Query         gi|254780511|ref|YP_003064924.1| flagellar biosynthesis protein FliR [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 248
No_of_seqs    114 out of 860
Neff          6.8 
Searched_HMMs 39220
Date          Sun May 29 23:09:32 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780511.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12772 bifunctional flagella 100.0       0       0  400.1  32.7  241    4-245     2-242 (609)
  2 PRK12780 fliR flagellar biosyn 100.0       0       0  394.0  33.4  246    1-246     1-247 (250)
  3 PRK05701 fliR flagellar biosyn 100.0       0       0  392.5  32.4  242    4-247     3-244 (250)
  4 pfam01311 Bac_export_1 Bacteri 100.0       0       0  385.3  32.5  240    6-247     4-245 (249)
  5 TIGR01400 fliR flagellar biosy 100.0       0       0  384.5  30.4  237   10-247     2-241 (248)
  6 COG1684 FliR Flagellar biosynt 100.0       0       0  373.3  29.9  241    4-247     7-247 (258)
  7 TIGR01401 fliR_like_III type I 100.0       0       0  335.7  29.5  240    5-244     4-251 (262)
  8 COG4791 EscT Type III secretor 100.0       0       0  306.1  26.8  243    2-246     3-246 (259)
  9 PRK05700 fliQ flagellar biosyn  95.9   0.098 2.5E-06   28.1  11.8   79  168-247     3-81  (89)
 10 pfam01313 Bac_export_3 Bacteri  95.8    0.11 2.8E-06   27.9  10.6   75  170-245     2-76  (76)
 11 PRK09617 type III secretion sy  95.6    0.06 1.5E-06   29.4   7.0   76  146-223   204-286 (305)
 12 PRK12781 fliQ flagellar biosyn  95.5    0.14 3.6E-06   27.2  11.6   78  169-247     4-81  (88)
 13 PRK12797 type III secretion sy  95.4    0.15 3.9E-06   27.0  12.5   55  167-223   142-196 (215)
 14 PRK06010 fliQ flagellar biosyn  95.4    0.16 4.2E-06   26.8  11.7   77  169-246     4-80  (88)
 15 PRK12796 spaP surface presenta  95.0    0.16 4.1E-06   26.9   7.5   72  168-243   143-214 (219)
 16 COG1987 FliQ Flagellar biosynt  94.9    0.22 5.7E-06   26.0  11.7   78  169-247     4-81  (89)
 17 PRK12783 fliP flagellar biosyn  94.5    0.28 7.2E-06   25.4  13.7   55  167-223   179-233 (252)
 18 PRK05699 fliP flagellar biosyn  94.5    0.29 7.3E-06   25.4  13.1   66  167-236   171-236 (245)
 19 PRK12430 type III secretion sy  94.5    0.29 7.3E-06   25.4  12.5   69  167-239   305-373 (379)
 20 TIGR01402 fliQ flagellar biosy  93.7    0.41   1E-05   24.5  11.6   79  168-247     3-81  (88)
 21 COG1338 FliP Flagellar biosynt  88.2     1.5 3.8E-05   21.1  12.4   54  168-223   176-229 (248)
 22 TIGR01103 fliP flagellar biosy  84.4     2.4 6.1E-05   19.9   8.4   71   71-153   132-202 (202)
 23 COG4790 EscR Type III secretor  78.9     3.8 9.7E-05   18.7   8.7   52  169-223   142-194 (214)
 24 pfam05799 COX5C Cytochrome c o  53.4      11 0.00027   16.1   2.3   19   73-91     15-33  (62)
 25 COG5110 RPN1 26S proteasome re  41.0     9.8 0.00025   16.3   0.6   20  196-215   661-680 (881)
 26 TIGR01102 yscR type III secret  31.6      29 0.00074   13.5   7.3   85  136-223    96-195 (209)
 27 COG4794 EscS Type III secretor  22.7      42  0.0011   12.5  10.9   74  169-243     4-77  (89)
 28 KOG0508 consensus               21.2      45  0.0012   12.3   4.1   61   88-158    85-145 (615)

No 1  
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=100.00  E-value=0  Score=400.15  Aligned_cols=241  Identities=19%  Similarity=0.348  Sum_probs=228.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             83699999999999999999998552788862889999999999999952144456000122068999999999999999
Q gi|254780511|r    4 SPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVH   83 (248)
Q Consensus         4 ~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~l   83 (248)
                      .+-.++++|+++++|+++++..+|+||++.+|.++|+++++.+|+.++|.+... +.+.+.+...+...+++|+.+|+.+
T Consensus         2 i~~~yflaf~Lvf~Risa~~~~aPiF~~~~iP~~vKi~lal~ls~~i~p~v~~~-~~~~~~~~~~~~l~vl~E~liGl~l   80 (609)
T PRK12772          2 ISAAYFTALILIFLRLFSFFSMVPIFFPKGTPVIVKVSLALIISYMLVGGIDIS-TVNTINNSTALIFYGINEILTGLIL   80 (609)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             756999999999999999999865418888859999999999999996568887-6555433599999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99999999999999999999875422202688887530169999999999999994518999999999997555665568
Q gi|254780511|r   84 GLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQELN  163 (248)
Q Consensus        84 G~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~~~  163 (248)
                      |+..+++|++++.|||++|+|+|+++++.+||.+|+|++++|++++++++++|++.||||++++++.|||+.+|+|++..
T Consensus        81 Gf~~~l~F~av~~AG~lI~~qmGlsmA~~~DP~~g~q~~vig~f~~lla~llFla~~GH~~li~al~~Sf~~iP~G~~~~  160 (609)
T PRK12772         81 GYITNLCFVCVRYAGSMMDLQVGFSMMSMFDPSSNSNTTLIERLLYWFSTVVFFIVDGHHMLIRALVESFNVIKLGAFFL  160 (609)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999999999999999998764899980488778876489999999999999996769999999999731108996545


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  164 FGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       164 ~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      .++..+.+++.++++|..|+++|+|++++++++|+++|++||++||+|+|++|+|+|+++|+.++.+++|.+.+...+.|
T Consensus       161 ~~~~~~~~~~~~~~~F~~a~~iA~Pii~~lll~dv~lGilaR~~PQmNVF~vGfPlkIlvGl~~l~i~lP~~~~~~~~~~  240 (609)
T PRK12772        161 NQESIMHVINVFIQYFVIGIKIAIPIVLIILITDLTLGLISRTVPQLNIMILGLPIKILLGLTAFVIALPLILKVLGSAF  240 (609)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             52699999999999999999999999999999999999999813688799999789999999999999899999999998


Q ss_pred             HH
Q ss_conf             95
Q gi|254780511|r  244 LY  245 (248)
Q Consensus       244 ~~  245 (248)
                      -+
T Consensus       241 ~~  242 (609)
T PRK12772        241 GN  242 (609)
T ss_pred             HH
T ss_conf             63


No 2  
>PRK12780 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=100.00  E-value=0  Score=393.99  Aligned_cols=246  Identities=32%  Similarity=0.566  Sum_probs=233.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHHHHHHHH
Q ss_conf             986836999999999999999999985527888628899999999999999521444560-0012206899999999999
Q gi|254780511|r    1 MTISPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDL-QNFVNRAYYSKLVMVELFL   79 (248)
Q Consensus         1 m~~~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~-~~~~~~~~~~~l~l~E~~i   79 (248)
                      ||++..+.+.++++++||+++++..+|+||++.+|.++|+++++++|+.++|.+.+..+. ..+.+...+...+++|+.+
T Consensus         1 ~~~~lp~~~l~~lLvf~Ri~~~~~~~P~f~~~~vP~~vR~~lal~la~~l~P~l~~~~~~~~~~~~~~~~~~~~~~E~~i   80 (250)
T PRK12780          1 MSLPLPDSVLGVFLIFCRIGGCLMVVPGYSSARIPVQVRLFIALSVTLALTPLLLPLFRPFLEGAAPAETLLWIGSEMLT   80 (250)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99887799999999999999999986652777784999999999999999987354457644544279999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999999999999987542220268888753016999999999999999451899999999999755566
Q gi|254780511|r   80 GCVHGLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIG  159 (248)
Q Consensus        80 Gl~lG~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g  159 (248)
                      |+.+|+..|++|++++.|||++|+|+|+++++.+||++++|++++|+++++.++++|++.||||.+++++.|||+.+|+|
T Consensus        81 Gl~lG~~~~l~f~a~~~AG~ii~~q~Gl~~a~~~dP~~~~~~~~l~~f~~~~~~llFl~~~gH~~li~~l~~Sf~~~P~g  160 (250)
T PRK12780         81 GLLIGLLGRVFFFALETMATAVATAIGLGSIPGTPVEDTEPAPALVSLIVLAATALFFATDLHWELLRGLIASYDRIPPG  160 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999999999987075143479878897759999999999999999786999999999976210799


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55685799999999999999999999999999999999999999985332548999999999999999999999999999
Q gi|254780511|r  160 QELNFGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQF  239 (248)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~  239 (248)
                      +....++..+.+++..+++|..|+++|+|++++++++|+++|++||++||+|+|++|+|+|+.+|+.++++++|.+..+|
T Consensus       161 ~~~~~~~~~~~~~~~~~~~F~lal~lAaPvi~~~ll~nv~lGil~R~~PQlNvf~vg~P~~i~~Gl~vL~l~~p~l~~~f  240 (250)
T PRK12780        161 EGFGGQAALVQLVDQLSEAFTLALRIASPFIIYSVIVNLAVGLANKLTPTIPVYFISTPFVLFGGLLLLYLLSDEMLTQF  240 (250)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             77563789999999999999999999999999999999999999980335558999956999999999999999999999


Q ss_pred             HHHHHHH
Q ss_conf             9999950
Q gi|254780511|r  240 SHSFLYG  246 (248)
Q Consensus       240 ~~~f~~~  246 (248)
                      ++.|.+-
T Consensus       241 ~~~f~~~  247 (250)
T PRK12780        241 SLAYAAW  247 (250)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 3  
>PRK05701 fliR flagellar biosynthesis protein FliR; Reviewed
Probab=100.00  E-value=0  Score=392.46  Aligned_cols=242  Identities=30%  Similarity=0.517  Sum_probs=230.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             83699999999999999999998552788862889999999999999952144456000122068999999999999999
Q gi|254780511|r    4 SPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVH   83 (248)
Q Consensus         4 ~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~l   83 (248)
                      ..++|+.+|++++||+++++..+|+|+++.+|.++|.++++++|+.++|.+++..+  .+.+...+...++||.++|+.+
T Consensus         3 ~~~~~~~~fllv~~Rv~~~~~~~P~f~~~~vP~~vR~~lal~ls~~l~p~v~~~~~--~~~~~~~~~~~~~~E~~iGl~l   80 (250)
T PRK05701          3 QLLEWVAAFFLPFCRIGALLMTMPGFSERNIPARVKLGLALALTFAIAPLLPPVPQ--VDLFSLTALLLVLQEILIGLAL   80 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999999999997760777562999999999999999844877677--8851399999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99999999999999999999875422202688887530169999999999999994518999999999997555665568
Q gi|254780511|r   84 GLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQELN  163 (248)
Q Consensus        84 G~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~~~  163 (248)
                      |+.++++||+++.|||++|+|+|+++++.+||.+++|++++|+++++++.++|++.||||.+++++.|||+.||+|+...
T Consensus        81 G~~~~l~f~a~~~AG~~i~~q~G~s~a~~~DP~~~~q~~~~~~~~~~~~~~lF~~~~gh~~~l~~l~~Sf~~~P~g~~~~  160 (250)
T PRK05701         81 GLVAQIIFAALQFAGQIIAMQMGLSFASMVDPTSGQQSPLLGQFLTLLALLLFLALDGHHLLIRALVDSFQTLPIGGFLL  160 (250)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999999999998754631324798777755389999999999999997719999999999987648987756


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  164 FGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       164 ~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      .++..+.+.+.++++|..|+++|+|++++++++|+++|++||++||+|+|++|+|+|+++|++++.+++|.+.+.+++.|
T Consensus       161 ~~~~~~~~~~~~~~~f~~al~lAaPi~~~~ll~~~~lG~l~R~~PQlnvf~vg~p~ki~~gl~~l~l~l~~l~~~~~~~f  240 (250)
T PRK05701        161 NGNAFLLLAKALSAMFLIGLQLALPIIVALLLVNLALGLLNRAAPQLNIFVIGFPLKITVGLLILALILPALLSVFENLF  240 (250)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68999999999999999999999899999999999999999707300089999779999999999999999999999999


Q ss_pred             HHHC
Q ss_conf             9504
Q gi|254780511|r  244 LYGF  247 (248)
Q Consensus       244 ~~~f  247 (248)
                      ++.+
T Consensus       241 ~~~~  244 (250)
T PRK05701        241 SEAF  244 (250)
T ss_pred             HHHH
T ss_conf             9999


No 4  
>pfam01311 Bac_export_1 Bacterial export proteins, family 1. This family includes the following members; FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways.
Probab=100.00  E-value=0  Score=385.32  Aligned_cols=240  Identities=23%  Similarity=0.387  Sum_probs=226.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69999999999999999999855278886288999999999999995214445600012206899999999999999999
Q gi|254780511|r    6 EIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVHGL   85 (248)
Q Consensus         6 ~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~lG~   85 (248)
                      ++|+.+++++++|+++++..+|+|+++.+|.++|..+++.+|+.++|.++...+.  ..+...+...++||.++|+.+|+
T Consensus         4 ~~~l~~fllv~~Rv~~~~~~~P~f~~~~iP~~vr~~lal~ls~~l~p~v~~~~~~--~~~~~~~~~~~~~E~~iGl~lG~   81 (249)
T pfam01311         4 LVLLAALFLAFVRVLALFSTLPFFSDRSLGGVVRNGVALLLALIVAPSIPNQAAP--IISEAQLILLVLKEALLGLLLGF   81 (249)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999864527886729999999999999998568766667--64268999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC--
Q ss_conf             999999999999999999875422202688887530169999999999999994518999999999997555665568--
Q gi|254780511|r   86 LIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQELN--  163 (248)
Q Consensus        86 ~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~~~--  163 (248)
                      .++++|++++.|||++|+|+|+++++.+||++++|++++|+++++++.++|++.||||.+++++.|||+.+|+|++.+  
T Consensus        82 ~~~l~f~a~~~AG~~i~~q~Gls~a~~~DP~~~~~~~~~~~l~~~~~~~lFl~~~gh~~~i~~l~~Sf~~iP~g~~~~~~  161 (249)
T pfam01311        82 FLSIPFWAFHAAGELIDNQRGATMASSFDPASGSQSSPVGQFLNQLAILLFLASGGHLLLLSALYDSYQIWPVGQFLPNM  161 (249)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             99999999999999999986676461559877875418999999999999999481999999999998655887666765


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  164 FGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       164 ~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      ..+..+.+++..+++|..|+++|+|++++++++|+++|++||++||+|+|++|+|+|+.+|++++.+++|.+.+++++.+
T Consensus       162 ~~~~~~~~~~~~~~~F~~al~lAaPii~~~ll~~l~lGll~R~~PQlnvf~lg~pvki~~gl~~l~~~lp~~~~~~~~~~  241 (249)
T pfam01311       162 NAQAAKFLLKALSQLFSIALLLAAPVIILLLLIDLALGLLSRFAPQLNVFVLSFPIKSAVGLLLLALYLPYILPLFKEEL  241 (249)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             48999999999999999999999999999999999999999717310069989669999999999999999999999999


Q ss_pred             HHHC
Q ss_conf             9504
Q gi|254780511|r  244 LYGF  247 (248)
Q Consensus       244 ~~~f  247 (248)
                      ++.|
T Consensus       242 ~~~f  245 (249)
T pfam01311       242 SLLF  245 (249)
T ss_pred             HHHH
T ss_conf             9998


No 5  
>TIGR01400 fliR flagellar biosynthetic protein FliR; InterPro: IPR006303   These sequences represent the FliR protein of bacterial flagellar biosynthesis. It distinguishes FliR from the homologous proteins bacterial type III protein secretion systems, known by names such as YopT, EscT, and HrcT.; GO: 0015031 protein transport, 0016021 integral to membrane, 0019861 flagellum.
Probab=100.00  E-value=0  Score=384.53  Aligned_cols=237  Identities=28%  Similarity=0.524  Sum_probs=227.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998552788862889999999999999952144456000122068999999999999999999999
Q gi|254780511|r   10 MSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVHGLLIRV   89 (248)
Q Consensus        10 ~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~lG~~~~i   89 (248)
                      ..++++++|++|++.++|+||+|.+|.++|..+++.+|+.++|.++...+ +.......+..++++|+.+|..+|+..++
T Consensus         2 ~~~~l~~~R~~a~l~~~P~fs~~~vP~~vR~~lal~~~~~~~p~l~~~~~-~~~~~~~~~~~~~~~E~l~G~~~G~~~~~   80 (248)
T TIGR01400         2 STFFLVFVRVGAFLMTMPFFSERLVPVRVRLYLALALTFIVLPFLPPTPG-QVNLFSLFFVLLLLQEILIGLLIGFILQL   80 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             56899999999999971664234054068999999999999845100345-20011799999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHH-HHHHHHHHCCCCCCCCCH--H
Q ss_conf             9999999999999987542220268888753016999999999999999451899999-999999755566556857--9
Q gi|254780511|r   90 YTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFY-ALVKSYGTIPIGQELNFG--N  166 (248)
Q Consensus        90 ~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~-~l~~Sf~~iP~g~~~~~~--~  166 (248)
                      .|++++.|||++|.|+|+++|+.+||.+++|++++||++++.++++|++.||||++++ ++.|||+.+|+|+...++  +
T Consensus        81 ~f~a~~~AG~~I~~~~GLg~A~~~dp~~~~~~p~~~~~l~~lall~FL~~~gh~~~i~~~l~~S~~~~P~g~~~~~~~e~  160 (248)
T TIGR01400        81 LFAAFVLAGEIISFQMGLGFASMVDPSSGEQTPVLGQILYLLALLLFLALDGHHLLILIGLVDSFKSLPVGSFFLNGSEN  160 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             99999999999998898899876312356661289999999999999984648999999999776540367666786148


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999999999853325489999999999999999999999999999999950
Q gi|254780511|r  167 IFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYG  246 (248)
Q Consensus       167 ~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~  246 (248)
                      ..+.+++..+++|..|+++|+|+++.++++|+++|++||++||+|+|++|+|+|+.+|+++++..+|.+.+.+++.++|.
T Consensus       161 ~~~~~~~~~~~~F~~gl~~a~P~~~~lLl~nl~~G~~~R~~PQ~N~F~iG~Pl~~~~Gl~ll~~~~p~~~~~~~~~~~~~  240 (248)
T TIGR01400       161 LFELILKALSDMFLLGLLLALPIIAALLLINLVLGLVNRAAPQLNIFSIGFPLKILLGLILLYLILPVIASLFKKLFEEL  240 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999998799999999999999998775799999998559999999999999999999999999999


Q ss_pred             C
Q ss_conf             4
Q gi|254780511|r  247 F  247 (248)
Q Consensus       247 f  247 (248)
                      +
T Consensus       241 ~  241 (248)
T TIGR01400       241 L  241 (248)
T ss_pred             H
T ss_conf             9


No 6  
>COG1684 FliR Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=100.00  E-value=0  Score=373.33  Aligned_cols=241  Identities=30%  Similarity=0.507  Sum_probs=231.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             83699999999999999999998552788862889999999999999952144456000122068999999999999999
Q gi|254780511|r    4 SPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGCVH   83 (248)
Q Consensus         4 ~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl~l   83 (248)
                      -.++|+.++++++||+++++.++|+|++|.+|.++|+.+++++|+.++|.+++ .+.  ......+..++.+|+.+|.++
T Consensus         7 ~~~~~v~~~~l~f~Rv~afl~~~P~~s~~~IP~~vrl~lal~ls~~v~p~l~~-~p~--~~~~~~~~ll~~~EiliG~~~   83 (258)
T COG1684           7 QLEEWVLAFFLPFVRVLAFLMTMPFFSERSIPARVRLGLALALSFAVLPLLPA-VPA--PLFSLEFLLLALSEILIGLAL   83 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCC--CCCCHHHHHHHHHHHHHHHHH
T ss_conf             76899999999999999999982010556553789999999999999945767-885--434488999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99999999999999999999875422202688887530169999999999999994518999999999997555665568
Q gi|254780511|r   84 GLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQELN  163 (248)
Q Consensus        84 G~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~~~  163 (248)
                      |+.+|+.|++++.|||++|.|+|+|+++.+||.+++|++++||+++..++++|++.||||++++++.|||+.+|+|+...
T Consensus        84 G~~~~l~f~a~~~aG~~i~~qmGls~a~~~Dp~~~~~~~~l~~~l~~~all~fl~~dgh~~li~~l~~Sf~~~Pv~~~~~  163 (258)
T COG1684          84 GFFAQLLFAALQFAGEIISMQMGLSFATMVDPSSGEQSPLLGQFLNFLALLLFLSLDGHLLLILGLVDSFKALPVGGFFL  163 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHEEECCCCCC
T ss_conf             99999999999999999999872242024688788763399999999999999990775999999998732200466667


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57999999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  164 FGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       164 ~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      +++..+.+.+..++.|..++++|+|+++.++++|+++|++||++||+|+|++|+|+|+.+|+.++++.+|.+.++++|.+
T Consensus       164 ~~~~~~~l~~~l~~~F~~~l~iAlPii~~lLlvnlalGlv~R~~PQinvf~ig~Pl~i~~Gl~lL~~~lp~i~~~~~~~~  243 (258)
T COG1684         164 NDNAFLLLAKALSAIFLIGLRLALPIIALLLLVNLALGLLNRLAPQLNVFFIGFPLKIAVGLLLLYLILPLIAPVFKHLF  243 (258)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             74099999999999999999999899999999999999998425420068755319999999999999999999999999


Q ss_pred             HHHC
Q ss_conf             9504
Q gi|254780511|r  244 LYGF  247 (248)
Q Consensus       244 ~~~f  247 (248)
                      ++.+
T Consensus       244 ~~~~  247 (258)
T COG1684         244 SELF  247 (258)
T ss_pred             HHHH
T ss_conf             9999


No 7  
>TIGR01401 fliR_like_III type III secretion apparatus protein SpaR/YscT/HrcT; InterPro: IPR006304   These sequences represent members of bacterial type III secretion systems homologous to the flagellar biosynthetic protein FliR (IPR006303 from INTERPRO).; GO: 0006810 transport, 0016021 integral to membrane.
Probab=100.00  E-value=0  Score=335.73  Aligned_cols=240  Identities=19%  Similarity=0.306  Sum_probs=224.3

Q ss_pred             CHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             36999999999999999----999985527888628-8999999999999995214445600012206899999999999
Q gi|254780511|r    5 PEIIMMSLFLIVCRVGS----CIMLLPGLSMSYIPM-QVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFL   79 (248)
Q Consensus         5 ~~~~l~~f~li~~Ri~~----~~~~~P~f~~~~iP~-~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~i   79 (248)
                      -.+++.+..++.+|+.+    ++++.|+|+++.+|. .+|.+++..++..++|...+.....+...+.....++.||+.+
T Consensus         4 ~~~~L~~lal~~~R~~~fylP~f~~LP~l~~~~L~g~~~R~~V~~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~kE~~i   83 (262)
T TIGR01401         4 LQELLITLALAFARILPFYLPLFLLLPFLASGSLPGGLIRNGVIVVLALPILPIVSTALLALDEEKWFSLAGLLLKEVII   83 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999999989998889899999896541035677414899999999999997546788603410289999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999999999999999875422-2026888875301699999999999999945189999999999975556
Q gi|254780511|r   80 GCVHGLLIRVYTLGLQFTGSVISTAIGLNL-QTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPI  158 (248)
Q Consensus        80 Gl~lG~~~~i~f~a~~~AG~~id~q~Gls~-a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~  158 (248)
                      |+.+|++..++||+++++|++||+|||.+. ++.+||.+|.|+|++|.+++++..++|++.||...+++.++|||++||+
T Consensus        84 GlllG~~l~~PFW~~~a~G~lIDnQRGAt~Ps~~~nPa~G~~tS~~g~lf~~~~~v~Fl~~GG~~~ll~~L~~SY~~wP~  163 (262)
T TIGR01401        84 GLLLGFLLALPFWIFEAVGFLIDNQRGATLPSSILNPATGVDTSPLGVLFNQFLIVIFLTSGGMELLLEALYESYRLWPL  163 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_conf             99999999989999999999998664230341010666652166899999999999999986999999999999865122


Q ss_pred             CCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6556--85799999999999999999999999999999999999999985332548999999999999999999999999
Q gi|254780511|r  159 GQEL--NFGNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIV  236 (248)
Q Consensus       159 g~~~--~~~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~  236 (248)
                      .++.  ......+.+.+....+...++.+|+|+++++++.|+++|++||.|||+|+|.+++|+|.+++++++.++.+.+.
T Consensus       164 ~~~~P~~~~~~~~~~~~~~~~~~~~~~~la~P~i~~l~L~e~~lgLl~RfApQLNvF~LslpiKS~~a~~~Llly~~~l~  243 (262)
T TIGR01401       164 TAFLPAFSAQGLSFLLAQLDQLMALALLLAAPVIIVLLLAELALGLLSRFAPQLNVFILSLPIKSLLALLILLLYFATLL  243 (262)
T ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             53057888415899999999999999999999999999999999999855225337778678999999999999999999


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254780511|r  237 YQFSHSFL  244 (248)
Q Consensus       237 ~~~~~~f~  244 (248)
                      .+..+...
T Consensus       244 ~~~~~~~~  251 (262)
T TIGR01401       244 EEALEELL  251 (262)
T ss_pred             HHHHHHHH
T ss_conf             99999987


No 8  
>COG4791 EscT Type III secretory pathway, component EscT [Intracellular trafficking and secretion]
Probab=100.00  E-value=0  Score=306.07  Aligned_cols=243  Identities=18%  Similarity=0.344  Sum_probs=226.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             86836999999999999999999985527888628899999999999999521444560001220689999999999999
Q gi|254780511|r    2 TISPEIIMMSLFLIVCRVGSCIMLLPGLSMSYIPMQVRLCFAMAFSIVLLPFLWDTIDLQNFVNRAYYSKLVMVELFLGC   81 (248)
Q Consensus         2 ~~~~~~~l~~f~li~~Ri~~~~~~~P~f~~~~iP~~vr~~l~l~ls~~~~p~v~~~~~~~~~~~~~~~~~l~l~E~~iGl   81 (248)
                      .+..+.++.++.+.++|..+++.+.|+++++-.+..+|.+++..++..++|.+.+..+..+  +...+..+..||+.+|+
T Consensus         3 ~~~~~~~l~~~~L~~~R~l~if~iLP~l~~~l~~~liRngi~~s~al~v~p~v~~~~~~~~--~~~~~~~L~~kEi~iG~   80 (259)
T COG4791           3 MHEIQTLLVALALLLARPLGIFSILPVLNAGLLSGLIRNGIAISLALPVLPHVLQALQILL--SAFQLAGLLLKEILIGA   80 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC--CHHHHHHHHHHHHHHHH
T ss_conf             0017999999999999998999989987553432244548999999998462505653346--08999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999999998754222026888875301699999999999999945189999999999975556655
Q gi|254780511|r   82 VHGLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPIGQE  161 (248)
Q Consensus        82 ~lG~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~g~~  161 (248)
                      ++||+..++|||.|.||+++|+|+|.++.+.+||..+.|++++|.+++++..++|++.|||+.+++.+.+||+.||+++.
T Consensus        81 ~iGf~~s~pFWa~~aAG~~IDnqrG~t~~s~~np~~~~~tS~~G~ll~~f~~viF~~~GG~~~ll~~L~~Sy~~~Pl~~~  160 (259)
T COG4791          81 LIGFVASIPFWAAQAAGFIIDNQRGATILSIFNPLLGAETSPFGVLLTQFAIVIFFASGGILTLLGVLYESYESWPLGAF  160 (259)
T ss_pred             HHHHHHHHHHHHHHHCCCEECCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHH
T ss_conf             99999951999997355010134320444117974333246279999999999999818959999999888635730300


Q ss_pred             CCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6857-999999999999999999999999999999999999999853325489999999999999999999999999999
Q gi|254780511|r  162 LNFG-NIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFS  240 (248)
Q Consensus       162 ~~~~-~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~  240 (248)
                      .+.. ..+..+.+....++..++++|+|++.++++.|..+|++||.|||+|+|.+++|+|..++..++..+++.+.++++
T Consensus       161 ~p~~~~~~~fll~~~~~~l~~al~la~P~~iaMlLad~~lglL~R~Apqlnvf~LslpiKs~vall~l~l~~~~l~~~~~  240 (259)
T COG4791         161 YPFELSQLVFLLNEWDQILLLALVLAAPVIIAMLLADLFLGLLNRFAPQLNVFALSLPIKSAVALLLLLLYLGYLLPHFS  240 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             53024689999999999999999998689999999999999999714263025645538888999999999999998899


Q ss_pred             HHHHHH
Q ss_conf             999950
Q gi|254780511|r  241 HSFLYG  246 (248)
Q Consensus       241 ~~f~~~  246 (248)
                      ..-...
T Consensus       241 ~~~~~~  246 (259)
T COG4791         241 LALLLT  246 (259)
T ss_pred             HHHHHH
T ss_conf             999986


No 9  
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=95.94  E-value=0.098  Score=28.14  Aligned_cols=79  Identities=15%  Similarity=0.160  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999999999999998533254899999999999999999999999999999999504
Q gi|254780511|r  168 FSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYGF  247 (248)
Q Consensus       168 ~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~f  247 (248)
                      .+.+++...+.+..++.+++|+++..+++-+..++. .++-|+|=..++|--|+..-...+.+..|-+.....+.+.+-|
T Consensus         3 ~~~~i~l~~~al~~~l~ls~P~L~~alvVGl~Isi~-QA~TqIqEqTLsFvPKliav~~~l~~~g~Wm~~~l~~f~~~if   81 (89)
T PRK05700          3 PESVMDLFREAMKVALMLAAPLLLVALIVGLVVSIF-QAATQINEQTLSFIPKILAVLLTLIIAGPWMLNTLLDYTRTLF   81 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             889999999999999999888999999999999999-9999999989987999999999999987899999999999999


No 10 
>pfam01313 Bac_export_3 Bacterial export proteins, family 3. This family includes the following members; FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways.
Probab=95.84  E-value=0.11  Score=27.88  Aligned_cols=75  Identities=17%  Similarity=0.162  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999985332548999999999999999999999999999999995
Q gi|254780511|r  170 SFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLY  245 (248)
Q Consensus       170 ~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~  245 (248)
                      .+++...+.+...+.+++|.+++-+++-+..+++ .++-|+|=..++|--|+..-+..+.+..|-+.+...+...+
T Consensus         2 ~~i~l~~~al~~~l~~s~P~l~~alvVGlvIsi~-QA~TqIqEqTLsFvPKliav~~~l~~~~pwm~~~l~~f~~~   76 (76)
T pfam01313         2 DVIDLGRQALWLVLLLSAPLLLVALVVGLVVSLF-QAATQIQEQTLSFVPKLLAVLLTLLLAGPWMLQTLLDFTRE   76 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             4899999999999999988999999999999999-99999989689869999999999999878999999987529


No 11 
>PRK09617 type III secretion system protein; Reviewed
Probab=95.64  E-value=0.06  Score=29.39  Aligned_cols=76  Identities=20%  Similarity=0.161  Sum_probs=48.7

Q ss_pred             HHHHHH-HHHHCCCCCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999-9975556655685------799999999999999999999999999999999999999985332548999999
Q gi|254780511|r  146 FYALVK-SYGTIPIGQELNF------GNIFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTP  218 (248)
Q Consensus       146 i~~l~~-Sf~~iP~g~~~~~------~~~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~p  218 (248)
                      ++.+.+ +-+.||.......      --....++......|.+|+.+=.|+++.=+++-=.  +++--+=.+..-.++.|
T Consensus       204 l~~F~~~a~~~~p~~~~~~~~~~~l~vLiPAFvlSELktAFqIGFlIYLPFlVIDLVVAsV--LmAMGMMMlpP~~ISLP  281 (305)
T PRK09617        204 IQSFYKISQKTFPPEIRDALTPSDFVIIIPAFIMGQIKNAFEIGVLIYLPFFVIDLVTANV--LVAMQMMMLSPLSISLP  281 (305)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHCCCCCCHHHHHH
T ss_conf             9999998454488752235677873110579999999999999999999999999999999--99800210580465445


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780511|r  219 YLIGL  223 (248)
Q Consensus       219 iki~i  223 (248)
                      .|+++
T Consensus       282 fKLLL  286 (305)
T PRK09617        282 LKLLL  286 (305)
T ss_pred             HHHHH
T ss_conf             77778


No 12 
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=95.55  E-value=0.14  Score=27.21  Aligned_cols=78  Identities=13%  Similarity=0.105  Sum_probs=68.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999999999999998533254899999999999999999999999999999999504
Q gi|254780511|r  169 SSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYGF  247 (248)
Q Consensus       169 ~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~f  247 (248)
                      +..++...+..-..+.+++|++++-+++-+..++. .++-|+|=..++|--|+..-++.+.+..|.+.+...+..++-|
T Consensus         4 ~~vi~l~r~al~~~l~~s~PiL~~aL~VGl~Isif-QA~TQIQE~TLsFVPKi~av~~~l~l~g~wm~~~l~~ft~~lf   81 (88)
T PRK12781          4 RDALELVRAAIWTIIVASGPAVGAAMLVGIAIALL-QALTQIQEVTLTFVPKIVVILIVMAVTGSFVGAQIYAFTEMVY   81 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999774999999999999999-9999999999985998999999999987799999999999999


No 13 
>PRK12797 type III secretion system protein; Provisional
Probab=95.45  E-value=0.15  Score=27.00  Aligned_cols=55  Identities=25%  Similarity=0.248  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999999998533254899999999999
Q gi|254780511|r  167 IFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGL  223 (248)
Q Consensus       167 ~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~i  223 (248)
                      ....++......|.+|+.+=.|+++.=+++--.  +++--+-.++.-.++.|.|+++
T Consensus       142 iPAF~iSELk~AF~IGFliyLPFlvIDlVVasi--LmamGMmMlpP~~ISlPfKllL  196 (215)
T PRK12797        142 IPAFTLSELTRAFEIGFLLYLPFIVIDLVISNI--LLAMGMMMVSPTTISLPFKLLL  196 (215)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCHHCCHHHHHHHHHHHH
T ss_conf             079999999999999999999999999999999--9982010058268757788889


No 14 
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=95.35  E-value=0.16  Score=26.80  Aligned_cols=77  Identities=18%  Similarity=0.154  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999999853325489999999999999999999999999999999950
Q gi|254780511|r  169 SSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYG  246 (248)
Q Consensus       169 ~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~  246 (248)
                      +..++...+.....+.+++|.+++-+++-+..++. .++-|+|=..++|--|+..-...+.+..|-+.+...+...+-
T Consensus         4 ~~vi~l~~~al~~~l~ls~P~L~valvVGl~Islf-QA~TQIqEqTLsFvPKliav~~~l~~~~pwm~~~l~~ft~~i   80 (88)
T PRK06010          4 ADALDVVRDAIWTVLIASGPAVLAAMVVGVAIALF-QALTQIQEMTLTFVPKIVAIFVTLLLTLPFMGAQISAFTLRI   80 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999876999999999999999-999999998998799999999999998889999999999999


No 15 
>PRK12796 spaP surface presentation of antigens protein SpaP; Provisional
Probab=95.02  E-value=0.16  Score=26.87  Aligned_cols=72  Identities=17%  Similarity=0.159  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  168 FSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       168 ~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      ...++......|.+|+.+=.|+++.=+++--.  +++--+-.+..-.++.|.|+++  .++.=.+..+..-.-+.|
T Consensus       143 PAF~iSEL~~AF~IGfllylPFlvIDlvVAsv--LmamGMmMlpP~~ISLPfKlll--FVlvDGW~ll~~~Lv~Sy  214 (219)
T PRK12796        143 PAYALSEIKSAFKIGFYLYLPFVVVDLVVSSV--LLALGMMMMSPVTISVPIKLIL--FVAMDGWTLLSKGLILQY  214 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHHHHHH--HHHCCHHHHHHHHHHHHH
T ss_conf             89999999999999999999999999999999--9982120058058766678889--863161999999999999


No 16 
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.90  E-value=0.22  Score=26.01  Aligned_cols=78  Identities=22%  Similarity=0.183  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999999999999998533254899999999999999999999999999999999504
Q gi|254780511|r  169 SSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYGF  247 (248)
Q Consensus       169 ~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~f  247 (248)
                      +.+.+...+.+...+.+++|.+.+-+++-+..++. .++-|+|=..++|-=|+..-+..+.+.-|-+..+..|.+.+-|
T Consensus         4 ~~~l~i~~~ai~~~L~l~~P~ll~alvvGLvIsif-QA~TQIqEqTLsFiPKIiai~~~l~~~gpWm~~~l~dft~~if   81 (89)
T COG1987           4 EDVLDIGQEAIWLVLMLSAPVLLVALVVGLVISIF-QAATQIQEQTLSFIPKIIAVFLVLILLGPWMLNQLLDFTVTIF   81 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999999999999998999999999999999-9999999999985998999999999975899999999999999


No 17 
>PRK12783 fliP flagellar biosynthesis protein FliP; Reviewed
Probab=94.48  E-value=0.28  Score=25.39  Aligned_cols=55  Identities=20%  Similarity=0.310  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999999998533254899999999999
Q gi|254780511|r  167 IFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGL  223 (248)
Q Consensus       167 ~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~i  223 (248)
                      ....++......|.+|+.+=.|+++.=+++--.  +++--+=.++.-.++.|.|+++
T Consensus       179 iPAF~iSELk~AF~IGFliyLPFlvIDLVVasi--LmaMGMmMlpP~~ISLPfKLlL  233 (252)
T PRK12783        179 IPAFMISELRRGFEIGFLIVLPFLVIDMIVATL--VMSMGMMMLPPTVISLPFKVLF  233 (252)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCHHCCHHHHHHHHHHHH
T ss_conf             489999999999999999999999999999999--9981010048167655678889


No 18 
>PRK05699 fliP flagellar biosynthesis protein FliP; Reviewed
Probab=94.46  E-value=0.29  Score=25.37  Aligned_cols=66  Identities=24%  Similarity=0.347  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999999985332548999999999999999999999999
Q gi|254780511|r  167 IFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIV  236 (248)
Q Consensus       167 ~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~  236 (248)
                      ....++......|.+|+.+-.|+++.=+++-=.  +++--+=.+....++.|.|+++  .++.=.+..+.
T Consensus       171 iPAF~~SELk~AF~IGFliylPFlvIDlVVasi--LmamGMmMlpP~~ISlPfKllL--FVlvDGW~ll~  236 (245)
T PRK05699        171 VPAFVLSELKTAFQIGFLIFLPFLIIDLVVASV--LMSMGMMMLPPVIISLPFKLLL--FVLVDGWNLLV  236 (245)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHCHHCCHHHHHHHHHHHH--HHHCCHHHHHH
T ss_conf             657789999999999999999999999999999--9982021148167645678889--85116199999


No 19 
>PRK12430 type III secretion system protein; Provisional
Probab=94.45  E-value=0.29  Score=25.36  Aligned_cols=69  Identities=23%  Similarity=0.324  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999999985332548999999999999999999999999999
Q gi|254780511|r  167 IFSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQF  239 (248)
Q Consensus       167 ~~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~  239 (248)
                      ....++......|.+|+.+-.|+++.=+++-=.  +++--+=.++.-.++.|.|+++  .++.=.+..+..-.
T Consensus       305 iPAFviSELktAFqIGFLIyLPFLVIDLVVASI--LMAMGMMMlpP~~ISLPFKLLL--FVlVDGW~Lli~sL  373 (379)
T PRK12430        305 LPSFITSELKTAFQIGFTIFIPFLIIDLVVASV--LMALGMMMVPPSTISLPFKLML--FVLVDGWQLLITSL  373 (379)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCCCHHHHHHHHHHHH--HHEECCHHHHHHHH
T ss_conf             978999999999999999999999999999999--9975053358046555367666--41337299999999


No 20 
>TIGR01402 fliQ flagellar biosynthetic protein FliQ; InterPro: IPR006305   These sequences represent FliQ, a protein involved in biosynthesis of bacterial flagella. A related family of proteins, excluded from this model, participate in bacterial type III protein secretion systems. ; GO: 0016021 integral to membrane, 0019861 flagellum.
Probab=93.70  E-value=0.41  Score=24.46  Aligned_cols=79  Identities=19%  Similarity=0.124  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999999999999998533254899999999999999999999999999999999504
Q gi|254780511|r  168 FSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSFLYGF  247 (248)
Q Consensus       168 ~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f~~~f  247 (248)
                      .+.+++...+.....+.+++|++.+-+++=+..++. -++-|+|=..++|-=|+.+-++.+.+..|-+.+...|.+.+=|
T Consensus         3 ~~~~l~l~~~a~~~~L~l~aP~L~~aL~VGLvIsIf-QA~TqIqE~TLsF~PKii~~ll~l~l~gpWM~~~l~dF~~~~f   81 (88)
T TIGR01402         3 EETVLDLGREALWLTLLLSAPVLLVALVVGLVISIF-QAATQIQEQTLSFIPKIIAVLLALILLGPWMLQKLLDFTREIF   81 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999989999999999999999-9987885768866989999999999985899998999999999


No 21 
>COG1338 FliP Flagellar biosynthesis pathway, component FliP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=88.24  E-value=1.5  Score=21.11  Aligned_cols=54  Identities=24%  Similarity=0.307  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999999998533254899999999999
Q gi|254780511|r  168 FSSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGL  223 (248)
Q Consensus       168 ~~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~i  223 (248)
                      ...++......|.+|+.+-.|+++.=+++-=.+=  +--+==++.-+++.|.|+++
T Consensus       176 PAFi~sELk~aFqIGflIylPFlVIDLVVAsvLM--aMGMMMlpP~~ISLPFKill  229 (248)
T COG1338         176 PAFMISELKTAFQIGFLIYLPFLVIDLVVASVLM--AMGMMMLPPVMISLPFKLLL  229 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCHHCCHHHHCCCHHHHH
T ss_conf             8999999999998889999899999999999999--81122059145213355540


No 22 
>TIGR01103 fliP flagellar biosynthetic protein FliP; InterPro: IPR005837    This model describes bacterial flagellar biogenesis protein fliP, which is one of the genes within the motility locus on the bacterial chromosome that is involved in structure and function of bacterial flagellum. It was demonstrated that mutants in fliP locus were non-flagellated and non-motile, while revertants were flagellated and motile. In Escherichia coli and related proteins the fliP protein probably  plays a role in the transport of flagellar proteins. FliP is a protein of about 30 Kd which contains three or four transmembrane regions. Proteins evolutionary related to fliP have been found in a wide range of bacteria (mopC, hrcR, hrpW, spaP, yscR, etc.) and are involved in a variety of signal-peptide independent secretion systems. ; GO: 0009306 protein secretion, 0016020 membrane.
Probab=84.40  E-value=2.4  Score=19.90  Aligned_cols=71  Identities=23%  Similarity=0.284  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             99999999999999999999999999999999987542220268888753016999999999999999451899999999
Q gi|254780511|r   71 KLVMVELFLGCVHGLLIRVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALV  150 (248)
Q Consensus        71 ~l~l~E~~iGl~lG~~~~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~  150 (248)
                      .-++.|+=.++=+||..-++|-.++..=.=+=..+|--|    =|...-+ =|       +=+++|+..||..++.+.++
T Consensus       132 AF~~sELk~AF~IGfliflPFLiiDlvVASvLMaMGMmM----LPP~~IS-LP-------FKl~LFVLVDGW~Ll~~sL~  199 (202)
T TIGR01103       132 AFILSELKTAFQIGFLIFLPFLIIDLVVASVLMAMGMMM----LPPVSIS-LP-------FKLLLFVLVDGWNLLVGSLV  199 (202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----CCCCHHH-HH-------HHHHHHHHHHHHHHHHHHHH
T ss_conf             999999898998859999999999999999997422404----5731033-00-------68888888877899986541


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780511|r  151 KSY  153 (248)
Q Consensus       151 ~Sf  153 (248)
                      |||
T Consensus       200 ~SF  202 (202)
T TIGR01103       200 QSF  202 (202)
T ss_pred             CCC
T ss_conf             259


No 23 
>COG4790 EscR Type III secretory pathway, component EscR [Intracellular trafficking and secretion]
Probab=78.91  E-value=3.8  Score=18.70  Aligned_cols=52  Identities=25%  Similarity=0.345  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999-999999998533254899999999999
Q gi|254780511|r  169 SSFVNMLQTTFMIMLRLSSPFLFFYIVF-NISIGLLNKLVPQIPIYFISTPYLIGL  223 (248)
Q Consensus       169 ~~~~~~~~~~f~~al~lA~P~i~~lll~-~i~lgil~R~aPQlnvf~vg~piki~i  223 (248)
                      ...+....+.|.+|+.+=.|+++.-+++ |+-++.   -+-++....++.|.|.++
T Consensus       142 AftlseL~~AF~IGfllYLPFivIDLiISniLlAm---GMmMvSP~tIS~PfKLll  194 (214)
T COG4790         142 AFTLSELTSAFKIGFLLYLPFIVIDLIISNILLAL---GMMMVSPVTISLPFKLLL  194 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHCCCCEECCCHHHHH
T ss_conf             87799999999999999979999999999999996---625408500141379899


No 24 
>pfam05799 COX5C Cytochrome c oxidase subunit Vc (COX5C). This family consists of plant cytochrome c oxidase subunit 5c proteins.
Probab=53.42  E-value=11  Score=16.07  Aligned_cols=19  Identities=26%  Similarity=0.293  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999
Q gi|254780511|r   73 VMVELFLGCVHGLLIRVYT   91 (248)
Q Consensus        73 ~l~E~~iGl~lG~~~~i~f   91 (248)
                      ++||+++|+.+|+...-.+
T Consensus        15 vvKEi~~G~~lgl~aGglW   33 (62)
T pfam05799        15 VVKEIVIGLTLGLAAGGLW   33 (62)
T ss_pred             HHHHHHHHHHHHHHHCHHH
T ss_conf             8999999999998614156


No 25 
>COG5110 RPN1 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=41.00  E-value=9.8  Score=16.26  Aligned_cols=20  Identities=20%  Similarity=0.479  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999985332548999
Q gi|254780511|r  196 FNISIGLLNKLVPQIPIYFI  215 (248)
Q Consensus       196 ~~i~lgil~R~aPQlnvf~v  215 (248)
                      +-+++|+++-+-||||+|-.
T Consensus       661 ~PLa~gils~SnPQm~vfDt  680 (881)
T COG5110         661 LPLAYGILSPSNPQMNVFDT  680 (881)
T ss_pred             HHHHHHCCCCCCCCHHHHHH
T ss_conf             77887303678962279998


No 26 
>TIGR01102 yscR type III secretion apparatus protein, YscR/HrcR family; InterPro: IPR005773    This model identifies the generic virulence translocation proteins in bacteria. It derives its name:'Yop' from Yersinia enterocolitica species, where this virulence protein was identified. In bacterial pathogenesis, Yop effector proteins are translocated into the eukaryotic cells.; GO: 0015031 protein transport, 0016021 integral to membrane.
Probab=31.65  E-value=29  Score=13.47  Aligned_cols=85  Identities=19%  Similarity=0.188  Sum_probs=58.2

Q ss_pred             HHHHCCHHHHHHHHHHHHH-HCC-------CCC--CCCCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Q ss_conf             9994518999999999997-555-------665--568579----99999999999999999999999999999-99999
Q gi|254780511|r  136 LWVIDFHHQVFYALVKSYG-TIP-------IGQ--ELNFGN----IFSSFVNMLQTTFMIMLRLSSPFLFFYIV-FNISI  200 (248)
Q Consensus       136 F~~~ggh~~li~~l~~Sf~-~iP-------~g~--~~~~~~----~~~~~~~~~~~~f~~al~lA~P~i~~lll-~~i~l  200 (248)
                      |+.-+-...-.+-+.+|-+ .||       -..  ....++    .....+....+.|++|+.+=.|+++.=++ .|+-+
T Consensus        96 fL~k~t~~~~~~FF~~~~~k~wPGeeteav~~~~~~~~~D~L~iL~PAF~lSEL~~AF~IGFLlYLPFIVIDLivSNiLL  175 (209)
T TIGR01102        96 FLKKNTDEDEVAFFERSTQKLWPGEETEAVKEMADRLKKDSLLILLPAFTLSELTAAFKIGFLLYLPFIVIDLIVSNILL  175 (209)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98861738999999998874148740244478996228884545766899999999888779999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998533254899999999999
Q gi|254780511|r  201 GLLNKLVPQIPIYFISTPYLIGL  223 (248)
Q Consensus       201 gil~R~aPQlnvf~vg~piki~i  223 (248)
                      +.   =+-|+....++.|.|.++
T Consensus       176 Al---GM~MVSP~tiS~PfKLLL  195 (209)
T TIGR01102       176 AL---GMMMVSPMTISLPFKLLL  195 (209)
T ss_pred             HH---HCCCCCHHHHHHHHHHHH
T ss_conf             82---021201579999999999


No 27 
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=22.74  E-value=42  Score=12.50  Aligned_cols=74  Identities=16%  Similarity=0.102  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999999853325489999999999999999999999999999999
Q gi|254780511|r  169 SSFVNMLQTTFMIMLRLSSPFLFFYIVFNISIGLLNKLVPQIPIYFISTPYLIGLGSLFLCLSIEIIVYQFSHSF  243 (248)
Q Consensus       169 ~~~~~~~~~~f~~al~lA~P~i~~lll~~i~lgil~R~aPQlnvf~vg~piki~ig~~~l~l~l~~~~~~~~~~f  243 (248)
                      +.+++..++.+-+-+-+++|.+++--.+-+..++. .++-|++=-.++|-+|..+-...+.++-|-......+.=
T Consensus         4 ~~i~~~~~qaL~liLilSlPpvivAsvvGllVslv-QA~TQiQdQTl~f~iKLl~V~~tl~lt~~Wlg~~ll~fa   77 (89)
T COG4794           4 DDIVFLTSQALWLILILSLPPVIVASVVGLLVSLV-QALTQIQDQTLPFGIKLLAVSATLFLTAGWLGATLLNFA   77 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999999611999999999999999-999999986788999999999999997077588999999


No 28 
>KOG0508 consensus
Probab=21.19  E-value=45  Score=12.31  Aligned_cols=61  Identities=18%  Similarity=0.112  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999998754222026888875301699999999999999945189999999999975556
Q gi|254780511|r   88 RVYTLGLQFTGSVISTAIGLNLQTSMGISDSLAETPLNSLIGIIGLLALWVIDFHHQVFYALVKSYGTIPI  158 (248)
Q Consensus        88 ~i~f~a~~~AG~~id~q~Gls~a~~~dP~~~~~~~~~~~l~~~~~~~lF~~~ggh~~li~~l~~Sf~~iP~  158 (248)
                      ..+.|+...||.+==.+.=...+...|-++.++++|+-.-          ..|||..+.+-+.++=.-..+
T Consensus        85 appLWaAsaAGHl~vVk~L~~~ga~VN~tT~TNStPLraA----------CfDG~leivKyLvE~gad~~I  145 (615)
T KOG0508          85 APPLWAASAAGHLEVVKLLLRRGASVNDTTRTNSTPLRAA----------CFDGHLEIVKYLVEHGADPEI  145 (615)
T ss_pred             CCHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHH----------HHCCHHHHHHHHHHCCCCCCC
T ss_conf             7355677505809999999983475455445577308888----------834606999999972899765


Done!