+|+++|++|||||+|++|++|+++||++|+++||||||++||||||||||||
T Consensus       111 ~~d~~l~~g~laY~~Gr~~ea~~~L~~i~~~~lp~~lg~~laLv~a~l~~~~dP~~Al~~lD~aRL~aPGTLvEEAALRR  190 (416)
T PRK12798        111 EVDQRLADGALAYLSGRGREARKLLSGVDPETLPAELGAYLALVQGNLMAATDPATALDRLDQARLLAPGTLVEEAALRR  190 (416)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             03299999999997698799998851378010472245779999888751368899999988999818815899999987


Q ss_pred             HHHHHHC-CCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
Q ss_conf             7887522-525899999999999720484656699999998520013577878999998578102579999999999853
Q gi|254780528|r  189 LLEITQN-EVGERAFGYIRAYVTQFHHSIYKDHFISVLLRFFLHGQLKLPDEDIVFTISFFSLEEQRAIYLKIAQNSVIS  267 (396)
Q Consensus       189 si~la~~-g~~~k~~~~a~~Y~rRf~~S~YA~~F~~~f~~~~v~~~~~~~~~~l~~ils~~d~~~q~~lYL~IAR~Ali~  267 (396)
                      ||+|+.. |+++||+.|++||+|||+||||+||||++|+.+++++++++++++|+++|++||+++|+++||+|||+|+|+
T Consensus       191 ~i~la~~~g~~~r~~~~a~~Y~rRf~~S~Ya~~F~~~F~~~vv~~~~~~~~~~l~~ils~~d~~~qr~lYL~IAR~A~i~  270 (416)
T PRK12798        191 SLFIAAQLGDADKFEALSRNYLRRFRHSPYAGNFAQRFVLAVVRLSDRIRDERLVEILSEMDPESQRELYLRIARAALID  270 (416)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC
T ss_conf             76999863767899999999999850680067899999999987403442879999998449687899999999999870


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             96479999999999631578886556899999997501789899999984399788897539999999999998530456
Q gi|254780528|r  268 GKRKIGFLAIKQLKRIIDRLDYKDLATIQLYENILNIPFVDIMSLQRSTCNIPYYSLMEQDRYLKKASEIIMSEIGKSLI  347 (396)
Q Consensus       268 G~~~lA~~As~rA~~L~~~~~~~~~~ra~LY~aaa~i~s~d~~~a~~~L~~Id~~~L~~~Dr~L~~AA~~ia~~I~r~~~  347 (396)
                      ||+++++||++||++|+++ ++.+.+|++||+++++|+|+++++++++|++||+++|+++||+|++||++||++|+|++.
T Consensus       271 Gk~~~a~~As~rA~~La~~-~~~~~~~A~LY~~aa~v~s~~~~~al~~L~~I~~~~L~~~Dr~Ll~AA~~iA~~V~r~p~  349 (416)
T PRK12798        271 GKTELARFAAERALKLAAE-DSAEATRARLYRAAALVASDDADSALEELSQIDRAKLSERDRALLDAALSVARQVRRPPD  349 (416)
T ss_pred             CHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             4289999999999974567-887507999999987379876999999986699654790239999999999997507999


Q ss_pred             CCCCCCCC-----------------CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             76744466-----------------22445444534566543057678978999999999864149
Q gi|254780528|r  348 DIDFEHIQ-----------------KDLLLDKKEPRHTNVSMGIESFIKKNRSQIESIDVLLAEAR  396 (396)
Q Consensus       348 ~a~~~~~q-----------------~~~~~~~~~~~~~~~~~~~~~~v~~ar~~l~eiD~LL~~~r  396 (396)
                      +.+.+..+                 ++..+...++...+..++.++||+++|+||+|||.||++.+
T Consensus       350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fi~~arskL~eID~lL~~~~  415 (416)
T PRK12798        350 ASSLAQASAPSTSRPRPTVADAAALEAQQGVAFTSARTSSDPDLQAFIARARSKLDEIDALLGKTG  415 (416)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             986222457566787556676200112345555433688770199999973877999999986536


No 2  
>pfam07219 HemY_N HemY protein N-terminus. This family represents the N-terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. This is a membrane protein involved in a late step of protoheme IX synthesis.
Probab=81.56  E-value=2.1  Score=21.62  Aligned_cols=65  Identities=9%  Similarity=-0.040  Sum_probs=47.4

Q ss_pred             CCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCHHCCCCCCCHHHHHHHHHHH
Q ss_conf             898899999986188984326999999997269879999983126710036100013888766664
Q gi|254780528|r   92 SQDLSVVDDLIAKDTKGYFDIAIVYALKKYFSGQLEESSKELSKIKDKDNTRGIVPYLHLLIGRAM  157 (396)
Q Consensus        92 GG~P~~lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a~l~  157 (396)
                      -+-|..++.-..+-......+.+.+|++++.+|+-.+|++.+.+-.. ..+...-.|+.=++++..
T Consensus        67 ~~~p~~~~~~~~~rr~~k~~~al~~Gl~a~~~Gd~~~A~k~~~ka~k-~~~~p~l~~LlaA~aA~~  131 (134)
T pfam07219        67 IRLPRRVRRYFRRRKRRRGRKALSEGLLALAEGDWALAERLARKAAE-LEDQPPLALLLAARAAQA  131 (134)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHH
T ss_conf             73658999999999999999999999999978999999999999876-379935799999999988


No 3  
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF; InterPro: IPR014162   Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, and a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction..
Probab=76.80  E-value=5.3  Score=19.17  Aligned_cols=103  Identities=10%  Similarity=0.133  Sum_probs=76.9

Q ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCCCHHH--HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHH-HHHHH
Q ss_conf             9877678875-225258999999999997204846566--9999999852001357787899999857810257-99999
Q gi|254780528|r  184 IALRNLLEIT-QNEVGERAFGYIRAYVTQFHHSIYKDH--FISVLLRFFLHGQLKLPDEDIVFTISFFSLEEQR-AIYLK  259 (396)
Q Consensus       184 AALRRsi~la-~~g~~~k~~~~a~~Y~rRf~~S~YA~~--F~~~f~~~~v~~~~~~~~~~l~~ils~~d~~~q~-~lYL~  259 (396)
                      .+.=..+... ..|+-+......++++..|+.|+|+.|  ||-= -+.+..++.+.-...+..+++.-+-...+ +-.|.
T Consensus         3 ~~~y~aa~~~lk~gdY~~A~~~F~~F~~~YP~S~y~pnA~YWLG-e~~y~~~~~~~A~~~f~~v~~~yp~s~KaPdALLK   81 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLG-EAYYAQGDYADAAKAFLAVVKKYPKSPKAPDALLK   81 (119)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH
T ss_conf             67899999998538878999999999886879876710547999-99999733999999999998645899860689999


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9999985396479999999999631578
Q gi|254780528|r  260 IAQNSVISGKRKIGFLAIKQLKRIIDRL  287 (396)
Q Consensus       260 IAR~Ali~G~~~lA~~As~rA~~L~~~~  287 (396)
                      ++....--|+.+-|+..-+++.+-=+..
T Consensus        82 lg~~~~~~g~~~~A~~~l~~V~~~YP~s  109 (119)
T TIGR02795        82 LGMSLQELGDKEKAKATLQQVIKRYPGS  109 (119)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf             9999987289889999999998566998


No 4  
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.66  E-value=6.4  Score=18.68  Aligned_cols=97  Identities=10%  Similarity=0.125  Sum_probs=71.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCHHH--HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHH-HHHHHHHHHHHHC
Q ss_conf             875225258999999999997204846566--9999999852001357787899999857810257-9999999999853
Q gi|254780528|r  191 EITQNEVGERAFGYIRAYVTQFHHSIYKDH--FISVLLRFFLHGQLKLPDEDIVFTISFFSLEEQR-AIYLKIAQNSVIS  267 (396)
Q Consensus       191 ~la~~g~~~k~~~~a~~Y~rRf~~S~YA~~--F~~~f~~~~v~~~~~~~~~~l~~ils~~d~~~q~-~lYL~IAR~Ali~  267 (396)
                      -+...|+........+.|+.+|+.|+|..|  ||=- -..+..+..+.--..+..+....+..-.. +.+|.++..-.--
T Consensus       150 ~~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLG-e~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l  228 (262)
T COG1729         150 DLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLG-ESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRL  228 (262)
T ss_pred             HHHHCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHH-HHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             999838788999999999970999755602499988-9998624616799999999983899998828999999999982


Q ss_pred             CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             964799999999996315788
Q gi|254780528|r  268 GKRKIGFLAIKQLKRIIDRLD  288 (396)
Q Consensus       268 G~~~lA~~As~rA~~L~~~~~  288 (396)
                      |+.+-|+.--+++.+-=+..+
T Consensus       229 ~~~d~A~atl~qv~k~YP~t~  249 (262)
T COG1729         229 GNTDEACATLQQVIKRYPGTD  249 (262)
T ss_pred             CCHHHHHHHHHHHHHHCCCCH
T ss_conf             177999999999998789977


No 5  
>PHA00368 internal virion protein D
Probab=72.46  E-value=4.1  Score=19.82  Aligned_cols=17  Identities=18%  Similarity=0.171  Sum_probs=10.1

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             76689999999999999
Q gi|254780528|r   30 IVPYQCVRSLQRALDEA   46 (396)
Q Consensus        30 l~Py~lvRSLq~lQD~V   46 (396)
                      =.||.++|.+.+.-++-
T Consensus        23 gvsyd~l~k~~~~es~f   39 (1316)
T PHA00368         23 GVSYDLLRKVAWDESRF   39 (1316)
T ss_pred             CCCHHHHHHHHHHHHCC
T ss_conf             98799999876533036


No 6  
>PRK10803 hypothetical protein; Provisional
Probab=63.69  E-value=10  Score=17.42  Aligned_cols=104  Identities=8%  Similarity=0.081  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCCHHH--HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHH-HHHHH
Q ss_conf             99987767887522-5258999999999997204846566--99999998520013577878999998578102-57999
Q gi|254780528|r  182 EEIALRNLLEITQN-EVGERAFGYIRAYVTQFHHSIYKDH--FISVLLRFFLHGQLKLPDEDIVFTISFFSLEE-QRAIY  257 (396)
Q Consensus       182 EEAALRRsi~la~~-g~~~k~~~~a~~Y~rRf~~S~YA~~--F~~~f~~~~v~~~~~~~~~~l~~ils~~d~~~-q~~lY  257 (396)
                      |..+-..-+.+... ++.+........|+..|+.|+|+.|  ||--- ..+.....+.-...+..++...+... .-+-+
T Consensus       141 e~~~Y~~A~~Lvl~~k~y~~Ai~aF~~Fi~~yP~s~y~~nA~YWLGe-~~y~~~~~~~A~~~F~~vv~~yP~s~K~pdAl  219 (262)
T PRK10803        141 ANTDYNAAIALVQDKSRQDDAIVAFQNFIKKYPDSTYQPNANYWLGQ-LNYNKGKKDDAAYYFASVVKNYPKSPKAADAM  219 (262)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHH-HHHHHCCHHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             27789999999997356999999999999878799877430999999-99974378999999999998677998678999


Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             99999998539647999999999963157
Q gi|254780528|r  258 LKIAQNSVISGKRKIGFLAIKQLKRIIDR  286 (396)
Q Consensus       258 L~IAR~Ali~G~~~lA~~As~rA~~L~~~  286 (396)
                      +.++....--|+..-|+..-++...-=+.
T Consensus       220 lklg~~~~~lg~~~~Ak~~l~~vi~~YP~  248 (262)
T PRK10803        220 FKVGVIMQDKGDTAKAKAVYQQVIKKYPG  248 (262)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCC
T ss_conf             99999999859999999999999998859


No 7  
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=57.79  E-value=13  Score=16.79  Aligned_cols=230  Identities=11%  Similarity=0.019  Sum_probs=116.4

Q ss_pred             HHCCCCHHHHHHHHHCCCCCCCCHHHH---HHH-HHHHCCCHHHHHHHHCCCCHHCCCCCCCHHHHHHHHHH-HHHCCHH
Q ss_conf             974898899999986188984326999---999-99726987999998312671003610001388876666-4321989
Q gi|254780528|r   89 TIISQDLSVVDDLIAKDTKGYFDIAIV---YAL-KKYFSGQLEESSKELSKIKDKDNTRGIVPYLHLLIGRA-MMPFSSQ  163 (396)
Q Consensus        89 ~lSGG~P~~lr~l~~~d~~~~~d~~L~---~g~-laY~~Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a~l-~~~~dp~  163 (396)
                      .|..||....++.+.+... +.|.+++   -++ -++-.|........|....  +..+.=.-.+.|+++.+ +.+.++.
T Consensus        94 ~l~EG~~~~AeK~l~k~a~-~~~~pllnyL~AArAA~~~g~~~~rd~yL~~A~--e~~p~a~lav~lt~Ael~l~~~q~e  170 (398)
T PRK10747         94 KLAEGDYQQVEKLMAKNAD-HAEQPVVNYLLAAEAAQQRGDEARANQHLERAA--ELAGNDTIPVEITRVRLQLARNENH  170 (398)
T ss_pred             HHHCCCHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHCCCHH
T ss_conf             9877799999999986343-567748899999999998889899999999988--8589848899999999999779989


Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHH----------HHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99999999999678529999987767887522-52589999999999----------97204846566999999985200
Q gi|254780528|r  164 QAVHFFDYVRLTSPGTFLEEIALRNLLEITQN-EVGERAFGYIRAYV----------TQFHHSIYKDHFISVLLRFFLHG  232 (396)
Q Consensus       164 ~Al~llD~aRLlaPGTLvEEAALRRsi~la~~-g~~~k~~~~a~~Y~----------rRf~~S~YA~~F~~~f~~~~v~~  232 (396)
                      .|+.-++..+-..|.--   ..||-...+... ++-+.-..+....-          .+...-.|.+.+.+.        
T Consensus       171 ~Ala~L~~L~~~~p~~~---~VL~Ll~~~y~~~~dW~aL~~LLp~L~K~~~l~~~e~~~L~~~a~~~ll~~~--------  239 (398)
T PRK10747        171 AARHGVDKLLEVTPRHP---EVLRLAEQAYIRTGAWSSLLDIIPSMAKAHVGDEEHRAMLEQQAWIGLMDQA--------  239 (398)
T ss_pred             HHHHHHHHHHHCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH--------
T ss_conf             99999999986199999---9999999999987459999999999987579999999999999999999998--------


Q ss_pred             CCCCCHHHHHHHHHHCCCHHHHHHHHHHH--HHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHH
Q ss_conf             13577878999998578102579999999--9998539647999999999963157888655689999999750178989
Q gi|254780528|r  233 QLKLPDEDIVFTISFFSLEEQRAIYLKIA--QNSVISGKRKIGFLAIKQLKRIIDRLDYKDLATIQLYENILNIPFVDIM  310 (396)
Q Consensus       233 ~~~~~~~~l~~ils~~d~~~q~~lYL~IA--R~Ali~G~~~lA~~As~rA~~L~~~~~~~~~~ra~LY~aaa~i~s~d~~  310 (396)
                      ..+.+.+.|...-..+++..+.+..+..+  +.=+-.|..+-|..-..+.+.-.     -+.....+|   ..+.+.|..
T Consensus       240 ~~~~~~~~L~~~W~~lp~~~r~~~~l~~~ya~~Li~~g~~~~A~~ll~~~Lkk~-----wd~~Lv~ly---~~l~~~d~~  311 (398)
T PRK10747        240 RADNGSEGLRNWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIIIDGLKRQ-----YDDRLVLPI---PRLKTNNPE  311 (398)
T ss_pred             HHHCCHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-----CCHHHHHHH---HHCCCCCHH
T ss_conf             732347999999986899875699999999999986899689999999998618-----998999998---756779989


Q ss_pred             HHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999843997888975399999999999985
Q gi|254780528|r  311 SLQRSTCNIPYYSLMEQDRYLKKASEIIMSEI  342 (396)
Q Consensus       311 ~a~~~L~~Id~~~L~~~Dr~L~~AA~~ia~~I  342 (396)
                      ..++.+.+--  +=.++|..|+-+-..++-.-
T Consensus       312 ~~l~~~e~wl--k~~~~~~~Ll~aLGrL~~~~  341 (398)
T PRK10747        312 QLEKVLRQQI--KQVGDRPLLWSTLGQSLMKH  341 (398)
T ss_pred             HHHHHHHHHH--HCCCCCHHHHHHHHHHHHHH
T ss_conf             9999999987--31899989999999999973


No 8  
>pfam10602 RPN7 26S proteasome subunit RPN7. RPN7 (known as the non ATPase regulatory subunit 6 in higher eukaryotes) is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity. The 26S proteasome is is involved in the ATP-dependent degradation of ubiquitinated proteins.
Probab=57.54  E-value=13  Score=16.76  Aligned_cols=86  Identities=12%  Similarity=0.094  Sum_probs=66.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCC-CCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHH-----
Q ss_conf             81025799999999998539647999999999963157888-655689999999750178989999998439978-----
Q gi|254780528|r  249 SLEEQRAIYLKIAQNSVISGKRKIGFLAIKQLKRIIDRLDY-KDLATIQLYENILNIPFVDIMSLQRSTCNIPYY-----  322 (396)
Q Consensus       249 d~~~q~~lYL~IAR~Ali~G~~~lA~~As~rA~~L~~~~~~-~~~~ra~LY~aaa~i~s~d~~~a~~~L~~Id~~-----  322 (396)
                      -+....+++|.+-|-++.-|......--..||.++...++. ..+.+...|.|.+.+...++.+|...+-.....     
T Consensus        68 s~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~e~ggDw~r~nrlk~y~Gl~~l~~r~f~~AA~~fl~~~~tf~~~e  147 (174)
T pfam10602        68 SLGHKIDMCLNLIRVGIFFNDWDHVSKYIEKAKSLIEKGGDWERRNRLKVYEGLALLAIRDFKEAAKLFLDSLSTFTSTE  147 (174)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCC
T ss_conf             84599999999999999970099999999999856514455878988999999999971649999999963767888463


Q ss_pred             HCCHHHHHHHHH
Q ss_conf             889753999999
Q gi|254780528|r  323 SLMEQDRYLKKA  334 (396)
Q Consensus       323 ~L~~~Dr~L~~A  334 (396)
                      -++..|...-..
T Consensus       148 lis~~dia~Y~~  159 (174)
T pfam10602       148 LISYEDVAVYGV  159 (174)
T ss_pred             CCCHHHHHHHHH
T ss_conf             426768899999


No 9  
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=52.88  E-value=11  Score=17.18  Aligned_cols=49  Identities=12%  Similarity=0.092  Sum_probs=33.5

Q ss_pred             HCCCCHHHHHHHHHCCCHHHCCHHHHHH-H--------------HHHHHHHHHHHCCCCCCCCC
Q ss_conf             0178989999998439978889753999-9--------------99999999853045676744
Q gi|254780528|r  304 IPFVDIMSLQRSTCNIPYYSLMEQDRYL-K--------------KASEIIMSEIGKSLIDIDFE  352 (396)
Q Consensus       304 i~s~d~~~a~~~L~~Id~~~L~~~Dr~L-~--------------~AA~~ia~~I~r~~~~a~~~  352 (396)
                      |...++.+.......||..++...+..- +              +|..+|+..|+++-...+..
T Consensus       529 V~~~~ia~vvs~~tgIPv~~l~~~e~~~l~~le~~L~~~ViGQ~~Av~~v~~ai~~sraGl~d~  592 (852)
T TIGR03345       529 VDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDP  592 (852)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             6899999999999689878861788888886799999997284999999999999987179999


No 10 
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=46.20  E-value=20  Score=15.67  Aligned_cols=186  Identities=10%  Similarity=-0.051  Sum_probs=121.3

Q ss_pred             CCHHHHHHHHHHHCCCHHHHHHHHCCCCHHCCCCCCCHHHHHHHH-HHHHHCCHHHHHHHHHHHHHHCCCC-HHHHHHHH
Q ss_conf             326999999997269879999983126710036100013888766-6643219899999999999967852-99999877
Q gi|254780528|r  110 FDIAIVYALKKYFSGQLEESSKELSKIKDKDNTRGIVPYLHLLIG-RAMMPFSSQQAVHFFDYVRLTSPGT-FLEEIALR  187 (396)
Q Consensus       110 ~d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a-~l~~~~dp~~Al~llD~aRLlaPGT-LvEEAALR  187 (396)
                      .+.---.|...+-+|+-.+|.+.|..+...+--+..+...-+-.| ......+...|+..++.---.-|+. -++.|--.
T Consensus        33 ~~~lY~~a~~~~~~~~y~~A~~~fe~l~~~yp~s~~a~~A~l~~a~a~y~~~~y~~A~~~~~~Fi~~yP~~~~~~ya~y~  112 (235)
T TIGR03302        33 AEELYNEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYL  112 (235)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             99999999999987899999999999998689931379999999999997643999999999999988774349999999


Q ss_pred             HHHHHH-H------C-CCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             678875-2------2-5258999999999997204846566999999985200135778789999985781025799999
Q gi|254780528|r  188 NLLEIT-Q------N-EVGERAFGYIRAYVTQFHHSIYKDHFISVLLRFFLHGQLKLPDEDIVFTISFFSLEEQRAIYLK  259 (396)
Q Consensus       188 Rsi~la-~------~-g~~~k~~~~a~~Y~rRf~~S~YA~~F~~~f~~~~v~~~~~~~~~~l~~ils~~d~~~q~~lYL~  259 (396)
                      +.+.-- +      + ....+.+..-+.++++|++|+|+.+-...+...--+...                   ++  +.
T Consensus       113 ~a~s~~~~~~~~~rDq~~~~~A~~~f~~~i~~yP~S~ya~dA~~~i~~l~~~LA~-------------------~e--~~  171 (235)
T TIGR03302       113 RGLSNYKQIDDSDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAG-------------------KE--LY  171 (235)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-------------------HH--HH
T ss_conf             8799887366544580899999999999998889965799999999999999999-------------------99--99


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf             99999853964799999999996315788865568999999975017898999999843
Q gi|254780528|r  260 IAQNSVISGKRKIGFLAIKQLKRIIDRLDYKDLATIQLYENILNIPFVDIMSLQRSTCN  318 (396)
Q Consensus       260 IAR~Ali~G~~~lA~~As~rA~~L~~~~~~~~~~ra~LY~aaa~i~s~d~~~a~~~L~~  318 (396)
                      ||+-=.-.|+-.-|.--.+.+..-=++.  ...+.|..+-+-+-..-+..+++..+.+.
T Consensus       172 ia~~Y~k~~~y~aAi~r~~~vl~~Yp~t--~~~~eAl~~l~eay~~lg~~~~A~~~~~~  228 (235)
T TIGR03302       172 VARFYLKRGAYVAAINRFETVVENYPDT--PATEEALARLVEAYLALGLTDLAQDAAAV  228 (235)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999998417099999999999868998--51399999999999986998999999999


No 11 
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=44.79  E-value=21  Score=15.54  Aligned_cols=49  Identities=18%  Similarity=0.205  Sum_probs=34.3

Q ss_pred             HCCCCHHHHHHHHHCCCHHHCCHHHHHHH---------------HHHHHHHHHHHCCCCCCCCC
Q ss_conf             01789899999984399788897539999---------------99999999853045676744
Q gi|254780528|r  304 IPFVDIMSLQRSTCNIPYYSLMEQDRYLK---------------KASEIIMSEIGKSLIDIDFE  352 (396)
Q Consensus       304 i~s~d~~~a~~~L~~Id~~~L~~~Dr~L~---------------~AA~~ia~~I~r~~~~a~~~  352 (396)
                      |...++.+.......||..++...+..-+               +|..+|+..|+++-...+..
T Consensus       528 V~~~~ia~vvs~~tgIPv~~~~~~e~~~L~~Le~~L~~rViGQd~AI~~I~~aI~~sraGL~dp  591 (852)
T TIGR03346       528 VTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDP  591 (852)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             7999999999999688667666547999987888899897170999999999999997188889


No 12 
>pfam02530 Porin_2 Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.
Probab=44.39  E-value=9.6  Score=17.61  Aligned_cols=36  Identities=28%  Similarity=0.280  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHH
Q ss_conf             9715778999999998743432024435--776689999
Q gi|254780528|r    1 MNQKYLICTMMVAMDVFFSFATDQDLVR--TIVPYQCVR   37 (396)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~--~l~Py~lvR   37 (396)
                      ||-|-++--++.|+....| |++.|..=  ++||.|-||
T Consensus         1 MNiKsLlLgSaaalvA~sg-A~AAD~iV~aePEpvEYVr   38 (378)
T pfam02530         1 MNIKSLLLGSAAALAAVSG-AQAADAIVAAEPEPVEYVR   38 (378)
T ss_pred             CCHHHHHHHHHHHHHHHCC-HHHCCCCCCCCCCCCCEEE
T ss_conf             9567888888999998400-2013653347877632589


No 13 
>PRK10716 long-chain fatty acid outer membrane transporter; Provisional
Probab=42.00  E-value=20  Score=15.69  Aligned_cols=25  Identities=24%  Similarity=0.186  Sum_probs=20.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9715778999999998743432024
Q gi|254780528|r    1 MNQKYLICTMMVAMDVFFSFATDQD   25 (396)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~a~~~~   25 (396)
                      ||||.++-+.+||+.+.+...++..
T Consensus         3 ~~~~~~~~k~~la~~~~l~ss~a~A   27 (437)
T PRK10716          3 MSQKTLFTKSALAVAVALISTQAWS   27 (437)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4451177899999999988503111


No 14 
>pfam11768 DUF3312 Protein of unknown function (DUF3312). This is a eukaryotic family of uncharacterized proteins.
Probab=41.12  E-value=24  Score=15.19  Aligned_cols=152  Identities=15%  Similarity=0.201  Sum_probs=82.0

Q ss_pred             HHHHHHHHCCCCHHHHHHHH---HCCCCCCCCHHHHHHHHHHHC-CCHHHHHHHHCCCCHHCCCCCCCHHHHHHHHHHHH
Q ss_conf             99999897489889999998---618898432699999999726-98799999831267100361000138887666643
Q gi|254780528|r   83 DAVWIYTIISQDLSVVDDLI---AKDTKGYFDIAIVYALKKYFS-GQLEESSKELSKIKDKDNTRGIVPYLHLLIGRAMM  158 (396)
Q Consensus        83 ~Aa~iY~lSGG~P~~lr~l~---~~d~~~~~d~~L~~g~laY~~-Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a~l~~  158 (396)
                      +..+.-.+.+|.-+++|-.+   .++..|..+     -.-+|+. ++-++|...|..++=.+....---.+..|.--++-
T Consensus       381 ~~~l~L~f~~GPLavlr~~lG~~~~G~lg~~~-----L~~~yl~~~qv~eAv~iL~smnW~t~G~~C~~~L~~I~N~Llk  455 (544)
T pfam11768       381 DCLLLLIFEQGPLACLRFKLGVGSRGDLGTSE-----LISKYIRLSQVEEAVNILLSMNWDTYGAMCLISLHLIANYLLR  455 (544)
T ss_pred             CCEEEEEECCCCEEEEEEECCCCCCCCCCHHH-----HHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             41589996388769999730323467446278-----8999875143899998775178342025899999999999960


Q ss_pred             H-CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH--HC---CCHHHHHHHHHHHHHHHCCCCCHHH-HHHHHHHHHHH
Q ss_conf             2-1989999999999996785299999877678875--22---5258999999999997204846566-99999998520
Q gi|254780528|r  159 P-FSSQQAVHFFDYVRLTSPGTFLEEIALRNLLEIT--QN---EVGERAFGYIRAYVTQFHHSIYKDH-FISVLLRFFLH  231 (396)
Q Consensus       159 ~-~dp~~Al~llD~aRLlaPGTLvEEAALRRsi~la--~~---g~~~k~~~~a~~Y~rRf~~S~YA~~-F~~~f~~~~v~  231 (396)
                      + -+|.+..-              =|+||.-  |-+  ..   .-..+|.--...|.|||-|---.-+ |...|.-++.-
T Consensus       456 q~L~~~RE~q--------------Le~alGs--FyaP~rPLs~~t~lEyrd~Is~laRRFFHhLLRy~rFEKAFlLAvDi  519 (544)
T pfam11768       456 QRLGPEREAQ--------------LEASLGS--FYAPARPLSDETILEYRDPVSDYARRFFHHLLRYKRFEKAFLLAVDI  519 (544)
T ss_pred             CCCCCHHHHH--------------HHHHHHC--CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             8798057899--------------9987505--31788567778999875188899999999999888888989887604


Q ss_pred             CCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             01357787899999857810257999999999985396479999
Q gi|254780528|r  232 GQLKLPDEDIVFTISFFSLEEQRAIYLKIAQNSVISGKRKIGFL  275 (396)
Q Consensus       232 ~~~~~~~~~l~~ils~~d~~~q~~lYL~IAR~Ali~G~~~lA~~  275 (396)
                      ++                    |++++-|-.-|+--|..++|..
T Consensus       520 g~--------------------rDLFMDihy~A~d~ge~~lA~v  543 (544)
T pfam11768       520 GD--------------------RDLFMDLHYLAKDKGELALAKV  543 (544)
T ss_pred             CC--------------------HHHHHHHHHHHHHCCHHHHHHC
T ss_conf             63--------------------7666778998872161555411


No 15 
>PRK10865 protein disaggregation chaperone; Provisional
Probab=38.78  E-value=27  Score=14.97  Aligned_cols=49  Identities=18%  Similarity=0.209  Sum_probs=34.9

Q ss_pred             HCCCCHHHHHHHHHCCCHHHCCHHHHHHH---------------HHHHHHHHHHHCCCCCCCCC
Q ss_conf             01789899999984399788897539999---------------99999999853045676744
Q gi|254780528|r  304 IPFVDIMSLQRSTCNIPYYSLMEQDRYLK---------------KASEIIMSEIGKSLIDIDFE  352 (396)
Q Consensus       304 i~s~d~~~a~~~L~~Id~~~L~~~Dr~L~---------------~AA~~ia~~I~r~~~~a~~~  352 (396)
                      |...++.+.......||-.++...+..-+               +|..+|+..|+++-...+..
T Consensus       531 V~~~~ia~vvs~~TgIPv~~l~~~e~~~L~~le~~L~~rViGQd~AI~~v~~aI~~sraGL~dp  594 (857)
T PRK10865        531 VTDAEIAEVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDP  594 (857)
T ss_pred             CCHHHHHHHHHHHHCCCCHHCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             6899999999999689830213105899999999998785280999999999999986389999


No 16 
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=33.03  E-value=33  Score=14.41  Aligned_cols=47  Identities=13%  Similarity=0.141  Sum_probs=32.6

Q ss_pred             HCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCHHCC
Q ss_conf             7489889999998618898432699999999726987999998312671003
Q gi|254780528|r   90 IISQDLSVVDDLIAKDTKGYFDIAIVYALKKYFSGQLEESSKELSKIKDKDN  141 (396)
Q Consensus        90 lSGG~P~~lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~l  141 (396)
                      |.|-+|.-|-.    .+..+++++|+..+++|..|-...|.++|. |...++
T Consensus        42 L~g~~~~~ly~----~vl~evE~pLl~~vL~~t~gNqskAA~~LG-InR~TL   88 (98)
T PRK00430         42 LDGQDVNDLYE----LVLAEVEAPLLDMVMQYTRGNQTRAALMLG-INRGTL   88 (98)
T ss_pred             CCCCCCHHHHH----HHHHHHHHHHHHHHHHHHCCCHHHHHHHHC-CCHHHH
T ss_conf             49999206999----999998999999999996695999999978-778899


No 17 
>KOG3928 consensus
Probab=29.67  E-value=38  Score=14.07  Aligned_cols=187  Identities=14%  Similarity=0.068  Sum_probs=80.1

Q ss_pred             CHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHH----------HHHHHHHCCCHHHHHHHHH
Q ss_conf             710036100013888766664321989999999999996785299999877----------6788752252589999999
Q gi|254780528|r  137 KDKDNTRGIVPYLHLLIGRAMMPFSSQQAVHFFDYVRLTSPGTFLEEIALR----------NLLEITQNEVGERAFGYIR  206 (396)
Q Consensus       137 ~~~~lp~~lg~~laLv~a~l~~~~dp~~Al~llD~aRLlaPGTLvEEAALR----------Rsi~la~~g~~~k~~~~a~  206 (396)
                      -+.-+|..+--++-.-+-..+.-..|+..  +++.-|+..|++=    +.|          ++|.++      ....|+.
T Consensus       137 ~~~G~p~~~~~q~~tf~ea~lLVRkpale--l~~~~r~~d~~~P----~~r~vL~Ge~GtGKSiaL~------qa~h~a~  204 (461)
T KOG3928         137 NPLGLPFKKSQQFKTFTEAVLLVRKPALE--LLLYKRLVDPMHP----VKRFVLDGEPGTGKSIALA------QAVHYAA  204 (461)
T ss_pred             CCCCCCHHHHHHHHHHHCCHHEECHHHHH--HHHHHHHCCCCCC----CEEEEEECCCCCCHHHHHH------HHHHHHH
T ss_conf             64789567778787640004202137899--9877640365676----3589985799876205999------9999873


Q ss_pred             HHHHHHCCCCCHHHHHHH----HHHHHHHCCCCCCHHHHHHHHHHCC---CHHHH-----HHHHHHHHHHHHCCCHHHHH
Q ss_conf             999972048465669999----9998520013577878999998578---10257-----99999999998539647999
Q gi|254780528|r  207 AYVTQFHHSIYKDHFISV----LLRFFLHGQLKLPDEDIVFTISFFS---LEEQR-----AIYLKIAQNSVISGKRKIGF  274 (396)
Q Consensus       207 ~Y~rRf~~S~YA~~F~~~----f~~~~v~~~~~~~~~~l~~ils~~d---~~~q~-----~lYL~IAR~Ali~G~~~lA~  274 (396)
                      .==+=-.|=||+-+|-..    +-+...++-.+.+..--.-+-.++.   +-.++     +=|----+.....|++-+-.
T Consensus       205 ~~~wlIlhip~a~~w~~~~~~~~y~~~~kg~~dqP~~a~~~L~~fkk~N~~~L~~~lkt~~~yvwsk~e~t~kG~pl~ei  284 (461)
T KOG3928         205 DQKWLILHIPYAELWTNGRKDYSYDSDLKGLWDQPLYAKKILKNFKKTNEPALKKQLKTSKDYVWSKRESTLKGKPLVEI  284 (461)
T ss_pred             CCCEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHCCCCCEEECCCCCCCCCCCCHHH
T ss_conf             17859997785787631631102455112441383689999999986262989877512444342156775678860556


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCC----------CCHHHH--HHHHHCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf             99999996315788865568999999975017----------898999--9998439978889753999999999999
Q gi|254780528|r  275 LAIKQLKRIIDRLDYKDLATIQLYENILNIPF----------VDIMSL--QRSTCNIPYYSLMEQDRYLKKASEIIMS  340 (396)
Q Consensus       275 ~As~rA~~L~~~~~~~~~~ra~LY~aaa~i~s----------~d~~~a--~~~L~~Id~~~L~~~Dr~L~~AA~~ia~  340 (396)
                      .-..    ++. ..++.....-|.+..-+..+          |++-..  ...+..=+...++|.|-.|-..-+-+-.
T Consensus       285 ~e~g----I~~-i~~a~~~vg~llrelk~~s~~~~~kVLvaID~~n~l~~~T~~k~~~~~~v~P~dl~li~~~~~~i~  357 (461)
T KOG3928         285 VETG----IAS-IKNAPDAVGILLRELKRLSVQSKVKVLVAIDNFNSLFTVTAYKSEDNKPVTPLDLTLIHLLRDIIS  357 (461)
T ss_pred             HHHH----HHH-HCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHEEEEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             7765----653-314567799999999975230376189997374023022111034467388154237899999870


No 18 
>COG3573 Predicted oxidoreductase [General function prediction only]
Probab=28.75  E-value=26  Score=15.07  Aligned_cols=152  Identities=8%  Similarity=0.028  Sum_probs=78.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHH--------------------HCCCCHHCCCCCCCHHHH
Q ss_conf             489889999998618898432699999999726987999998--------------------312671003610001388
Q gi|254780528|r   91 ISQDLSVVDDLIAKDTKGYFDIAIVYALKKYFSGQLEESSKE--------------------LSKIKDKDNTRGIVPYLH  150 (396)
Q Consensus        91 SGG~P~~lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~~a~~~--------------------L~~i~~~~lp~~lg~~la  150 (396)
                      .|||++.+|+-|.+.-.|.....++-|+-+++.||.......                    +.+|=|.---..|.++-.
T Consensus       227 IGGnhelVRrnWP~eRlG~~Pe~m~~GVPaHVDGrmi~i~~~aGg~vIN~DRMWHYtEGirNwdPiWp~HgIRIlPGPSS  306 (552)
T COG3573         227 IGGNHELVRRNWPTERLGRAPEQMLSGVPAHVDGRMIGIAVAAGGSVINPDRMWHYTEGIRNWDPIWPNHGIRILPGPSS  306 (552)
T ss_pred             CCCCHHHHHHCCCHHHCCCCHHHHHCCCCCCCCCHHHHHHHHHCCCEECCCCCEEHHHCCCCCCCCCCCCCEEECCCCCC
T ss_conf             68888888752956550897588762886013622677888707824465311013214556787676665065468732


Q ss_pred             H---HH-----HHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCH--H
Q ss_conf             8---76-----66643219899999999999967852999998776788752-252589999999999972048465--6
Q gi|254780528|r  151 L---LI-----GRAMMPFSSQQAVHFFDYVRLTSPGTFLEEIALRNLLEITQ-NEVGERAFGYIRAYVTQFHHSIYK--D  219 (396)
Q Consensus       151 L---v~-----a~l~~~~dp~~Al~llD~aRLlaPGTLvEEAALRRsi~la~-~g~~~k~~~~a~~Y~rRf~~S~YA--~  219 (396)
                      |   ..     .-++-.+|.-..++..-.------=-++.++-+++|..|.. ++..|-.-.--++.++|-..-|--  .
T Consensus       307 lWlDa~G~RLp~P~~PGfdtlgTL~hi~~~G~~ysWFiLt~kiI~kEFaLSGsEQNPDLTGkd~rlll~Ra~k~pPgPV~  386 (552)
T COG3573         307 LWLDAAGKRLPVPLFPGFDTLGTLKHITSTGYDYSWFILTRKIIKKEFALSGSEQNPDLTGKDLRLLLRRAGKGPPGPVQ  386 (552)
T ss_pred             EEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHH
T ss_conf             23877788188776788522558899862589832463308888877434665559886322499999871579995188


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHCC
Q ss_conf             699999998520013577878999998578
Q gi|254780528|r  220 HFISVLLRFFLHGQLKLPDEDIVFTISFFS  249 (396)
Q Consensus       220 ~F~~~f~~~~v~~~~~~~~~~l~~ils~~d  249 (396)
                      -|++       ++++=+..+.|.++++.|.
T Consensus       387 AFmd-------rGeDFvv~~~L~eLVa~MN  409 (552)
T COG3573         387 AFMD-------RGEDFVVADTLRELVAGMN  409 (552)
T ss_pred             HHHH-------CCCCEEHHHHHHHHHHHHH
T ss_conf             8876-------3763140624999999863


No 19 
>TIGR01163 rpe ribulose-phosphate 3-epimerase; InterPro: IPR000056 Ribulose-phosphate 3-epimerase (5.1.3.1 from EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Alcaligenes eutrophus two copies of the gene coding for PPE are known , one is chromosomally encoded P40117 from SWISSPROT, the other one is on a plasmid Q04539 from SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.; GO: 0004750 ribulose-phosphate 3-epimerase activity, 0005975 carbohydrate metabolic process.
Probab=28.45  E-value=39  Score=13.94  Aligned_cols=26  Identities=19%  Similarity=0.388  Sum_probs=23.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66543057678978999999999864
Q gi|254780528|r  368 TNVSMGIESFIKKNRSQIESIDVLLA  393 (396)
Q Consensus       368 ~~~~~~~~~~v~~ar~~l~eiD~LL~  393 (396)
                      -|+-+++|+||...-+||-++-.++.
T Consensus       137 VnPGFgGQkFIP~~~~Kir~~R~~id  162 (216)
T TIGR01163       137 VNPGFGGQKFIPETLEKIRELRKMID  162 (216)
T ss_pred             EECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             60799884110578999999999998


No 20 
>pfam10236 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=27.28  E-value=27  Score=14.95  Aligned_cols=19  Identities=16%  Similarity=0.097  Sum_probs=8.0

Q ss_pred             CHHHCCHHHHHHHHHHHHH
Q ss_conf             9788897539999999999
Q gi|254780528|r  320 PYYSLMEQDRYLKKASEII  338 (396)
Q Consensus       320 d~~~L~~~Dr~L~~AA~~i  338 (396)
                      +....++.|-.|-..-..+
T Consensus       178 ~~~~I~~~~L~lv~~f~~~  196 (274)
T pfam10236       178 DYKPIHPHDLTLVRLFLDL  196 (274)
T ss_pred             CCCCCCHHHHHHHHHHHHH
T ss_conf             8856578984499999998


No 21 
>PRK10866 outer membrane protein assembly complex subunit YfiO; Provisional
Probab=25.37  E-value=45  Score=13.61  Aligned_cols=116  Identities=13%  Similarity=0.104  Sum_probs=73.0

Q ss_pred             CHHHHHHHHHHHCCCHHHHHHHHCCCCHHCCCCCCCHHHHHHHH-HHHHHCCHHHHHHHHHHHHHHCCCC-HHHHHHHHH
Q ss_conf             26999999997269879999983126710036100013888766-6643219899999999999967852-999998776
Q gi|254780528|r  111 DIAIVYALKKYFSGQLEESSKELSKIKDKDNTRGIVPYLHLLIG-RAMMPFSSQQAVHFFDYVRLTSPGT-FLEEIALRN  188 (396)
Q Consensus       111 d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~lp~~lg~~laLv~a-~l~~~~dp~~Al~llD~aRLlaPGT-LvEEAALRR  188 (396)
                      +.---.|..++-+|+=.+|.+.|..++..+--+..+..--|-.+ ......+...|+.-+|.=--+-|.. -|+-|--.+
T Consensus        33 ~~~Y~~A~~~~~~~~y~~A~~~fe~l~~~yP~s~~A~qA~L~~ayayy~~~~y~~A~~~~~rFi~lyP~~~~v~Ya~Yl~  112 (243)
T PRK10866         33 NEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFMRLNPTHPNIDYVMYMR  112 (243)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf             99999999999878999999999999986899767899999999998730778999999999998678999738999998


Q ss_pred             HHH--------------HHH---C-CCHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             788--------------752---2-5258999999999997204846566999999
Q gi|254780528|r  189 LLE--------------ITQ---N-EVGERAFGYIRAYVTQFHHSIYKDHFISVLL  226 (396)
Q Consensus       189 si~--------------la~---~-g~~~k~~~~a~~Y~rRf~~S~YA~~F~~~f~  226 (396)
                      .+.              +-.   + +..-+.+......++||++|.|+.+-..+..
T Consensus       113 gl~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~f~~li~~yP~S~Ya~dA~~r~~  168 (243)
T PRK10866        113 GLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLV  168 (243)
T ss_pred             HHHHHHCCHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             89877401358888743256430769999999999999987899845899999999


No 22 
>pfam08012 DUF1702 Protein of unknown function (DUF1702). This family of proteins contains many bacterial proteins that are encoded by the UnbL gene. The function of these proteins is unknown.
Probab=25.25  E-value=45  Score=13.59  Aligned_cols=139  Identities=9%  Similarity=-0.026  Sum_probs=84.1

Q ss_pred             HHHCC-CHHHHHHHHHHHHHHH-CCCCCHH--HHHHHHHHHHHH-------CCCCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             75225-2589999999999972-0484656--699999998520-------01357787899999857810257999999
Q gi|254780528|r  192 ITQNE-VGERAFGYIRAYVTQF-HHSIYKD--HFISVLLRFFLH-------GQLKLPDEDIVFTISFFSLEEQRAIYLKI  260 (396)
Q Consensus       192 la~~g-~~~k~~~~a~~Y~rRf-~~S~YA~--~F~~~f~~~~v~-------~~~~~~~~~l~~ils~~d~~~q~~lYL~I  260 (396)
                      |+.+| -+.+.++--.+|+++- ...+|.+  ...+.+...+..       +..-.+.+.+.+.++-+++.++.+||==|
T Consensus       141 LalDGYGFhqaYF~t~ryV~~~~~~~~~~w~~g~~~y~~ra~DQGiGRALWFV~G~dp~~va~~I~~Fp~~Rr~DLwsGv  220 (318)
T pfam08012       141 LALDGYGFHQAYFKTDRYVRGQHRERPFPWPGGPDDYAGRAVDQGIGRALWFVGGTDPDVVADLIERFPEDRRADLWSGV  220 (318)
T ss_pred             HHHCCCCCCCEEECCCHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             53036662302205504542226788899999963888888861414777622788889999999856832102344238


Q ss_pred             HHHHHHCCCHHHHHHH------HHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHCCHHHHHHHHH
Q ss_conf             9999853964799999------9999963157888655689999999750178989999998439978889753999999
Q gi|254780528|r  261 AQNSVISGKRKIGFLA------IKQLKRIIDRLDYKDLATIQLYENILNIPFVDIMSLQRSTCNIPYYSLMEQDRYLKKA  334 (396)
Q Consensus       261 AR~Ali~G~~~lA~~A------s~rA~~L~~~~~~~~~~ra~LY~aaa~i~s~d~~~a~~~L~~Id~~~L~~~Dr~L~~A  334 (396)
                      -=++.-.|--.-.-+.      -+-.-.|+.  ++++...+..+   +..++..-+-+...||.++..           .
T Consensus       221 GLAatYAGG~~~~eL~~l~~~aG~~r~~lAQ--GaaFAa~AR~~---AG~v~~hT~~A~~vlcG~s~~-----------~  284 (318)
T pfam08012       221 GLAATYAGGADEDELRALAELAGEHRAALAQ--GAAFAAEARVR---AGLVPEHTELATRVLCGVTPA-----------E  284 (318)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHCHHHHHHHH--HHHHHHHHHHH---CCCCCCHHHHHHHHHHCCCHH-----------H
T ss_conf             9998870699999999999972310588886--89999999997---499860289999998199899-----------9


Q ss_pred             HHHHHHHHHCCC
Q ss_conf             999999853045
Q gi|254780528|r  335 SEIIMSEIGKSL  346 (396)
Q Consensus       335 A~~ia~~I~r~~  346 (396)
                      |..+.++..-.+
T Consensus       285 Aa~~~~~~~~~~  296 (318)
T pfam08012       285 AAAVTDEARPGL  296 (318)
T ss_pred             HHHHHHHHCCCC
T ss_conf             999999744256


No 23 
>TIGR01818 ntrC nitrogen regulation protein NR(I); InterPro: IPR010114   This entry represents Nitrogen regulatory protein C (NtrC), which is a bacterial enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism. It is phosphorylated by NtrB and interacts with sigma-54. One of the best studied examples is its activation of the gene glnA, which encodes the enzyme glutamine synthetase.. NtrC is composed of three domains , . The 124 residue N-terminal domain is homologous to receiver domains of other response regulator proteins in two-component signal transduction systems , . The 240 residue central domain of NtrC is homologous to a domain found in all activators of the sigma-54 RNA polymerase holoenzyme , . The C-terminal domain has been indicated to contain the determinants necessary for both DNA-binding and dimerization of full-length NtrC.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0009399 nitrogen fixation, 0050906 detection of stimulus during sensory perception.
Probab=24.21  E-value=47  Score=13.47  Aligned_cols=59  Identities=17%  Similarity=0.162  Sum_probs=37.0

Q ss_pred             HHHHCCHHHHHHHHHHHHCCCCHHH-HHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHC
Q ss_conf             6760562337999998974898899-9999861889843269999999972698799999831
Q gi|254780528|r   73 MDVFVDNRNIDAVWIYTIISQDLSV-VDDLIAKDTKGYFDIAIVYALKKYFSGQLEESSKELS  134 (396)
Q Consensus        73 ~~vw~d~rNv~Aa~iY~lSGG~P~~-lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~~a~~~L~  134 (396)
                      .+.|..  .+..-+--.++.|.-.+ -..|+ ....+++|+.|+..+|+...|+..+|...|.
T Consensus       399 ~~~w~~--~l~~~~~~~~~~~~~G~P~~~L~-~~~~~~~er~Ll~~AL~~T~G~~~~AA~~LG  458 (471)
T TIGR01818       399 QDDWEE--ALEAWAKQALSSGKDGVPEQGLL-DEALPELERTLLEAALQHTRGRKQEAAKLLG  458 (471)
T ss_pred             HHHHHH--HHHHHHHHHHHCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf             346999--99999999862145678816689-9999987399999999734550689998618


No 24 
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.99  E-value=48  Score=13.45  Aligned_cols=48  Identities=10%  Similarity=0.058  Sum_probs=33.3

Q ss_pred             HHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHCCCCHHCC
Q ss_conf             97489889999998618898432699999999726987999998312671003
Q gi|254780528|r   89 TIISQDLSVVDDLIAKDTKGYFDIAIVYALKKYFSGQLEESSKELSKIKDKDN  141 (396)
Q Consensus        89 ~lSGG~P~~lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~~a~~~L~~i~~~~l  141 (396)
                      -|.|.+|.-+-.    -+..+++++|+..++.+..|-...|.++|+ |..-++
T Consensus        20 ~L~g~~~~~ly~----~vl~evE~pLi~~vl~~~~gNQ~kAA~~LG-inR~TL   67 (77)
T PRK01905         20 DLDGSNPHDVYD----MVLSCVEKPLLEVVMEQAGGNQSLAAEYLG-INRNTL   67 (77)
T ss_pred             HCCCCCHHHHHH----HHHHHHHHHHHHHHHHHHCCCHHHHHHHHC-CCHHHH
T ss_conf             838998046999----999998999999999984594999999978-658889


No 25 
>TIGR00207 fliG flagellar motor switch protein FliG; InterPro: IPR000090   The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour . The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour . CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated.    The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN . Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important . Such clustering suggests that FliG-FliM interaction plays a central role in switching.   Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins . This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring , . FliG is present in about 25 copies per flagellum. This structure of the C-terminal domain is known, this domain functions specifically in motor rotation .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 flagellin-based flagellum.
Probab=22.32  E-value=51  Score=13.25  Aligned_cols=167  Identities=14%  Similarity=0.150  Sum_probs=87.8

Q ss_pred             HHHHHHHHHCCCHH----HHHHHHCCCCHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             99999997269879----99998312671003610001388876666432198999999999999678529999987767
Q gi|254780528|r  114 IVYALKKYFSGQLE----ESSKELSKIKDKDNTRGIVPYLHLLIGRAMMPFSSQQAVHFFDYVRLTSPGTFLEEIALRNL  189 (396)
Q Consensus       114 L~~g~laY~~Gr~~----~a~~~L~~i~~~~lp~~lg~~laLv~a~l~~~~dp~~Al~llD~aRLlaPGTLvEEAALRRs  189 (396)
                      .+--+.+|++-++.    .....+..|+-+..+..|-=.-.+..++-++.+.-      +|++|=+.-=||=||-|--=-
T Consensus        33 ~~a~vfkhL~~~ei~~Ls~~i~~l~~i~~~~~~~VL~EF~~~~~~~~yi~~gg------~~YaR~lL~kaLG~e~A~~~l  106 (346)
T TIGR00207        33 VSAEVFKHLSQEEIEELSAEIAKLEQIDKQQKDDVLEEFEEIAEAQEYINKGG------LDYARELLEKALGEEKAKKIL  106 (346)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH------HHHHHHHHHHHCCHHHHHHHH
T ss_conf             45578641788899999999885322348887899999999999999885063------789999988614158999999


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHH------------HHHCCCHHHHHHH
Q ss_conf             8875225258999999999997204846566999999985200135778789999------------9857810257999
Q gi|254780528|r  190 LEITQNEVGERAFGYIRAYVTQFHHSIYKDHFISVLLRFFLHGQLKLPDEDIVFT------------ISFFSLEEQRAIY  257 (396)
Q Consensus       190 i~la~~g~~~k~~~~a~~Y~rRf~~S~YA~~F~~~f~~~~v~~~~~~~~~~l~~i------------ls~~d~~~q~~lY  257 (396)
                      =-|...-+..+.|.|.+    + ..---.-||        ++.+   +++.++-|            ||.+|++.|.++-
T Consensus       107 ~~l~~slq~~~~f~~~~----~-~~P~~~~df--------I~~E---HPQtiAlIL~hL~~~~Aa~iLs~l~~e~~~~v~  170 (346)
T TIGR00207       107 NKLTSSLQTKPGFEFLR----K-AEPQQIADF--------IQQE---HPQTIALILSHLDPAQAAEILSLLPEEVQAEVA  170 (346)
T ss_pred             HHHHHHHCCCCCHHHHH----C-CCHHHHHHH--------HHCC---CHHHHHHHHHHHCHHHHHHHHHCCCHHHHHHHH
T ss_conf             98887531631156763----1-586889987--------7505---867999999851830478887306856899999


Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHC
Q ss_conf             9999999853964799999999996315-78886556899999997501
Q gi|254780528|r  258 LKIAQNSVISGKRKIGFLAIKQLKRIID-RLDYKDLATIQLYENILNIP  305 (396)
Q Consensus       258 L~IAR~Ali~G~~~lA~~As~rA~~L~~-~~~~~~~~ra~LY~aaa~i~  305 (396)
                      +|||-.   ++=-+-+..-.++++.-.= ...+.+.+..-=-++++.|-
T Consensus       171 ~RiA~~---g~~sP~vv~ev~~VLe~kL~s~~~~~~~~~GGv~~vaEi~  216 (346)
T TIGR00207       171 RRIAVM---GRTSPEVVKEVERVLEKKLESLTSEDYTKVGGVRAVAEII  216 (346)
T ss_pred             HHHHHC---CCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHH
T ss_conf             999850---7867899999999997762244212355416257899987


No 26 
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=21.41  E-value=54  Score=13.14  Aligned_cols=79  Identities=13%  Similarity=-0.061  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCC----------------------------CCHHHHHHHHHHHHHC-
Q ss_conf             99999999998539647999999999963157888----------------------------6556899999997501-
Q gi|254780528|r  255 AIYLKIAQNSVISGKRKIGFLAIKQLKRIIDRLDY----------------------------KDLATIQLYENILNIP-  305 (396)
Q Consensus       255 ~lYL~IAR~Ali~G~~~lA~~As~rA~~L~~~~~~----------------------------~~~~ra~LY~aaa~i~-  305 (396)
                      +++-.-|+.++-.|+...|.-.-+++..+.++.+=                            .+..-..+|.++.-.. 
T Consensus       463 ~~l~~qA~~~~~~Gd~~~A~~~l~qa~~~~P~dpWlR~~LAr~~~~~G~~~~A~~lM~~l~~~~p~~pe~~yA~ALyls~  542 (1158)
T PRK11447        463 DRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWITYRLAQDLWQAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSG  542 (1158)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             99999999999788999999999999971899704999999999977998899999999984499998999999999876


Q ss_pred             CCCHHHHHHHHHCCCHHHCCHHHHHHHH
Q ss_conf             7898999999843997888975399999
Q gi|254780528|r  306 FVDIMSLQRSTCNIPYYSLMEQDRYLKK  333 (396)
Q Consensus       306 s~d~~~a~~~L~~Id~~~L~~~Dr~L~~  333 (396)
                      +++...++..|..||..+.++.=+.|..
T Consensus       543 ~~~~~~A~a~L~~IP~a~~t~~mr~L~~  570 (1158)
T PRK11447        543 SDRDRAALAHLNTLPRAQWNSNIQELAQ  570 (1158)
T ss_pred             CCCHHHHHHHHHHCCHHHCCHHHHHHHH
T ss_conf             7887999999973994337978999999


No 27 
>pfam10037 MRP-S27 Mitochondrial 28S ribosomal protein S27. Members of this family of small ribosomal proteins possess one of three conserved blocks of sequence found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins, leaving open the possibility that MRP-S27 might be a functional partner of GTP-binding ribosomal proteins.
Probab=21.30  E-value=47  Score=13.46  Aligned_cols=25  Identities=12%  Similarity=-0.110  Sum_probs=11.4

Q ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             5623379999989748988999999
Q gi|254780528|r   77 VDNRNIDAVWIYTIISQDLSVVDDL  101 (396)
Q Consensus        77 ~d~rNv~Aa~iY~lSGG~P~~lr~l  101 (396)
                      .-|--.+|.|=..|.-|+|+.+=++
T Consensus        99 ll~sT~Ha~VRq~L~~~~~d~lL~~  123 (417)
T pfam10037        99 LRDSTIHAWIRQCLKYQAPDKALYT  123 (417)
T ss_pred             CCCCCHHHHHHHHHHCCCHHHHHHH
T ss_conf             5787479999999946888889999


No 28 
>pfam07624 PSD2 Protein of unknown function (DUF1585). A conserved sequence region at the C terminus of several cytochrome-like proteins in Rhodopirellula baltica.
Probab=20.82  E-value=55  Score=13.06  Aligned_cols=34  Identities=18%  Similarity=0.230  Sum_probs=24.5

Q ss_pred             CCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             98899999986188984326999999997269879
Q gi|254780528|r   93 QDLSVVDDLIAKDTKGYFDIAIVYALKKYFSGQLE  127 (396)
Q Consensus        93 G~P~~lr~l~~~d~~~~~d~~L~~g~laY~~Gr~~  127 (396)
                      -|+.-+++++..+ .+.+-+.++.-++.|+-||..
T Consensus         7 ~~~~~lk~~L~~~-~d~~~r~~~~kLl~YAlGR~l   40 (76)
T pfam07624         7 EGPAELKKLLLER-KDQFARSLTEKLLTYALGRSL   40 (76)
T ss_pred             CCHHHHHHHHHHC-HHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999989-899999999999999808999


Done!