Query         gi|254780138|ref|YP_003064551.1| ABC transporter [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 373
No_of_seqs    186 out of 1048
Neff          6.2 
Searched_HMMs 39220
Date          Sun May 22 12:36:25 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780138.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00056 TIGR00056 conserved  100.0       0       0  532.2  29.0  264  110-373     6-275 (275)
  2 COG0767 Ttg2B ABC-type transpo 100.0       0       0  506.1  31.7  262  105-373     6-267 (267)
  3 pfam02405 DUF140 Domain of unk 100.0       0       0  473.1  29.2  215  154-368     1-215 (215)
  4 cd06844 STAS Sulphate Transpor  98.3   3E-06 7.7E-11   62.4   7.9   85    3-88      6-93  (100)
  5 cd07043 STAS_anti-anti-sigma_f  98.3   5E-06 1.3E-10   60.9   7.6   84    3-88      6-92  (99)
  6 COG3113 Predicted NTP binding   98.2 3.4E-06 8.5E-11   62.1   6.4   80    7-89     12-94  (99)
  7 pfam01740 STAS STAS domain. Th  98.1 2.7E-05   7E-10   55.7   8.2   86    3-89      7-95  (106)
  8 TIGR02886 spore_II_AA anti-sig  97.7 7.7E-06   2E-10   59.6   0.8   86    3-89      6-94  (106)
  9 COG1366 SpoIIAA Anti-anti-sigm  97.6 0.00041   1E-08   47.5   7.6   83    7-90     15-100 (117)
 10 cd07042 STAS_SulP_like_sulfate  97.4   0.001 2.6E-08   44.7   7.3   87    2-88      6-95  (107)
 11 cd07041 STAS_RsbR_RsbS_like Su  96.7   0.011 2.9E-07   37.4   7.7   82    4-86      9-93  (109)
 12 TIGR00377 ant_ant_sig anti-ant  96.0   0.023 5.7E-07   35.3   6.1   87    3-89     10-99  (109)
 13 PRK10782 DL-methionine transpo  79.1     4.2 0.00011   19.3   5.9   51  238-288   117-175 (217)
 14 COG0795 Predicted permeases [G  76.3     5.1 0.00013   18.8  13.4   23  248-270   336-358 (364)
 15 COG4591 LolE ABC-type transpor  69.5     7.2 0.00018   17.7  12.5   96  234-334   295-398 (408)
 16 pfam03739 YjgP_YjgQ Predicted   69.2     7.3 0.00019   17.6  12.7   21  165-185   274-294 (353)
 17 KOG0236 consensus               68.5     7.6 0.00019   17.5   7.4   67  125-191   111-188 (665)
 18 COG5439 Uncharacterized conser  58.3     9.8 0.00025   16.7   2.8   53    9-63     17-72  (112)
 19 COG4215 ArtQ ABC-type arginine  54.5      13 0.00033   15.8  11.6  125  130-268    24-156 (230)
 20 pfam02687 FtsX Predicted perme  48.7      16 0.00041   15.2  12.5   97  230-331    72-168 (174)
 21 PRK11146 outer membrane-specif  47.4      17 0.00043   15.1  12.2   96  234-334   293-402 (412)
 22 TIGR01253 thiP thiamine/thiami  42.9      19  0.0005   14.6   3.0   22  304-325   446-467 (519)
 23 PRK08456 flagellar motor prote  41.4      20 0.00052   14.5   6.4   57  157-219   142-198 (257)
 24 TIGR02182 GRXB Glutaredoxin, G  40.7     7.1 0.00018   17.7  -0.2   14   44-57    108-121 (212)
 25 pfam09838 DUF2065 Uncharacteri  40.4      21 0.00054   14.4   2.9   33  152-184    22-54  (57)
 26 KOG2927 consensus               39.3      22 0.00056   14.3   3.1   50  184-234   215-268 (372)
 27 pfam05197 TRIC TRIC channel. T  39.3      22 0.00056   14.3   4.1   35  268-302    15-49  (197)
 28 COG4177 LivM ABC-type branched  39.2      22 0.00056   14.3   6.6   69  212-298   170-238 (314)
 29 COG1079 Uncharacterized ABC-ty  38.8      22 0.00057   14.2   4.6   88  235-333   170-262 (304)
 30 TIGR00815 sulP sulfate permeas  38.1      23 0.00059   14.1   2.9   21  201-221   307-327 (638)
 31 PRK13108 prolipoprotein diacyl  37.9      23 0.00059   14.1   2.3   22  212-233   133-154 (460)
 32 PRK10814 outer membrane-specif  37.0      24 0.00061   14.0  13.4   97  234-335   290-390 (396)
 33 pfam11964 DUF3478 Protein of u  36.6      24 0.00062   14.0   7.5   84    2-86      8-94  (118)
 34 pfam04123 DUF373 Domain of unk  35.8      25 0.00063   13.9   8.3   29  176-204   184-213 (344)
 35 TIGR03004 ectoine_ehuC ectoine  34.0      26 0.00068   13.7  11.1  116  209-327    77-200 (216)
 36 PRK08124 flagellar motor prote  33.0      27  0.0007   13.6   6.3   58  157-220   143-200 (263)
 37 PRK08990 flagellar motor prote  31.9      29 0.00073   13.5   6.3   62  156-223   138-199 (253)
 38 COG1291 MotA Flagellar motor c  31.6      29 0.00074   13.4   5.4   63  158-226   144-206 (266)
 39 PRK11301 livM leucine/isoleuci  31.5      29 0.00074   13.4   4.7   52  236-299   292-343 (416)
 40 pfam08566 Pam17 Mitochondrial   28.9      32 0.00081   13.1   6.1   50  238-299    62-113 (174)
 41 PRK00965 tetrahydromethanopter  27.9      33 0.00085   13.0   2.2   29   66-94     25-56  (108)
 42 COG1987 FliQ Flagellar biosynt  26.9      34 0.00088   12.9   9.7   66  155-221     8-75  (89)
 43 PRK06926 flagellar motor prote  26.9      35 0.00088   12.9   6.3   47  159-211   149-195 (272)
 44 pfam04710 Pellino Pellino. Pel  26.7     7.5 0.00019   17.6  -2.0   64    1-64    181-256 (416)
 45 pfam03683 UPF0175 Uncharacteri  26.5      14 0.00037   15.6  -0.6   36  218-254    29-64  (76)
 46 PRK11123 arginine transporter   26.4      35  0.0009   12.8  16.6  126  142-273    33-168 (238)
 47 pfam08496 Peptidase_S49_N Pept  26.4      35  0.0009   12.8   4.1   14   70-83     43-56  (154)
 48 PRK09109 motC flagellar motor   25.5      36 0.00093   12.7   6.2   58  157-220   142-199 (246)
 49 TIGR00780 ccoN cytochrome c ox  25.5      36 0.00093   12.7   3.9   98  158-282     7-112 (485)
 50 COG2239 MgtE Mg/Co/Ni transpor  25.4      37 0.00093   12.7   8.5  130  168-334   287-418 (451)
 51 pfam07297 DPM2 Dolichol phosph  24.1      39 0.00098   12.6   3.0   34  250-283    37-70  (80)
 52 COG2120 Uncharacterized protei  23.5      22 0.00056   14.3  -0.1   11   58-68    101-111 (237)
 53 KOG3944 consensus               23.3      39 0.00099   12.5   1.2   23  307-329   235-257 (291)
 54 PRK06743 flagellar motor prote  23.0      40   0.001   12.4   6.4   57  157-219   139-195 (254)
 55 pfam01312 Bac_export_2 FlhB Hr  22.8      41   0.001   12.4  16.2   35  292-326   123-157 (343)
 56 PRK10535 macrolide transporter  22.2      42  0.0011   12.3  13.6   94  226-329   532-633 (648)
 57 KOG0539 consensus               22.0      34 0.00087   12.9   0.7   40  254-293   137-182 (240)
 58 pfam03095 PTPA Phosphotyrosyl   21.8      43  0.0011   12.3   8.1  109   41-149     5-125 (298)
 59 COG2011 AbcD ABC-type metal io  21.7      43  0.0011   12.2   3.9  105  163-293    66-185 (222)
 60 TIGR01389 recQ ATP-dependent D  21.4      37 0.00095   12.6   0.8   13   74-86    146-158 (607)
 61 COG3763 Uncharacterized protei  20.7      45  0.0011   12.1   3.9   21  269-289     8-28  (71)
 62 COG4062 MtrB Tetrahydromethano  20.5      45  0.0012   12.1   3.0   33   66-98     25-60  (108)

No 1  
>TIGR00056 TIGR00056 conserved hypothetical protein; InterPro: IPR003453 This domain has no known function nor do any of the proteins that possess it. The aligned region is approximately 150 amino acids long..
Probab=100.00  E-value=0  Score=532.18  Aligned_cols=264  Identities=35%  Similarity=0.540  Sum_probs=244.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999859999999999999999999999999997402678----872899999999983776999999999999999999
Q gi|254780138|r  110 LHYHIGKKIVKFINDSCSQAHILGLVISNTGEFCASSYKF----KGFLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQQ  185 (373)
Q Consensus       110 ~~~~iG~~~~~~~~~~~~~~~f~G~~~~~~~~~~~~~~~~----r~~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~q  185 (373)
                      ...++|+...+..+.....+.+.|........-..++++.    ..+...+++|++..|++|+||+.++++++|+|+++|
T Consensus         6 ~~~~L~k~~~~~~ntfl~Af~l~g~~~F~~~~g~~~~r~~kyikqf~~~~~~~ql~~vG~~s~~i~l~t~~~iG~v~alQ   85 (275)
T TIGR00056         6 LIAKLGKEIIETGNTFLRAFLLTGLMLFQLLKGKPNIRKHKYIKQFPLSALLKQLNTVGVESLPIILVTSLFIGMVIALQ   85 (275)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             26533336789999999999999999999973787765413000121018999998888999999999999999999999


Q ss_pred             HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             99987542756689999999999998999999999996457899999999875001344442786899999999999999
Q gi|254780138|r  186 GAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALII  265 (373)
Q Consensus       186 ~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i  265 (373)
                      +|.+|++|||+..+|+++++++.|||||++||+++|||+|||+|||||+||+||||||||+|++||++|||.||++|+++
T Consensus        86 ~a~~l~~fgA~~~~g~~vals~~RELgPvltal~~AGRvgSa~TA~IG~MriTEqlDAL~~m~~~P~~~LV~PR~lA~~i  165 (275)
T TIGR00056        86 GALQLIAFGAETSIGGLVALSLLRELGPVLTALVVAGRVGSAFTAEIGLMRITEQLDALEMMAVNPVEFLVLPRVLACVI  165 (275)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             99999971742589999999998889999999999998788988875134566687788862458266577889999998


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHH--HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             9999999999999999999999861139899999999861699--99999999999999999998317704559865899
Q gi|254780138|r  266 SLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLA--NIFTGLIKAPFMACAIGIVAMKEGFAVGVHSNSLG  343 (373)
Q Consensus       266 ~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~--d~~~~~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG  343 (373)
                      ++|+|+++++++|++||++++...+|++...||+++++.++.|  |+..|++|+++||++|++||||+||.++|++||||
T Consensus       166 ~~PlLt~L~~~~gi~GG~~~~~~~~gi~~~~f~~~~~~~v~~w~~D~~~G~~Ka~fFGv~Ia~igc~~Gf~t~g~~~g~G  245 (275)
T TIGR00056       166 MLPLLTVLSLVAGILGGAFIASSLLGIGSESFWSKMQNAVEKWNYDIFAGLVKAVFFGVAIAIIGCYYGFTTKGGTEGVG  245 (275)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             88899999999998614987887751440467887622211104421441135789999999999732654458866313


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999999999999999985089
Q gi|254780138|r  344 KKVTTCVVQSISIVIIIDSLFAIFYFAIGI  373 (373)
Q Consensus       344 ~att~aVV~si~~ii~~d~~~~~~~~~~gi  373 (373)
                      ++||+|||+|+.+|++.|++||.++.++|+
T Consensus       246 ~~TT~sVVts~l~I~~lDf~ls~i~f~LG~  275 (275)
T TIGR00056       246 RSTTRSVVTSLLAILILDFVLSAIMFQLGI  275 (275)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             789999999999999999999999985079


No 2  
>COG0767 Ttg2B ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=100.00  E-value=0  Score=506.09  Aligned_cols=262  Identities=39%  Similarity=0.611  Sum_probs=248.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             13665899985999999999999999999999999999740267887289999999998377699999999999999999
Q gi|254780138|r  105 NSFKNLHYHIGKKIVKFINDSCSQAHILGLVISNTGEFCASSYKFKGFLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQ  184 (373)
Q Consensus       105 ~~~~~~~~~iG~~~~~~~~~~~~~~~f~G~~~~~~~~~~~~~~~~r~~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~  184 (373)
                      +...+.+.++|+.+.+..++.+....|+|..+..       .++.+.+|+++.+|+++.|.+|+||+.++++++|+++++
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~g~~~~~~~~~l~~-------~~~~~~~~~~~~~q~~~vg~~sl~Iv~~~~~~vG~vla~   78 (267)
T COG0767           6 PRLIALLRRLGKALLKTLRSLGRAFLFLGNALRG-------LFREPFRPRELVRQLYFVGVGSLPIVALTSLFVGAVLAL   78 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1389999999898999999999999999999998-------402436689999999998600379999999999999999


Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             99998754275668999999999999899999999999645789999999987500134444278689999999999999
Q gi|254780138|r  185 QGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALI  264 (373)
Q Consensus       185 q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~  264 (373)
                      |++.||.+|||+.+++++++++.+||+||++|++++|||+|||+|||||+||+||||||||+||+||++|||.||++|++
T Consensus        79 qg~~~L~~fGAe~~~g~lval~~~RElgPvlTal~~AGr~gSa~tAeIG~MritEEIDAlevmgidPi~~LV~PRvlA~~  158 (267)
T COG0767          79 QGYTQLRDFGAEDFSGFLVALSLLRELGPVLTALVVAGRVGSAITAEIGAMRITEEIDALEVMGIDPISRLVAPRVLAGV  158 (267)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             99999998089999999999999999878999999985338899999812669889999998577943888788899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             99999999999999999999999861139899999999861699999999999999999999983177045598658999
Q gi|254780138|r  265 ISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFAVGVHSNSLGK  344 (373)
Q Consensus       265 i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG~  344 (373)
                      +++|+|+.+++.+|++||+++++..+|+++..|++++++.++++|++.|++|+++||++|++|+||+||+++|++|+||+
T Consensus       159 i~~plL~~l~~~~gi~GG~~v~~~~~gi~~g~f~~~l~~~v~~~dv~~g~iKa~~fg~ii~li~cy~G~~~~gg~~gvG~  238 (267)
T COG0767         159 IVLPLLTALADAAGILGGYLVAVFLLGISPGAFLSRLQTFVGPEDVLIGLIKAPVFGVIIGLIGCYYGYTVGGGPEGVGR  238 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCEECCCCCCHHHH
T ss_conf             99999999999999850250014441798689999998625899999999999999999999996647102899552737


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999999999999985089
Q gi|254780138|r  345 KVTTCVVQSISIVIIIDSLFAIFYFAIGI  373 (373)
Q Consensus       345 att~aVV~si~~ii~~d~~~~~~~~~~gi  373 (373)
                      +||+|||.|+++|++.|++++.+++..|+
T Consensus       239 att~sVV~s~~~v~~~d~v~t~~~~~~~~  267 (267)
T COG0767         239 ATTRSVVTSILVVIVLDFVLTALMFGVGI  267 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             76589999999999999999999845689


No 3  
>pfam02405 DUF140 Domain of unknown function DUF140. This domain has no known function nor do any of the proteins that possess it. The aligned region is approximately 150 amino acids long.
Probab=100.00  E-value=0  Score=473.08  Aligned_cols=215  Identities=40%  Similarity=0.689  Sum_probs=212.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999983776999999999999999999999875427566899999999999989999999999964578999999
Q gi|254780138|r  154 LSLIRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIG  233 (373)
Q Consensus       154 ~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG  233 (373)
                      +++++|++++|++|+|++.++++++|+++++|++.+|++||++.+++++++++++||+||++||+++|||+||++|||||
T Consensus         1 ~~~~~Q~~~~G~~sl~iv~~~~~~~G~v~~~q~~~~l~~~G~~~~ig~~~~~~~vRElgP~ltalilagR~Gsa~aAElG   80 (215)
T pfam02405         1 REILRQIYFVGVGSLPIVALTAFFIGAVLALQGAYQLRQFGAESFVGALVALSLVRELGPVLTALLVAGRVGSAITAELG   80 (215)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97899999998849999999999999999999999999849189999999999999998999999999987139999998


Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHH
Q ss_conf             99875001344442786899999999999999999999999999999999999986113989999999986169999999
Q gi|254780138|r  234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLANIFTG  313 (373)
Q Consensus       234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~  313 (373)
                      +||+||||||||+||+||++|||+||++|+++++|+|++++++++++|||++++..+|++++.|++++.+.++++|++.+
T Consensus        81 tM~v~eeIDAL~~mgi~P~~yLv~PRvlA~~i~~p~L~i~~~~~~~~gG~l~~~~~~~i~~~~f~~~~~~~~~~~Dl~~~  160 (215)
T pfam02405        81 TMRVTEEIDALEVMGIDPIRYLVLPRVLAGVIALPLLTIIADLVGILGGYLVAVVVLGISPGAFLHSFQSFVDPTDVLVG  160 (215)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHH
T ss_conf             72698899999984899247765989999999999999999999999999999997699999999999997789999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999983177045598658999999999999999999999999999
Q gi|254780138|r  314 LIKAPFMACAIGIVAMKEGFAVGVHSNSLGKKVTTCVVQSISIVIIIDSLFAIFY  368 (373)
Q Consensus       314 ~~K~~~fg~~i~~i~c~~Gl~~~~~a~~VG~att~aVV~si~~ii~~d~~~~~~~  368 (373)
                      ++|+++||++|++++||+||++++|+++||++||+|||+|+++|++.|++++.+|
T Consensus       161 l~K~~vFG~~I~~i~c~~Gl~~~~ga~~VG~att~aVV~s~~~I~~~d~~~s~l~  215 (215)
T pfam02405       161 LIKAVVFGLIIALIGCYYGLTAKGGAEGVGRATTRAVVTSIVAIIVLDFVLTALF  215 (215)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999999999996568157999748879999999999999999999999879


No 4  
>cd06844 STAS Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and "stressosome" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation.
Probab=98.32  E-value=3e-06  Score=62.43  Aligned_cols=85  Identities=15%  Similarity=0.329  Sum_probs=72.8

Q ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH
Q ss_conf             5882799984035635522007999986431167880899701051521299999999997---5187643158991269
Q gi|254780138|r    3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE   79 (373)
Q Consensus         3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~   79 (373)
                      .|+.++++++|+.+..+...+.+++...+.+. ..+.+++|+|+++++||+|.-.|....+   ..+.+....+.+|..+
T Consensus         6 ~d~~lVv~l~GelD~~ta~~lr~~l~~~i~~~-~~~~iVvDls~v~f~DSsGl~~Ll~~~k~~~~~Gg~l~l~~~~p~V~   84 (100)
T cd06844           6 VDDYWVVRLEGELDHHSVEQFKEELLHNITNV-AGKTIVIDISALEFMDSSGTGVLLERSRLAEAVGGQFVLTGISPAVR   84 (100)
T ss_pred             ECCEEEEEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCEEECHHHHHHHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             99999999779983888999999999999738-99789998768818847899999999999996699899983998999


Q ss_pred             HHHHHHHHH
Q ss_conf             999988642
Q gi|254780138|r   80 QLFSLISFT   88 (373)
Q Consensus        80 ~Ll~Ll~~~   88 (373)
                      +++++....
T Consensus        85 ~vf~~tGld   93 (100)
T cd06844          85 ITLTESGLD   93 (100)
T ss_pred             HHHHHHCCC
T ss_conf             999994868


No 5  
>cd07043 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes.
Probab=98.25  E-value=5e-06  Score=60.94  Aligned_cols=84  Identities=20%  Similarity=0.404  Sum_probs=71.3

Q ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH---CCCCCCCCCCCHHHH
Q ss_conf             58827999840356355220079999864311678808997010515212999999999975---187643158991269
Q gi|254780138|r    3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEK---YHGKIKLQGVSTHIE   79 (373)
Q Consensus         3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~---~~~~~~~~~l~~~~~   79 (373)
                      +++..++++.|+++..+...+.+.+.+.....  .+.+++|+++++++||+|...|..+.+.   .+.+....+.++..+
T Consensus         6 ~~~~~vi~l~G~ld~~~~~~~~~~~~~~~~~~--~~~vilDls~v~~idSsgl~~L~~~~~~~~~~~~~l~l~~~~~~v~   83 (99)
T cd07043           6 RGGVLVVRLSGELDAATAPELREALEELLAEG--PRRLVLDLSGVTFIDSSGLGVLLGAYKRARAAGGRLVLVNVSPAVR   83 (99)
T ss_pred             ECCEEEEEEEEEEEHHHHHHHHHHHHHHHHCC--CCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             89999999999985642899999999999769--9789998858876206899999999999872799199990998999


Q ss_pred             HHHHHHHHH
Q ss_conf             999988642
Q gi|254780138|r   80 QLFSLISFT   88 (373)
Q Consensus        80 ~Ll~Ll~~~   88 (373)
                      +++++....
T Consensus        84 ~il~~~gl~   92 (99)
T cd07043          84 RVLELTGLD   92 (99)
T ss_pred             HHHHHCCCC
T ss_conf             999981988


No 6  
>COG3113 Predicted NTP binding protein (contains STAS domain) [General function prediction only]
Probab=98.24  E-value=3.4e-06  Score=62.13  Aligned_cols=80  Identities=16%  Similarity=0.354  Sum_probs=65.2

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCHHHHHHHH
Q ss_conf             7999840356355220079999864311678808997010515212999999999975187---6431589912699999
Q gi|254780138|r    7 TVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEKYHG---KIKLQGVSTHIEQLFS   83 (373)
Q Consensus         7 ~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~~~~---~~~~~~l~~~~~~Ll~   83 (373)
                      -++.++|+.+-+++.++|....+.+.+   .+.+++|++++.+.||+|.++|.++.+.++.   ...+++.|+..+.|.+
T Consensus        12 ~tL~LsGeL~r~tl~~lw~~r~~~~~~---~~~~~idLs~v~rvDSaglALL~~~~~~~k~~g~~~~L~~~p~~L~tLa~   88 (99)
T COG3113          12 DTLVLSGELDRDTLLPLWSQREAQLKQ---LDTVRIDLSGVSRVDSAGLALLLHLIRLAKKQGNAVTLTGVPEQLRTLAE   88 (99)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHCCC---CCEEEEEHHHCCEECHHHHHHHHHHHHHHHHHCCEEEEECCCHHHHHHHH
T ss_conf             829995135487789999999986365---67589874344220227899999999999870880278637499999999


Q ss_pred             HHHHHH
Q ss_conf             886422
Q gi|254780138|r   84 LISFTH   89 (373)
Q Consensus        84 Ll~~~~   89 (373)
                      +++..+
T Consensus        89 Ly~l~~   94 (99)
T COG3113          89 LYNLSD   94 (99)
T ss_pred             HHCCHH
T ss_conf             969665


No 7  
>pfam01740 STAS STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=98.06  E-value=2.7e-05  Score=55.72  Aligned_cols=86  Identities=19%  Similarity=0.320  Sum_probs=71.1

Q ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH
Q ss_conf             5882799984035635522007999986431167880899701051521299999999997---5187643158991269
Q gi|254780138|r    3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE   79 (373)
Q Consensus         3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~   79 (373)
                      .+|..++++.|+++..+...+.+.+.+.+... +.+.+++|+++++++||+|+..|.++.+   +.+.+..+.++++..+
T Consensus         7 ~~gv~vi~l~G~Ld~~~a~~~~~~l~~~~~~~-~~~~vvlD~~~v~~iDssgl~~l~~~~~~~~~~g~~l~l~~~~~~v~   85 (106)
T pfam01740         7 IPGILILRLDGPLDFANAEAFRERLLRAIEEG-EIRHVILDLSGVPFIDSSGLGALLELYKELRRRGVELVLVGPSPEVR   85 (106)
T ss_pred             ECCEEEEEEEEEEEHHHHHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             69999999676897889999999999998658-99789999708988890299999999999997699099976998999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999886422
Q gi|254780138|r   80 QLFSLISFTH   89 (373)
Q Consensus        80 ~Ll~Ll~~~~   89 (373)
                      +.++......
T Consensus        86 ~~l~~~gl~~   95 (106)
T pfam01740        86 RTLEKTGLDD   95 (106)
T ss_pred             HHHHHHCCCC
T ss_conf             9999809986


No 8  
>TIGR02886 spore_II_AA anti-sigma F factor antagonist; InterPro: IPR014237   This represents the anti-sigma F factor antagonist, also known as stage II sporulation protein AA. This protein is universally conserved in the endospore-forming bacteria, all of which belong to the Firmcutes.; GO: 0045152 antisigma factor binding, 0006355 regulation of transcription DNA-dependent, 0030435 sporulation.
Probab=97.74  E-value=7.7e-06  Score=59.57  Aligned_cols=86  Identities=19%  Similarity=0.387  Sum_probs=73.4

Q ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHH-HH--HHHCCCCCCCCCCCHHHH
Q ss_conf             588279998403563552200799998643116788089970105152129999999-99--975187643158991269
Q gi|254780138|r    3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIM-YF--MEKYHGKIKLQGVSTHIE   79 (373)
Q Consensus         3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~-~l--~~~~~~~~~~~~l~~~~~   79 (373)
                      .++.++++++|..|.++...+..+....+.+. +-+.+++|+++|+++||||.-.+. |.  .+..+++...++.+|..+
T Consensus         6 ~~~~L~Vrl~GELDHH~aE~~R~~i~~~i~~~-~~~~~ilnL~~vtFMDSSGlGVilGRYK~i~~~gG~v~v~~v~p~vk   84 (106)
T TIGR02886         6 KGDVLIVRLSGELDHHTAEEVRRKIDDAIERR-PIKHLILNLKNVTFMDSSGLGVILGRYKKIKQEGGEVIVCNVSPAVK   84 (106)
T ss_pred             ECCEEEEEEEECCCHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCEEEECCCCEEEEEEEEEEECCCEEEEECCCCCCE
T ss_conf             18889999861004467899999999898507-98368986277647865122101110357730688898972993110


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999886422
Q gi|254780138|r   80 QLFSLISFTH   89 (373)
Q Consensus        80 ~Ll~Ll~~~~   89 (373)
                      +++++--...
T Consensus        85 r~felSGlFk   94 (106)
T TIGR02886        85 RVFELSGLFK   94 (106)
T ss_pred             EEEECCCCCC
T ss_conf             0011148750


No 9  
>COG1366 SpoIIAA Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms]
Probab=97.58  E-value=0.00041  Score=47.51  Aligned_cols=83  Identities=14%  Similarity=0.331  Sum_probs=67.6

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHHHHHH
Q ss_conf             799984035635522007999986431167880899701051521299999999997---51876431589912699999
Q gi|254780138|r    7 TVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIEQLFS   83 (373)
Q Consensus         7 ~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~~Ll~   83 (373)
                      .++.+.|+.+..+...+.+.+.+..... ..+.+++|+++++++||+|+-.|....+   ..+.+..+.+.+|+.++.+.
T Consensus        15 ~vl~l~G~lD~~~a~~~~e~~~~~~~~~-~~~~ivIDls~v~~~dS~gl~~L~~~~~~~~~~g~~~~l~~i~p~v~~~~~   93 (117)
T COG1366          15 LVLPLIGELDAARAPALKETLLEVIAAS-GARGLVIDLSGVDFMDSAGLGVLVALLKSARLRGVELVLVGIQPEVARTLE   93 (117)
T ss_pred             EEEEEEEEEEHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCEECCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH
T ss_conf             8999554871888999999999999746-997799988888774545899999999999866994899929999999999


Q ss_pred             HHHHHHH
Q ss_conf             8864222
Q gi|254780138|r   84 LISFTHR   90 (373)
Q Consensus        84 Ll~~~~~   90 (373)
                      +......
T Consensus        94 ~~gl~~~  100 (117)
T COG1366          94 LTGLDKS  100 (117)
T ss_pred             HHCCCCE
T ss_conf             9397412


No 10 
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=97.35  E-value=0.001  Score=44.69  Aligned_cols=87  Identities=18%  Similarity=0.306  Sum_probs=70.2

Q ss_pred             CCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHH---CCCCCCCCCCCHHH
Q ss_conf             858827999840356355220079999864311678808997010515212999999999975---18764315899126
Q gi|254780138|r    2 SENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEK---YHGKIKLQGVSTHI   78 (373)
Q Consensus         2 s~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~---~~~~~~~~~l~~~~   78 (373)
                      ..++..++++.|+..-.+...+.+++.+.....+..+.+++|++++..+|++|+..|.++.+.   .+.+..+.++++..
T Consensus         6 ~~~~v~i~~~~g~LfF~~~~~~~~~i~~~~~~~~~~~~vvld~~~v~~iD~s~~~~L~~~~~~~~~~g~~l~~~~~~~~~   85 (107)
T cd07042           6 EPPGVLIYRIDGPLFFGNAEYFKDRLLRLVDEDPPLKVVILDLSAVNFIDSTAAEALEELVKDLRKRGVELYLAGLNPQV   85 (107)
T ss_pred             CCCCEEEEEECCEEEEEEHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHH
T ss_conf             68988999956706761799999999998715899729999984998547599999999999999779999998098799


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999988642
Q gi|254780138|r   79 EQLFSLISFT   88 (373)
Q Consensus        79 ~~Ll~Ll~~~   88 (373)
                      .+.++.....
T Consensus        86 ~~~l~~~g~~   95 (107)
T cd07042          86 RELLERAGLL   95 (107)
T ss_pred             HHHHHHCCCH
T ss_conf             9999986997


No 11 
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=96.69  E-value=0.011  Score=37.39  Aligned_cols=82  Identities=17%  Similarity=0.384  Sum_probs=69.0

Q ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHHH
Q ss_conf             882799984035635522007999986431167880899701051521299999999997---51876431589912699
Q gi|254780138|r    4 NGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIEQ   80 (373)
Q Consensus         4 dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~~   80 (373)
                      +|.+++-+-|+.+......+.+++...+.+. +.+.+.+|+|++..+|+..+-.|.++.+   -.+.+.-..|.+|+..+
T Consensus         9 ~~vlvlPliG~ld~~r~~~l~e~ll~~i~~~-~~~~viiDlsGv~~iD~~~~~~L~~l~~~~~LlG~~~il~Gi~P~vA~   87 (109)
T cd07041           9 DGVLVLPLIGDLDDERAEQLQERLLEAISRR-RARGVIIDLTGVPVIDSAVARHLLRLARALRLLGARTILTGIRPEVAQ   87 (109)
T ss_pred             CCEEEEEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHH
T ss_conf             9889998689885999999999999999972-988999974588637789999999999999963986999943999999


Q ss_pred             HHHHHH
Q ss_conf             999886
Q gi|254780138|r   81 LFSLIS   86 (373)
Q Consensus        81 Ll~Ll~   86 (373)
                      -+--..
T Consensus        88 ~lv~~g   93 (109)
T cd07041          88 TLVELG   93 (109)
T ss_pred             HHHHHC
T ss_conf             999929


No 12 
>TIGR00377 ant_ant_sig anti-anti-sigma factor; InterPro: IPR003658 An anti-sigma factor antagonist is an anti-anti-sigma factor, which relieves inhibition of sigma factor activity by the anti-sigma factor. Examples include the Bacillus subtilis SpoIIAA protein, which, in its phosphorylated form, acts as an anti-anti-sigma factor to relieve SpoIIAB inhibition of sigma F; and the anti-sigma B factor antagonist, RsbV, which counteracts the RsbW-mediated inhibition of sigma B by binding to RsbW.; GO: 0045152 antisigma factor binding, 0006355 regulation of transcription DNA-dependent.
Probab=96.03  E-value=0.023  Score=35.26  Aligned_cols=87  Identities=15%  Similarity=0.365  Sum_probs=69.6

Q ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH---HCCCCCCCCCCCHHHH
Q ss_conf             5882799984035635522007999986431167880899701051521299999999997---5187643158991269
Q gi|254780138|r    3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME---KYHGKIKLQGVSTHIE   79 (373)
Q Consensus         3 ~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~---~~~~~~~~~~l~~~~~   79 (373)
                      .++..+++++|+.+..+.+...+.+.....+......+.+|+.+++++|++|...+....+   +.+.+....+..+...
T Consensus        10 ~~~~~~~~~~g~~d~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (109)
T TIGR00377        10 QGGVLVVRLSGELDAHTAPALRELLTPLAERGTGIRPIVLDLEGLEFMDSSGLGVLLGLYKQVKRNGGELVLVGLSPRVA   89 (109)
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHH
T ss_conf             37556887425323301688999988876215776514775056431110037999999888751786079960766788


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999886422
Q gi|254780138|r   80 QLFSLISFTH   89 (373)
Q Consensus        80 ~Ll~Ll~~~~   89 (373)
                      +.++......
T Consensus        90 ~~~~~~gl~~   99 (109)
T TIGR00377        90 RLLEITGLLD   99 (109)
T ss_pred             HHHHHHCCCC
T ss_conf             8998713100


No 13 
>PRK10782 DL-methionine transporter permease subunit; Provisional
Probab=79.08  E-value=4.2  Score=19.28  Aligned_cols=51  Identities=22%  Similarity=0.196  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHCCCHHHHH---HHH----HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             500134444278689999---999----99999999-9999999999999999999998
Q gi|254780138|r  238 NEEIDAIRTMGLDFVRIL---ISP----RIWALIIS-LPLLTILANFSAIIGASIVIWK  288 (373)
Q Consensus       238 ~eeidAL~~~Gi~p~~~L---v~P----Rv~A~~i~-~p~L~~~~~~~~i~gg~~~~~~  288 (373)
                      .+|+||-++||.+|.+.+   ++|    +++..... .-.+.-++.+.|+.|+.-....
T Consensus       117 ~g~~EAa~alG~s~~q~i~~viLPqAlp~ii~~~~~~~i~~i~~tsl~g~IG~ggLG~~  175 (217)
T PRK10782        117 TGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQI  175 (217)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             87999999839898899485107921999999999999999999999999810478999


No 14 
>COG0795 Predicted permeases [General function prediction only]
Probab=76.31  E-value=5.1  Score=18.75  Aligned_cols=23  Identities=26%  Similarity=0.141  Sum_probs=10.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78689999999999999999999
Q gi|254780138|r  248 GLDFVRILISPRIWALIISLPLL  270 (373)
Q Consensus       248 Gi~p~~~Lv~PRv~A~~i~~p~L  270 (373)
                      .++|+--...|-+++..+..-++
T Consensus       336 ~l~p~~a~~~p~~v~l~~~~~l~  358 (364)
T COG0795         336 KLPPFLAAWLPNLVFLALGLWLL  358 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             82279999999999999999999


No 15 
>COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]
Probab=69.54  E-value=7.2  Score=17.68  Aligned_cols=96  Identities=13%  Similarity=0.123  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCHHHH----HHHHHHHC
Q ss_conf             9987500134444278689999999999999999999999999999999999998611----398999----99999861
Q gi|254780138|r  234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYD----IPFAVF----FSRFHSTA  305 (373)
Q Consensus       234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~----i~~~~f----~~~~~~~~  305 (373)
                      .|.=+.||.-||+||.+|-+-.-.==     .---.+.+++.+.|..-|++++...-.    +++..+    .+.++..+
T Consensus       295 V~ek~~eIAILrtmGa~~~~I~~iFl-----~~G~~iG~iG~llG~iLG~~~~~~i~~~~~~~~~~~~~~~~~~~lP~~~  369 (408)
T COG4591         295 VKEKTREIAILRAMGASPSHIMRIFL-----LQGLIIGLIGALLGVILGVLLALNLNSIIIFIEPLLGHTFGISTLPIEL  369 (408)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCEE
T ss_conf             66455578999982998678999999-----9989999999999999999999998778740565344100112477350


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             69999999999999999999998317704
Q gi|254780138|r  306 TLANIFTGLIKAPFMACAIGIVAMKEGFA  334 (373)
Q Consensus       306 ~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~  334 (373)
                      ++.|++...+=+++..++-++...++.-+
T Consensus       370 ~~~di~~v~~~al~ls~lAtlyPA~rAsk  398 (408)
T COG4591         370 SLLDVVLVLVFALLLSLLATLYPARRASK  398 (408)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             09999999999999999999978888866


No 16 
>pfam03739 YjgP_YjgQ Predicted permease YjgP/YjgQ family. Members of this family are predicted integral membrane proteins of unknown function. They are about 350 amino acids long and contain about 6 transmembrane regions. They are predicted to be permeases although there is no verification of this.
Probab=69.15  E-value=7.3  Score=17.62  Aligned_cols=21  Identities=10%  Similarity=0.112  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             776999999999999999999
Q gi|254780138|r  165 VSGVPVVILISFVTGAVIAQQ  185 (373)
Q Consensus       165 ~~alpiv~l~~~~~G~v~a~q  185 (373)
                      --+.|+..+...++|+-++..
T Consensus       274 r~~~pl~~l~l~ll~~~l~~~  294 (353)
T pfam03739       274 RLALPLSCLVLALLALPLGLG  294 (353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHC
T ss_conf             999899999999999998316


No 17 
>KOG0236 consensus
Probab=68.47  E-value=7.6  Score=17.53  Aligned_cols=67  Identities=12%  Similarity=0.061  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHH-----HHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999997402678872899-999-----999983-----776999999999999999999999875
Q gi|254780138|r  125 SCSQAHILGLVISNTGEFCASSYKFKGFLLS-LIR-----QMYYVG-----VSGVPVVILISFVTGAVIAQQGAFQLS  191 (373)
Q Consensus       125 ~~~~~~f~G~~~~~~~~~~~~~~~~r~~~~~-~~~-----q~~~~G-----~~alpiv~l~~~~~G~v~a~q~~~~l~  191 (373)
                      .+-+..|++-..+.+....++..-.....-. .+.     ..+..+     ..++-+...++|+.|.+-...|..+|.
T Consensus       111 yGLYssf~~~~iY~~fGtsr~isiG~~av~sLmv~~~v~~~v~~~~~~~~~~~~i~va~~lt~l~Giiq~~mG~lrLG  188 (665)
T KOG0236         111 YGLYSSFFPPLIYAIFGTSRHVSIGPFAVVSLMVGTVVSQVVLSEAPSNDIATTIQVATTLTFLTGIIQLILGLLRLG  188 (665)
T ss_pred             HHHHHHHHHHHHHEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             988988887888357067875563589999999988898876303566674236799999999999999999998235


No 18 
>COG5439 Uncharacterized conserved protein [Function unknown]
Probab=58.35  E-value=9.8  Score=16.73  Aligned_cols=53  Identities=13%  Similarity=0.267  Sum_probs=36.6

Q ss_pred             EEEECCCCHHH---HHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             99840356355---22007999986431167880899701051521299999999997
Q gi|254780138|r    9 FRFAGNWKSPE---ISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME   63 (373)
Q Consensus         9 L~LsGdWTl~~---l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~   63 (373)
                      +-+.|-..+.+   +.++-.-....++..  ..+.++|+.+++.+.|+|.-+|..+--
T Consensus        17 iyFdG~mRL~s~eayaPIm~l~~~~L~a~--ps~mtinL~gL~FLNSSGInlLakfti   72 (112)
T COG5439          17 IYFDGFMRLESMEAYAPIMNLMLEILSAD--PSEMTINLEGLEFLNSSGINLLAKFTI   72 (112)
T ss_pred             EEEEEEEECCCCCCCCHHHHHHHHHHHCC--HHHHEEECCCCEEECCCCHHHHHHHHH
T ss_conf             47743775054401063999999998549--177288023313402214578876634


No 19 
>COG4215 ArtQ ABC-type arginine transport system, permease component [Amino acid transport and metabolism]
Probab=54.46  E-value=13  Score=15.85  Aligned_cols=125  Identities=24%  Similarity=0.340  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
Q ss_conf             999999999999974026788728999999999837769999999-9999999999999987542756689999999999
Q gi|254780138|r  130 HILGLVISNTGEFCASSYKFKGFLLSLIRQMYYVGVSGVPVVILI-SFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQL  208 (373)
Q Consensus       130 ~f~G~~~~~~~~~~~~~~~~r~~~~~~~~q~~~~G~~alpiv~l~-~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~  208 (373)
                      ..+-..+..+.-+..+..+.|  +-.....+|-+=++.+|=..++ -++.|.-..++....  -++...+        -.
T Consensus        24 sl~lgl~lGl~~A~~kls~~r--~lr~~~~~YtTv~RGvPELl~illiyfG~~~lL~~~~~--~~~~~g~--------~~   91 (230)
T COG4215          24 SLILGLLLGLLGALGKLSKNR--LLRLLGNVYTTVIRGVPELLLILLIYFGGQILLNTLAD--VTGALGV--------GF   91 (230)
T ss_pred             HHHHHHHHHHHHHHHHHCCCH--HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH--HHCCCCC--------CC
T ss_conf             999999999999999866660--67897543535542671999999999830999999998--7301477--------74


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH--HHHHH--HHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHH
Q ss_conf             998999999999996457899999--99987--5001344442786899---999999999999999
Q gi|254780138|r  209 REIGVLLTAVMIAGRSGSAIVAEI--GSMKI--NEEIDAIRTMGLDFVR---ILISPRIWALIISLP  268 (373)
Q Consensus       209 RElgPlltaii~agR~gsa~aAei--G~M~v--~eeidAL~~~Gi~p~~---~Lv~PRv~A~~i~~p  268 (373)
                      -|+.|..++++.-|=.=+|+++|-  |.-+.  .+|++|=+.+|.+|-+   ++++|-++-  .++|
T Consensus        92 idi~~FvaGviaL~~i~gAYatEt~RGA~~AVp~GQ~EAa~AlGms~~~~frrI~lPqm~R--~ALP  156 (230)
T COG4215          92 IDISPFVAGVIALGLIFGAYATETLRGAFKAVPKGQIEAARALGLSRSQTFRRIVLPQMWR--HALP  156 (230)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH--HHCC
T ss_conf             5567499999999999999989999999972896518899980998768899999888999--8278


No 20 
>pfam02687 FtsX Predicted permease. This is a family of predicted permeases and hypothetical transmembrane proteins. The lipoprotein-releasing system transmembrane protein lolC from Buchnera aphidicola has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both lolC and an ATP-binding cassette transporter-like protein from Streptococcus cristatus have been shown to require ATP.
Probab=48.75  E-value=16  Score=15.25  Aligned_cols=97  Identities=11%  Similarity=0.079  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCHHH
Q ss_conf             99999987500134444278689999999999999999999999999999999999998611398999999998616999
Q gi|254780138|r  230 AEIGSMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFHSTATLAN  309 (373)
Q Consensus       230 AeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~~~~~~~d  309 (373)
                      --.-.++-++|+--|+++|.++-+-.-.--.-++.     ..+.+...|+..|+...+.....-.........-.+++.+
T Consensus        72 ~~~~i~~r~~ei~ilka~G~~~~~i~~~~~~e~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (174)
T pfam02687        72 LSISIAERRREIGILKALGASKKQIFKLLLLEALL-----LGLIGSLLGLLLGFLLAYLLSSAIGYFSGFSLPLVIDPIV  146 (174)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHH
T ss_conf             99999999999999999299999999999999999-----9999999999999999999999999861434340018999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999998317
Q gi|254780138|r  310 IFTGLIKAPFMACAIGIVAMKE  331 (373)
Q Consensus       310 ~~~~~~K~~~fg~~i~~i~c~~  331 (373)
                      ++..++=..+..++.+..+.++
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~  168 (174)
T pfam02687       147 ILLVLLLILLIALLASLLPARR  168 (174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999


No 21 
>PRK11146 outer membrane-specific lipoprotein transporter subunit LolE; Provisional
Probab=47.39  E-value=17  Score=15.10  Aligned_cols=96  Identities=11%  Similarity=0.089  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HC---CCHHH-HHH
Q ss_conf             99875001344442786899999999999999999999999999999999999986----------11---39899-999
Q gi|254780138|r  234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKY----------YD---IPFAV-FFS  299 (373)
Q Consensus       234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~----------~~---i~~~~-f~~  299 (373)
                      .+.=+.||--|++||.++-+-.-.     .+.-.-++.+.+.++|++-|.+.+...          .+   .++.. |.+
T Consensus       293 V~eK~reIgiLkalG~~~~~I~~i-----Fl~eg~~ig~~G~~~G~~lG~~l~~~l~~~~~~~~~~~~~~~~~~~iy~i~  367 (412)
T PRK11146        293 VKDKSGDIAILRTLGAKDGLIRAI-----FVWYGLLAGLKGSLIGVVIGVVVSLNLTPIIKGIEKLIGHQFLSGDIYFID  367 (412)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEC
T ss_conf             998887999999948998899999-----999999999999999999999999999999999999837555897520120


Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99986169999999999999999999998317704
Q gi|254780138|r  300 RFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFA  334 (373)
Q Consensus       300 ~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c~~Gl~  334 (373)
                      .++..+++.|+....+-+.+.+++.++...++--+
T Consensus       368 ~lP~~i~~~~v~~i~~~~~i~~~las~~PA~rAa~  402 (412)
T PRK11146        368 FLPSELHWLDVAYVLVTALLLSLLASWYPARRASK  402 (412)
T ss_pred             CCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             35517139999999999999999999999999978


No 22 
>TIGR01253 thiP thiamine/thiamine pyrophosphate ABC transporter, permease protein; InterPro: IPR005947   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents thiamine ABC transporter, permease protein in bacteria, believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane. The protein belongs to the larger ABC transport system. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP).   Thiamine pyrophosphate (TPP)1 is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and -ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.; GO: 0005215 transporter activity, 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=42.91  E-value=19  Score=14.64  Aligned_cols=22  Identities=18%  Similarity=0.099  Sum_probs=10.7

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             6169999999999999999999
Q gi|254780138|r  304 TATLANIFTGLIKAPFMACAIG  325 (373)
Q Consensus       304 ~~~~~d~~~~~~K~~~fg~~i~  325 (373)
                      .++++.+-.-+-.+..||.+.+
T Consensus       446 ~~E~~~L~~PL~~AlAl~~~LS  467 (519)
T TIGR01253       446 LVELKALKAPLAYALALALVLS  467 (519)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8879998779999999999985


No 23 
>PRK08456 flagellar motor protein MotA; Validated
Probab=41.44  E-value=20  Score=14.49  Aligned_cols=57  Identities=11%  Similarity=-0.006  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999837769999999999999999999998754275668999999999999899999999
Q gi|254780138|r  157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVM  219 (373)
Q Consensus       157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii  219 (373)
                      -..+++.-.+..|-..+++.++|+|..++...      -..-+|..++.+++--+-=++.|=+
T Consensus       142 ~~~~~~~~~~~aPafGmiGtvlGLI~~l~~l~------dp~~iG~~mA~ALvtTfyGvllAn~  198 (257)
T PRK08456        142 AAHYWITAGETCPTMGLVGAVMGLMLALQLLD------NPAEMAAGIAGAFTATVTGIMGSYA  198 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             36899999987458879999999999998069------9999998999999999999999999


No 24 
>TIGR02182 GRXB Glutaredoxin, GrxB family; InterPro: IPR011901   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This family includes the highly abundant Escherichia coli GrxB (Grx2) glutaredoxin which is notably longer than either GrxA or GrxC. Unlike the other two E. coli glutaredoxins, GrxB appears to be unable to reduce ribonucleotide reductase , and may have more to do with resistance to redox stress .; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity.
Probab=40.68  E-value=7.1  Score=17.73  Aligned_cols=14  Identities=21%  Similarity=0.107  Sum_probs=5.7

Q ss_pred             ECCCHHHHHHHHHH
Q ss_conf             01051521299999
Q gi|254780138|r   44 LSAITEIDTIGAEL   57 (373)
Q Consensus        44 ls~i~~lDTAGA~l   57 (373)
                      ..++..+=|--|.-
T Consensus       108 k~~l~EFAT~~A~~  121 (212)
T TIGR02182       108 KLDLPEFATQSARK  121 (212)
T ss_pred             CCCCCCCCCHHHHH
T ss_conf             16886567688999


No 25 
>pfam09838 DUF2065 Uncharacterized protein conserved in bacteria (DUF2065). This domain, found in various prokaryotic proteins, has no known function.
Probab=40.39  E-value=21  Score=14.38  Aligned_cols=33  Identities=15%  Similarity=0.165  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             289999999998377699999999999999999
Q gi|254780138|r  152 FLLSLIRQMYYVGVSGVPVVILISFVTGAVIAQ  184 (373)
Q Consensus       152 ~~~~~~~q~~~~G~~alpiv~l~~~~~G~v~a~  184 (373)
                      .|++..+|+.+.-.+.+-++.+.+..+|.++.+
T Consensus        22 ~~r~~l~~l~~~~~~~LR~~Gl~~m~~G~~ll~   54 (57)
T pfam09838        22 AWRRMLLQLAQLPDRQLRLIGLVSMLLGLVLLW   54 (57)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999819872699995999999999872


No 26 
>KOG2927 consensus
Probab=39.32  E-value=22  Score=14.27  Aligned_cols=50  Identities=26%  Similarity=0.386  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHH
Q ss_conf             9999987542756689999999999998999999999996457----89999999
Q gi|254780138|r  184 QQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGS----AIVAEIGS  234 (373)
Q Consensus       184 ~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gs----a~aAeiG~  234 (373)
                      -|+.+.+.- |+..+++.+++++++|=+.=.+|.++.-|+.|-    ..+++.|.
T Consensus       215 R~gvyY~si-g~~gfl~~IlvLaIvRlILF~I~~il~~g~~g~W~FPNL~eDvGf  268 (372)
T KOG2927         215 RQGVYYLSI-GAGGFLAFILVLAIVRLILFGITWILTGGKHGFWLFPNLTEDVGF  268 (372)
T ss_pred             HCCEEEEEC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHH
T ss_conf             422113440-315999999999999999999999973787725753625654437


No 27 
>pfam05197 TRIC TRIC channel. TRIC (trimeric intracellular cation) channels are differentially expressed in intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel.
Probab=39.26  E-value=22  Score=14.26  Aligned_cols=35  Identities=17%  Similarity=0.133  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99999999999999999999861139899999999
Q gi|254780138|r  268 PLLTILANFSAIIGASIVIWKYYDIPFAVFFSRFH  302 (373)
Q Consensus       268 p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~~~~  302 (373)
                      |+=+.++.+...+||.+.+.+.+|-++-.++++..
T Consensus        15 P~a~Wls~ML~cFaG~iL~~llLGep~l~pl~n~~   49 (197)
T pfam05197        15 PLACWLSAMLMCFGGAILSSFLLGEPPIAPLKNTT   49 (197)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCH
T ss_conf             78999999999942899888780785245660860


No 28 
>COG4177 LivM ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=39.23  E-value=22  Score=14.26  Aligned_cols=69  Identities=25%  Similarity=0.332  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999645789999999987500134444278689999999999999999999999999999999999998611
Q gi|254780138|r  212 GVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYD  291 (373)
Q Consensus       212 gPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~  291 (373)
                      .-+++.-++-.|.|-++.|      ++|.=++-|.||+||..|-    +.|.+++       +.+.|+-| .+.+.....
T Consensus       170 ~~~~~~~l~~S~~Gr~l~A------iRedE~~a~alG~n~~~~K----l~aF~is-------a~~AGiAG-aL~a~~~~~  231 (314)
T COG4177         170 TLLVLERLVRSPFGRALRA------IREDEIAARALGINVTRYK----LLAFVIS-------AAIAGIAG-ALYALYLGF  231 (314)
T ss_pred             HHHHHHHHHCCCCCHHHHH------HCCCHHHHHHCCCCHHHHH----HHHHHHH-------HHHHHHHH-HHHHHHHCE
T ss_conf             9999999864970336866------6157899998599889999----9999999-------99999999-999998150


Q ss_pred             CCHHHHH
Q ss_conf             3989999
Q gi|254780138|r  292 IPFAVFF  298 (373)
Q Consensus       292 i~~~~f~  298 (373)
                      ++|..|.
T Consensus       232 v~p~~f~  238 (314)
T COG4177         232 VSPESFS  238 (314)
T ss_pred             ECCHHCC
T ss_conf             3800253


No 29 
>COG1079 Uncharacterized ABC-type transport system, permease component [General function prediction only]
Probab=38.80  E-value=22  Score=14.22  Aligned_cols=88  Identities=15%  Similarity=0.157  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHHCCHHH
Q ss_conf             9875001344442786899999999999999999999999999999999999986113-----98999999998616999
Q gi|254780138|r  235 MKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDI-----PFAVFFSRFHSTATLAN  309 (373)
Q Consensus       235 M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i-----~~~~f~~~~~~~~~~~d  309 (373)
                      +-+.|.=+|.++||+|..+|    |..|.++.       +...|+-|+|+.-......     .-.-|+.--......|+
T Consensus       170 ravGE~P~aad~~Gi~V~r~----R~~av~~s-------G~laGlaGa~Lsl~~~~~f~~~m~aGrGfIAlA~~ifa~W~  238 (304)
T COG1079         170 RAVGENPAAADAMGINVYRY----RYLAVLVS-------GALAGLAGAYLSLAYSGQFVEGMTAGRGFIALAAVIFARWR  238 (304)
T ss_pred             EEECCCHHHHHHCCCCHHHH----HHHHHHHH-------HHHHHHHHHHEEEEECCCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             98269826788679875678----89999999-------99987535213555045644466677219999999994787


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999999831770
Q gi|254780138|r  310 IFTGLIKAPFMACAIGIVAMKEGF  333 (373)
Q Consensus       310 ~~~~~~K~~~fg~~i~~i~c~~Gl  333 (373)
                      -+..+.-+.+||+.-++----|.+
T Consensus       239 Pl~~~~~allFg~~~~l~~~~q~~  262 (304)
T COG1079         239 PLGALVAALLFGFFEALAIQLQAL  262 (304)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             399999999999999999886124


No 30 
>TIGR00815 sulP sulfate permease; InterPro: IPR001902   A number of proteins involved in the transport of sulphate across a membrane as well as some yet uncharacterised proteins have been shown ,  to be evolutionary related. These proteins are:  Neurospora crassa sulphate permease II (gene cys-14). Yeast sulphate permeases (genes SUL1 and SUL2). Rat sulphate anion transporter 1 (SAT-1). Mammalian DTDST, a probable sulphate transporter which, in human, is involved in the genetic disease, diastrophic dysplasia (DTD). Sulphate transporters 1, 2 and 3 from the legume Stylosanthes hamata. Human pendrin (gene PDS), which is involved in a number of hearing loss genetic diseases. Human protein DRA (Down-Regulated in Adenoma). Soybean early nodulin 70. Escherichia coli hypothetical protein ychM. Caenorhabditis elegans hypothetical protein F41D9.5.    These proteins are highly hydrophobic and seem to contain about 12 transmembrane domains. ; GO: 0008271 secondary active sulfate transmembrane transporter activity, 0008272 sulfate transport, 0016020 membrane.
Probab=38.08  E-value=23  Score=14.14  Aligned_cols=21  Identities=10%  Similarity=0.167  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999989999999999
Q gi|254780138|r  201 DLMSILQLREIGVLLTAVMIA  221 (373)
Q Consensus       201 ~~~~~~~~RElgPlltaii~a  221 (373)
                      ++++..+..-++++..+....
T Consensus       307 e~~~~G~~n~~~~~f~~~~~~  327 (638)
T TIGR00815       307 ELVALGIANILGSFFGCYPAT  327 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             123431366654555577777


No 31 
>PRK13108 prolipoprotein diacylglyceryl transferase; Reviewed
Probab=37.87  E-value=23  Score=14.12  Aligned_cols=22  Identities=18%  Similarity=0.122  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999964578999999
Q gi|254780138|r  212 GVLLTAVMIAGRSGSAIVAEIG  233 (373)
Q Consensus       212 gPlltaii~agR~gsa~aAeiG  233 (373)
                      +|-+--=--.||-|.=|.-|+=
T Consensus       133 APgllLAQAIGRwGNFFNQELy  154 (460)
T PRK13108        133 APGVVLAQAIGRLGNYFNQELY  154 (460)
T ss_pred             HHHHHHHHHHCHHHHHHCHHHC
T ss_conf             3567999984404643051223


No 32 
>PRK10814 outer membrane-specific lipoprotein transporter subunit LolC; Provisional
Probab=37.02  E-value=24  Score=14.03  Aligned_cols=97  Identities=10%  Similarity=0.027  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHCCHHH
Q ss_conf             998750013444427868999999999999999999999999999999999999861139----8999999998616999
Q gi|254780138|r  234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIP----FAVFFSRFHSTATLAN  309 (373)
Q Consensus       234 ~M~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~----~~~f~~~~~~~~~~~d  309 (373)
                      .+.=+.||--|++||.++-+-.-.=-+-++     ++.+.+.++|+.-|.+.+.....+.    ...+...++..+++.|
T Consensus       290 V~eK~~eI~iL~alGa~~~~I~~iFl~~g~-----~ig~~G~~~G~~lG~~l~~~~~~~~~~~~~~~~~~~~Pv~i~~~~  364 (396)
T PRK10814        290 VMEKQGEVAILQTQGLTPRQIMMVFMVQGA-----SAGIIGALLGAALGALLASQLNNLMPIIGVLLDGAALPVAIEPLQ  364 (396)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHH
T ss_conf             997776899999838993559999999999-----999999999999999999999999854323236643568952999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999983177045
Q gi|254780138|r  310 IFTGLIKAPFMACAIGIVAMKEGFAV  335 (373)
Q Consensus       310 ~~~~~~K~~~fg~~i~~i~c~~Gl~~  335 (373)
                      ++...+-+.+.+++-++...++--+.
T Consensus       365 v~~v~~~~~~i~~la~~~PA~~Aa~l  390 (396)
T PRK10814        365 VIVIALVAMAIALLSTLYPSWRAAAT  390 (396)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999999999999587


No 33 
>pfam11964 DUF3478 Protein of unknown function (DUF3478). This family of proteins is functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important.
Probab=36.63  E-value=24  Score=13.99  Aligned_cols=84  Identities=11%  Similarity=0.126  Sum_probs=52.0

Q ss_pred             CCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCHHH
Q ss_conf             858827999840356355220079999864311678808997010515212999999999975187---64315899126
Q gi|254780138|r    2 SENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFMEKYHG---KIKLQGVSTHI   78 (373)
Q Consensus         2 s~dG~~vL~LsGdWTl~~l~~l~~~l~~~L~~~~~~~~i~iDls~i~~lDTAGA~lL~~l~~~~~~---~~~~~~l~~~~   78 (373)
                      .+++...++++|..|...+..+.+.+...++.+.+ -++.+|+.+...|+-..+|==.++-.++..   ++..++-+.=.
T Consensus         8 ~~~~v~~~~v~G~lt~~D~~~l~~~l~~~l~~~~~-i~ll~~~~~f~G~~~~a~~ed~k~~~~h~~~~~riAiV~d~~W~   86 (118)
T pfam11964         8 PDDNVLAFKVSGKLTHEDYEVLIPALEAKLEEHGK-VRLLIDLDDFEGWELGALWEDLKLGLKHLKDFDRIAIVGDKKWL   86 (118)
T ss_pred             CCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHCCC-EEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECHHHH
T ss_conf             99998999995168899999999999999974796-58999945788998889999999877655045489999185999


Q ss_pred             HHHHHHHH
Q ss_conf             99999886
Q gi|254780138|r   79 EQLFSLIS   86 (373)
Q Consensus        79 ~~Ll~Ll~   86 (373)
                      +.+.++..
T Consensus        87 ~~~~~~~~   94 (118)
T pfam11964        87 EWAAKLFG   94 (118)
T ss_pred             HHHHHHHH
T ss_conf             99999985


No 34 
>pfam04123 DUF373 Domain of unknown function (DUF373). Archaeal domain of unknown function. Predicted to be an integral membrane protein with six transmembrane regions.
Probab=35.78  E-value=25  Score=13.90  Aligned_cols=29  Identities=24%  Similarity=0.549  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHH-HCHHHHHHHHHH
Q ss_conf             99999999999998754-275668999999
Q gi|254780138|r  176 FVTGAVIAQQGAFQLSQ-FGAEIFSIDLMS  204 (373)
Q Consensus       176 ~~~G~v~a~q~~~~l~~-fGa~~~v~~~~~  204 (373)
                      ..+|.+...-|.+.|-+ ||.+.++.....
T Consensus       184 ~~~~~i~~~lG~y~l~kG~gid~~~~~~~~  213 (344)
T pfam04123       184 YALGVILLILGLYLLYRGFGLDDFLRELLK  213 (344)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             799999999999999997379999999999


No 35 
>TIGR03004 ectoine_ehuC ectoine/hydroxyectoine ABC transporter, permease protein EhuC; InterPro: IPR014342   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    Members of this entry are presumed to act as permease subunits of ectoine ABC transporters. Operons containing this gene also contain other genes of the ABC transporter and are typically found next to either ectoine utilization or ectoine biosynthesis operons. Permease subunits EhuC and EhuD are homologues..
Probab=33.98  E-value=26  Score=13.70  Aligned_cols=116  Identities=26%  Similarity=0.236  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH--HHHH--HHHHHHHHHHHCCCHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998999999999996457899999--9998--7500134444278689999---99999999999999999999999999
Q gi|254780138|r  209 REIGVLLTAVMIAGRSGSAIVAEI--GSMK--INEEIDAIRTMGLDFVRIL---ISPRIWALIISLPLLTILANFSAIIG  281 (373)
Q Consensus       209 RElgPlltaii~agR~gsa~aAei--G~M~--v~eeidAL~~~Gi~p~~~L---v~PRv~A~~i~~p~L~~~~~~~~i~g  281 (373)
                      -|+.|+-+|++.-|-.--||.|||  |..|  -.||.+|=+.+...|++.+   ++|-  |++.|||.-+=.+.= -+=+
T Consensus        77 l~l~P~t~gv~~Lglh~GaYGAEivRGA~~sv~~~Q~EAc~ALNftrfq~~rrI~LPQ--Al~~mmp~fgNlaIE-lLK~  153 (216)
T TIGR03004        77 LELDPLTVGVLALGLHVGAYGAEIVRGAVKSVSKEQLEACIALNFTRFQALRRIVLPQ--ALVEMMPAFGNLAIE-LLKL  153 (216)
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHHHHCCCCCHHHHH-HHHH
T ss_conf             4025189999999973265016888888997436589999984153677998763267--999743866158999-9987


Q ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999986-11398999999998616999999999999999999999
Q gi|254780138|r  282 ASIVIWKY-YDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGIV  327 (373)
Q Consensus       282 g~~~~~~~-~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i  327 (373)
                      ..+|+-.. -|++|..---+-...=+..-+...+.-=.+++.+|.++
T Consensus       154 tslVSLIslaDltF~Aq~~r~~T~~tl~~fa~~LL~YFvMa~~i~l~  200 (216)
T TIGR03004       154 TSLVSLISLADLTFRAQSVRALTLDTLKVFALILLLYFVMALIISLA  200 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999986769999999841002799999999999999999999


No 36 
>PRK08124 flagellar motor protein MotA; Validated
Probab=32.98  E-value=27  Score=13.59  Aligned_cols=58  Identities=10%  Similarity=0.015  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998377699999999999999999999987542756689999999999998999999999
Q gi|254780138|r  157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMI  220 (373)
Q Consensus       157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~  220 (373)
                      -..+++.--+..|-..+++.++|+|..++..      +-..-+|..++.+++--+-=++.|=++
T Consensus       143 ~~~v~~~~~~~aPafGmiGtvlGLI~~L~~l------~dp~~iG~~mA~ALvtT~yGvllAn~~  200 (263)
T PRK08124        143 GAAIFTQAGTYAPTLGVLGAVIGLIAALGNL------NDIEKLGHAISAAFVATLLGIFTGYVL  200 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1479999998736775999999999998725------999999988999999999999999999


No 37 
>PRK08990 flagellar motor protein PomA; Reviewed
Probab=31.92  E-value=29  Score=13.48  Aligned_cols=62  Identities=15%  Similarity=-0.013  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998377699999999999999999999987542756689999999999998999999999996
Q gi|254780138|r  156 LIRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGR  223 (373)
Q Consensus       156 ~~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR  223 (373)
                      ....+++.--+..|-..+++.++|+|..++..      +-..-+|..++.+++--+-=++.|=++.+-
T Consensus       138 ~~~~v~~~~g~~aPafGmiGTviGLI~mL~~l------~dp~~iG~~mA~ALvtTlYGillAnl~~~P  199 (253)
T PRK08990        138 TGIGIFRAFGDVAPAMGMIGTLIGLVAMLSNM------DDPKSIGPAMAVALLTTLYGAVLANMVAIP  199 (253)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             86789999998716887999999999999806------999999988899999999999999999999


No 38 
>COG1291 MotA Flagellar motor component [Cell motility and secretion]
Probab=31.58  E-value=29  Score=13.44  Aligned_cols=63  Identities=11%  Similarity=0.021  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998377699999999999999999999987542756689999999999998999999999996457
Q gi|254780138|r  158 RQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGS  226 (373)
Q Consensus       158 ~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gs  226 (373)
                      .+....--++.|-..+++..+|+|.+++....      ..-+|..++.+++--+--.+.|-.+.+-.++
T Consensus       144 a~~~~~~g~~aPa~GivgaV~GlI~~l~~l~~------p~~LG~~iA~Alv~T~~Gi~~ay~~~~P~a~  206 (266)
T COG1291         144 AHAFTTAGDYAPAFGIVGAVMGLIHALGNLDD------PAELGALIAAALVGTLYGIFLAYGLFGPLAN  206 (266)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999988458266699999999999882799------7888889999999999999999897868899


No 39 
>PRK11301 livM leucine/isoleucine/valine transporter permease subunit; Provisional
Probab=31.46  E-value=29  Score=13.43  Aligned_cols=52  Identities=23%  Similarity=0.251  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             8750013444427868999999999999999999999999999999999999861139899999
Q gi|254780138|r  236 KINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFS  299 (373)
Q Consensus       236 ~v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~  299 (373)
                      -++|.=||-|.||+|+.+|-    +.|.+++       +.+.|+- |.+.++...-++|+.|--
T Consensus       292 AIRedE~AA~alGInv~r~K----L~AFals-------A~~AGlA-GaLyA~~~g~IsP~~F~~  343 (416)
T PRK11301        292 ALREDEIACRSLGLNPTRIK----LSAFTIG-------AAFAGFA-GTFFAARQGFVSPESFTF  343 (416)
T ss_pred             HHHCCHHHHHHCCCCHHHHH----HHHHHHH-------HHHHHHH-HHHHHHHCCEECCCCCCH
T ss_conf             99627999998597769999----9999999-------9999999-999998816348330659


No 40 
>pfam08566 Pam17 Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins.
Probab=28.92  E-value=32  Score=13.14  Aligned_cols=50  Identities=22%  Similarity=0.163  Sum_probs=24.8

Q ss_pred             HHHHHH--HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             500134--44427868999999999999999999999999999999999999861139899999
Q gi|254780138|r  238 NEEIDA--IRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVFFS  299 (373)
Q Consensus       238 ~eeidA--L~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f~~  299 (373)
                      +.|+|+  -..||+||+-.+.            +.++.+..+|.+.|=.+......+....+..
T Consensus        62 ~~~~D~~~~~I~GlDP~~~~g------------~~~~a~~~~G~L~GP~iG~~vf~l~~r~~~~  113 (174)
T pfam08566        62 TLEIDSPTQQIMGLDPFMVLG------------LATIACGALGWLLGPFIGNAVFRLLNRSQLK  113 (174)
T ss_pred             CCCCCCCCCCCCCCCHHHHHH------------HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             433354203013858899999------------9999974255751636789999997377888


No 41 
>PRK00965 tetrahydromethanopterin S-methyltransferase subunit B; Provisional
Probab=27.87  E-value=33  Score=13.01  Aligned_cols=29  Identities=7%  Similarity=0.036  Sum_probs=10.1

Q ss_pred             CCCCCCCCCCH---HHHHHHHHHHHHHHHCCC
Q ss_conf             87643158991---269999988642220112
Q gi|254780138|r   66 HGKIKLQGVST---HIEQLFSLISFTHRKKIK   94 (373)
Q Consensus        66 ~~~~~~~~l~~---~~~~Ll~Ll~~~~~~~~~   94 (373)
                      +.+.-..++.|   +..+|-+..+...+...|
T Consensus        25 ~~dvi~~s~~PI~e~i~kLe~~addL~nsLdP   56 (108)
T PRK00965         25 REDVIVVDMDPVEEEINKLEAIADDLENSLDP   56 (108)
T ss_pred             CCCEEEEECHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             58759985047899999999999999864599


No 42 
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=26.92  E-value=34  Score=12.90  Aligned_cols=66  Identities=17%  Similarity=0.263  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             99999999837769999999999999999-9999987542756689999999999-9989999999999
Q gi|254780138|r  155 SLIRQMYYVGVSGVPVVILISFVTGAVIA-QQGAFQLSQFGAEIFSIDLMSILQL-REIGVLLTAVMIA  221 (373)
Q Consensus       155 ~~~~q~~~~G~~alpiv~l~~~~~G~v~a-~q~~~~l~~fGa~~~v~~~~~~~~~-RElgPlltaii~a  221 (373)
                      ++.++....+.-....+.+.++.+|.+++ +|...|.++-- -.|++.++++..+ -=+||-+...++.
T Consensus         8 ~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA~TQIqEqT-LsFiPKIiai~~~l~~~gpWm~~~l~d   75 (89)
T COG1987           8 DIGQEAIWLVLMLSAPVLLVALVVGLVISIFQAATQIQEQT-LSFIPKIIAVFLVLILLGPWMLNQLLD   75 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999989999999999999999999999999-985998999999999975899999999


No 43 
>PRK06926 flagellar motor protein MotP; Reviewed
Probab=26.88  E-value=35  Score=12.89  Aligned_cols=47  Identities=13%  Similarity=0.086  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH
Q ss_conf             99998377699999999999999999999987542756689999999999998
Q gi|254780138|r  159 QMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREI  211 (373)
Q Consensus       159 q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~REl  211 (373)
                      .+++.--+..|-..+++.++|+|..++..      +...-+|..++.+++--+
T Consensus       149 ~~~~~~g~~aPafGmiGTviGLI~mL~~l------~dp~~iG~~mAvALvtTl  195 (272)
T PRK06926        149 RLFEKAGEFAPAWGMIGTLVGLVLMLKNL------NDPHTLGPNMAVALLTTL  195 (272)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHH
T ss_conf             99999998725887999999999998816------999999888899999999


No 44 
>pfam04710 Pellino Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase.
Probab=26.69  E-value=7.5  Score=17.56  Aligned_cols=64  Identities=19%  Similarity=0.261  Sum_probs=37.5

Q ss_pred             CCCCCEEEEEEECCCCHHHHHHHHHHHH--------HHHHHCCCCCEEEEE----ECCCHHHHHHHHHHHHHHHHH
Q ss_conf             9858827999840356355220079999--------864311678808997----010515212999999999975
Q gi|254780138|r    1 MSENGITVFRFAGNWKSPEISEIADDVV--------MAINKSIQSDSAIVD----LSAITEIDTIGAELIMYFMEK   64 (373)
Q Consensus         1 ~s~dG~~vL~LsGdWTl~~l~~l~~~l~--------~~L~~~~~~~~i~iD----ls~i~~lDTAGA~lL~~l~~~   64 (373)
                      |+.+|.++++-.|.|+-.+.+..|+++.        +.-.+..+..+.+=|    +.+=+-+|=+||.+|||....
T Consensus       181 LTTNGVLimhP~~~f~~~s~pgvWrEvSVcG~Vy~lResRSaq~~G~~ve~e~NiL~DGtLIDLCGaTLlWRsa~g  256 (416)
T pfam04710       181 LTTNGVLVMHPRGGFTEDSKPGVWREISVCGDVYTLRETRSAQQPGKLVEEETNVLQDGTLIDLCGATLLWRTADG  256 (416)
T ss_pred             CCCCCEEEECCCCCCCCCCCCCEEEEEEECCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEECCCCEEEEECCCC
T ss_conf             4216659973688887788886458998777054540134545787302488870145647030531578733453


No 45 
>pfam03683 UPF0175 Uncharacterized protein family (UPF0175). This family contains small proteins of unknown function.
Probab=26.49  E-value=14  Score=15.58  Aligned_cols=36  Identities=17%  Similarity=0.202  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             9999964578999999998750013444427868999
Q gi|254780138|r  218 VMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRI  254 (373)
Q Consensus       218 ii~agR~gsa~aAeiG~M~v~eeidAL~~~Gi~p~~~  254 (373)
                      +---|+...+-||||..|...|=++-|.-.||+ +.|
T Consensus        29 lY~~g~iS~gkAaelag~s~~eF~~~L~~~~I~-~~y   64 (76)
T pfam03683        29 LYERGKISLGKAAELAGMSRWEFLELLARRGIP-RHY   64 (76)
T ss_pred             HHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC-CCC
T ss_conf             998498489999999799999999999987999-889


No 46 
>PRK11123 arginine transporter permease subunit ArtQ; Provisional
Probab=26.39  E-value=35  Score=12.83  Aligned_cols=126  Identities=14%  Similarity=0.141  Sum_probs=70.4

Q ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCHHH--HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             974026788728999999999837769999-99999999999999999875427566--899999999999989999999
Q gi|254780138|r  142 FCASSYKFKGFLLSLIRQMYYVGVSGVPVV-ILISFVTGAVIAQQGAFQLSQFGAEI--FSIDLMSILQLREIGVLLTAV  218 (373)
Q Consensus       142 ~~~~~~~~r~~~~~~~~q~~~~G~~alpiv-~l~~~~~G~v~a~q~~~~l~~fGa~~--~v~~~~~~~~~RElgPlltai  218 (373)
                      .+.+..+.|  +-......|-.=.+..|.. .+.-+..|.-.-+...  -..++...  .......-..--++.|..+|+
T Consensus        33 a~~r~s~~~--~l~~~~~~yv~~~RgtP~lv~l~~~yfg~p~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~f~~av  108 (238)
T PRK11123         33 AVWESAKWR--PVAWPGTALVTLLRGLPEILVVLFIYFGSSQLLLTL--SDGFTLNLGFVQIPVQMDIENFEVSPFLCGV  108 (238)
T ss_pred             HHHHHCCCH--HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH--HHHHCCCCHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf             999988868--899999999999916759999999999528988763--1000001001110100121345646999999


Q ss_pred             HHHHHHHHHHHHHH---HHHHH-HHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99996457899999---99987-5001344442786899---99999999999999999999
Q gi|254780138|r  219 MIAGRSGSAIVAEI---GSMKI-NEEIDAIRTMGLDFVR---ILISPRIWALIISLPLLTIL  273 (373)
Q Consensus       219 i~agR~gsa~aAei---G~M~v-~eeidAL~~~Gi~p~~---~Lv~PRv~A~~i~~p~L~~~  273 (373)
                      +.-+=..+|+.||+   |-..| .+|.||=+++|.++.+   +.++|-.  .-.++|-++-.
T Consensus       109 ial~l~~~Ay~aEi~R~gi~sVp~GQ~EAa~alGms~~q~~r~IilPQa--~r~~lP~l~n~  168 (238)
T PRK11123        109 IALSLLYAAYASQTLRGALKAVPVGQWESGQALGLSKSAIFFRLVMPQM--WRHALPGLGNQ  168 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHH
T ss_conf             9999999999999999999839999999999849899999999998999--99997389999


No 47 
>pfam08496 Peptidase_S49_N Peptidase family S49 N-terminal. This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343).
Probab=26.38  E-value=35  Score=12.83  Aligned_cols=14  Identities=7%  Similarity=0.226  Sum_probs=4.9

Q ss_pred             CCCCCCHHHHHHHH
Q ss_conf             31589912699999
Q gi|254780138|r   70 KLQGVSTHIEQLFS   83 (373)
Q Consensus        70 ~~~~l~~~~~~Ll~   83 (373)
                      +..++++.++++-+
T Consensus        43 ~v~~Lne~y~~~~~   56 (154)
T pfam08496        43 EITDLNEEYKDLKE   56 (154)
T ss_pred             EEEEHHHHHHHHHH
T ss_conf             98567999999999


No 48 
>PRK09109 motC flagellar motor protein; Reviewed
Probab=25.54  E-value=36  Score=12.73  Aligned_cols=58  Identities=10%  Similarity=0.039  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998377699999999999999999999987542756689999999999998999999999
Q gi|254780138|r  157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMI  220 (373)
Q Consensus       157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~  220 (373)
                      -..+++.-.+..|-..+++.++|+|..++.-      +-..-+|..++.+++--+-=++.|=++
T Consensus       142 ~~~~~~~~g~~aPafGmiGtviGLI~mL~~l------~dp~~lG~~mA~ALvtT~yGv~lAn~v  199 (246)
T PRK09109        142 AAKVFESMGGYAPTIGIIGAVMGLIHVMENL------ADPSQLGSGIAVAFVATIYGVASANLL  199 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7789999998726764999999999998806------999999988799999999999999999


No 49 
>TIGR00780 ccoN cytochrome c oxidase, cbb3-type, subunit I; InterPro: IPR004677 This family represents the largest subunit, I, of the ccb3-type cytochrome c oxidase 1.9.3.1 from EC, with two protohemes and copper. It shows strong homology to subunits of other types of cytochrome oxidases. Species with this type, all from the proteobacteria so far, include Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Rhodobacter sphaeroides, Rhizobium leguminosarum, and others.; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport, 0045278 plasma membrane respiratory chain complex IV.
Probab=25.53  E-value=36  Score=12.73  Aligned_cols=98  Identities=17%  Similarity=0.153  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999837769999999999999999999998754275668999999-99999989999999999964578999999998
Q gi|254780138|r  158 RQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMS-ILQLREIGVLLTAVMIAGRSGSAIVAEIGSMK  236 (373)
Q Consensus       158 ~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~-~~~~RElgPlltaii~agR~gsa~aAeiG~M~  236 (373)
                      +.+-+.++-+.-.-.++++|+|+|+|+|.+.---++      .|+.. ....=.|=||=|.=++=|=.|           
T Consensus         7 d~vvr~f~ia~v~wGiVGmLvGvv~Af~L~fPaLnl------S~I~~~y~~FGrLRPLHTnAVIfaFgg-----------   69 (485)
T TIGR00780         7 DSVVRLFLIATVVWGIVGMLVGVVVAFQLSFPALNL------SDIAGEYGIFGRLRPLHTNAVIFAFGG-----------   69 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC------HHCCCCCCCCCCCCCCCHHHHHHHHHC-----------
T ss_conf             899987877434321677899999999860564560------113565235786686502366653222-----------


Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q ss_conf             750013444427868999999999999999-------9999999999999999
Q gi|254780138|r  237 INEEIDAIRTMGLDFVRILISPRIWALIIS-------LPLLTILANFSAIIGA  282 (373)
Q Consensus       237 v~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~-------~p~L~~~~~~~~i~gg  282 (373)
                                .|+=.-.|=|.-|++-.+..       .|.++++.-.+=|.-|
T Consensus        70 ----------~GliatsyYvvQRvlkiT~~~rlfgg~~~~f~FWgw~~~ivla  112 (485)
T TIGR00780        70 ----------GGLIATSYYVVQRVLKITYAQRLFGGIVGLFVFWGWQILIVLA  112 (485)
T ss_pred             ----------CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             ----------2155446676565766511135111368999989999999999


No 50 
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=25.43  E-value=37  Score=12.72  Aligned_cols=130  Identities=15%  Similarity=0.204  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999987542756689999999999998999999999996457899999999875001344442
Q gi|254780138|r  168 VPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSMKINEEIDAIRTM  247 (373)
Q Consensus       168 lpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M~v~eeidAL~~~  247 (373)
                      |.+..+.+++.|-++...          +.-+..+++++.+   =|++++      +|..-.+|.-|+.    |.||.+=
T Consensus       287 Llvll~~~~~ta~vi~~F----------e~~l~~~vaLa~f---iPlv~g------~gGN~GsQ~~tvi----vRaLa~~  343 (451)
T COG2239         287 LLVLLVTATLTASVIGLF----------EDTLEQLVALAAF---IPLVAG------MGGNAGTQAATVI----VRALALG  343 (451)
T ss_pred             HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH---HHEEEC------CCCCHHHHHHHHH----HHHHCCC
T ss_conf             999999898899999999----------9779999999988---601006------8876999999999----9753103


Q ss_pred             CCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             78689999-9999999999999999999999999999-999986113989999999986169999999999999999999
Q gi|254780138|r  248 GLDFVRIL-ISPRIWALIISLPLLTILANFSAIIGAS-IVIWKYYDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIG  325 (373)
Q Consensus       248 Gi~p~~~L-v~PRv~A~~i~~p~L~~~~~~~~i~gg~-~~~~~~~~i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~  325 (373)
                      -+++.... +++|=+..-      ...+.+.|...|. +.+++..+.        ....+-..-+...++-+...|.++.
T Consensus       344 ~i~~~~~~~vl~rE~~vG------~~~G~vl~~~~~~~~~~~~~~~~--------~l~~~v~~al~~~~~~A~l~G~~iP  409 (451)
T COG2239         344 EISLKNVFRVLLKELGVG------LLLGLVLAIIIGLRVPAWLYGGL--------LLGLIVALALLLNILFAALVGVLIP  409 (451)
T ss_pred             CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHCCC--------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             063200999989999999------99999999999999899992662--------3899999999999999999853388


Q ss_pred             HHHHCCCCC
Q ss_conf             998317704
Q gi|254780138|r  326 IVAMKEGFA  334 (373)
Q Consensus       326 ~i~c~~Gl~  334 (373)
                      ++--..|+-
T Consensus       410 ~ll~kl~~D  418 (451)
T COG2239         410 ILLKKLGLD  418 (451)
T ss_pred             HHHHHCCCC
T ss_conf             999874999


No 51 
>pfam07297 DPM2 Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2). This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2.
Probab=24.14  E-value=39  Score=12.55  Aligned_cols=34  Identities=18%  Similarity=0.196  Sum_probs=17.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6899999999999999999999999999999999
Q gi|254780138|r  250 DFVRILISPRIWALIISLPLLTILANFSAIIGAS  283 (373)
Q Consensus       250 ~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~  283 (373)
                      +|++-+..||-.|..+-.-++.+....+|.+-|+
T Consensus        37 h~~~~~FlpReyAi~iP~~l~v~~~~~vg~Fig~   70 (80)
T pfam07297        37 HVIHSFFLPREYAIRIPVIAGLLLLLFVGSFIGV   70 (80)
T ss_pred             CHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6698817858899998999999999999988441


No 52 
>COG2120 Uncharacterized proteins, LmbE homologs [Function unknown]
Probab=23.46  E-value=22  Score=14.28  Aligned_cols=11  Identities=0%  Similarity=0.253  Sum_probs=4.6

Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999751876
Q gi|254780138|r   58 IMYFMEKYHGK   68 (373)
Q Consensus        58 L~~l~~~~~~~   68 (373)
                      |.++.++.+.+
T Consensus       101 L~~ii~~~~P~  111 (237)
T COG2120         101 LVAIIRRLRPD  111 (237)
T ss_pred             HHHHHHHCCCC
T ss_conf             99999853997


No 53 
>KOG3944 consensus
Probab=23.31  E-value=39  Score=12.54  Aligned_cols=23  Identities=13%  Similarity=0.037  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999983
Q gi|254780138|r  307 LANIFTGLIKAPFMACAIGIVAM  329 (373)
Q Consensus       307 ~~d~~~~~~K~~~fg~~i~~i~c  329 (373)
                      +.+=+..+.-+.+||-+....+|
T Consensus       235 pf~plEn~~cavffGgi~d~~s~  257 (291)
T KOG3944         235 PFAPLENLLCAVFFGGIWDASSC  257 (291)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHH
T ss_conf             53236667589986444763034


No 54 
>PRK06743 flagellar motor protein MotP; Reviewed
Probab=23.05  E-value=40  Score=12.41  Aligned_cols=57  Identities=16%  Similarity=-0.048  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999837769999999999999999999998754275668999999999999899999999
Q gi|254780138|r  157 IRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVM  219 (373)
Q Consensus       157 ~~q~~~~G~~alpiv~l~~~~~G~v~a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii  219 (373)
                      -..+++.--+.-|-..+++.++|+|..++..      +-..-+|..++.+++--+-=++.|=+
T Consensus       139 ~~~v~~~~g~~APafGmiGTviGLI~mL~~l------~dp~~iG~~mAvAlvtTlYG~~lAnl  195 (254)
T PRK06743        139 GAALLDKIGDFAPAWGMIGTLIGLIIMLQNL------QDTSQIGTGMAVAMLTTLYGSVLANM  195 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999997643788999999999998726------99999989999999999999999999


No 55 
>pfam01312 Bac_export_2 FlhB HrpN YscU SpaS Family. This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse.
Probab=22.81  E-value=41  Score=12.38  Aligned_cols=35  Identities=14%  Similarity=0.153  Sum_probs=22.5

Q ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             39899999999861699999999999999999999
Q gi|254780138|r  292 IPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGI  326 (373)
Q Consensus       292 i~~~~f~~~~~~~~~~~d~~~~~~K~~~fg~~i~~  326 (373)
                      ++|-.=+.++.+.=++.++.-+++|-.+.|.+...
T Consensus       123 lNPi~GlKriFS~~~LvEl~KsllKv~li~~v~~~  157 (343)
T pfam01312       123 INPIKGLKRIFSARSLVELLKSILKVVAVGLIFYF  157 (343)
T ss_pred             CCHHHCHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68744422003777899999999999999999999


No 56 
>PRK10535 macrolide transporter ATP-binding /permease protein; Provisional
Probab=22.17  E-value=42  Score=12.30  Aligned_cols=94  Identities=16%  Similarity=0.251  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHH--------HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             789999999987--------500134444278689999999999999999999999999999999999998611398999
Q gi|254780138|r  226 SAIVAEIGSMKI--------NEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIPFAVF  297 (373)
Q Consensus       226 sa~aAeiG~M~v--------~eeidAL~~~Gi~p~~~Lv~PRv~A~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~~~~f  297 (373)
                      |-+.+-||-|.+        |.||==.+++|-.+-+-+..  +   ++=..+|++++.++|+..|++.+....-     |
T Consensus       532 SLlVggIGImNIMlvSVtERTrEIGIRKAlGA~~~dI~~q--F---L~Ea~~l~~iGGiiGi~lg~~i~~~i~~-----~  601 (648)
T PRK10535        532 SLVVGGIGVMNIMLVSVTERTREIGIRMAVGARASDVLQQ--F---LIEAVLVCLVGGALGISLSLLIAFTLQL-----F  601 (648)
T ss_pred             HHHHHHHHHHHHHEEEHHHHHHHHHHHHHHCCCHHHHHHH--H---HHHHHHHHHHHHHHHHHHHHHHHHHHHH-----H
T ss_conf             9999999999673220178888999999838988899999--9---9999999999999999999999999998-----5


Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999861699999999999999999999983
Q gi|254780138|r  298 FSRFHSTATLANIFTGLIKAPFMACAIGIVAM  329 (373)
Q Consensus       298 ~~~~~~~~~~~d~~~~~~K~~~fg~~i~~i~c  329 (373)
                      +......++++.+..++.=+.+.|++-++...
T Consensus       602 l~~~~~~~~~~~i~~a~~~s~~iGvlfGlyPA  633 (648)
T PRK10535        602 LPGWEIGFSPLALLSAFLCSTVTGILFGWLPA  633 (648)
T ss_pred             CCCCCEECCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66771426889999999999999999999999


No 57 
>KOG0539 consensus
Probab=22.02  E-value=34  Score=12.92  Aligned_cols=40  Identities=23%  Similarity=0.322  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHCCC
Q ss_conf             99999999999999999999999------99999999999861139
Q gi|254780138|r  254 ILISPRIWALIISLPLLTILANF------SAIIGASIVIWKYYDIP  293 (373)
Q Consensus       254 ~Lv~PRv~A~~i~~p~L~~~~~~------~~i~gg~~~~~~~~~i~  293 (373)
                      .||.|-+.+.+++.|.-.++..+      .++++|.+.....+|++
T Consensus       137 RLVfPP~~~~il~~pfy~~~~~vl~~~~~~a~faG~l~GYV~YDmt  182 (240)
T KOG0539         137 RLVFPPTPFAILAAPFYLILSLVLPHPVAPAGFAGGLLGYVCYDMT  182 (240)
T ss_pred             EEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHH
T ss_conf             2736882189999999999998637503243431201321354454


No 58 
>pfam03095 PTPA Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognized phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1.
Probab=21.84  E-value=43  Score=12.25  Aligned_cols=109  Identities=8%  Similarity=0.076  Sum_probs=65.4

Q ss_pred             EEEECCCHHHHHHHHHH-----HHHHHHHCCC-C-CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC-CCC--CHHHHHH
Q ss_conf             99701051521299999-----9999975187-6-43158991269999988642220112456533-543--1136658
Q gi|254780138|r   41 IVDLSAITEIDTIGAEL-----IMYFMEKYHG-K-IKLQGVSTHIEQLFSLISFTHRKKIKNQKPQR-SFF--YNSFKNL  110 (373)
Q Consensus        41 ~iDls~i~~lDTAGA~l-----L~~l~~~~~~-~-~~~~~l~~~~~~Ll~Ll~~~~~~~~~~~~~~~-~~~--~~~~~~~  110 (373)
                      +.+.++++.|-.+-|..     +.++.+...+ + -.....++..++++++++...+-..+.||.+. +.+  -..++.|
T Consensus         5 I~~~~D~~~f~~S~ay~~i~~fI~~l~~sv~g~~~~~~~~~s~~i~~l~~il~~l~~~i~e~PP~~~~~~RFGN~afR~w   84 (298)
T pfam03095         5 ILSPSDLELFLRSQAYYDILAFIQKLSDSVQGKPISDTFPISPAVRKLLEILDKLDALIDETPPLDQNPSRFGNKAFRDW   84 (298)
T ss_pred             CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH
T ss_conf             37777898885379999999999999998538868988888989999999999999999858998898766687789999


Q ss_pred             HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99985999999999999--9999999999999997402678
Q gi|254780138|r  111 HYHIGKKIVKFINDSCS--QAHILGLVISNTGEFCASSYKF  149 (373)
Q Consensus       111 ~~~iG~~~~~~~~~~~~--~~~f~G~~~~~~~~~~~~~~~~  149 (373)
                      ..++-+.+..+.++...  .-..+-|....+.+.+.++.|.
T Consensus        85 ~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~~Ri  125 (298)
T pfam03095        85 HDKLEERAPSLLSELLPSSKDEAINELSYYLLNSFGNRTRI  125 (298)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999989999998658304658999999998675987005


No 59 
>COG2011 AbcD ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]
Probab=21.65  E-value=43  Score=12.23  Aligned_cols=105  Identities=20%  Similarity=0.213  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             83776999999999999999-------99999987542756689999999999998999999999996457899999999
Q gi|254780138|r  163 VGVSGVPVVILISFVTGAVI-------AQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIGSM  235 (373)
Q Consensus       163 ~G~~alpiv~l~~~~~G~v~-------a~q~~~~l~~fGa~~~v~~~~~~~~~RElgPlltaii~agR~gsa~aAeiG~M  235 (373)
                      .-.+|+|.+.++-.++-..-       .-..+..--..||--|...++-. -+||.-                       
T Consensus        66 Ni~Rs~PFiILlv~liP~Tr~ivGTsiG~~AAivPL~i~a~PF~ARlve~-aL~EVd-----------------------  121 (222)
T COG2011          66 NILRSIPFIILLVALIPLTRLIVGTSIGTTAAIVPLTIGAAPFVARLVES-ALREVD-----------------------  121 (222)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHCC-----------------------
T ss_conf             98751209999999998899997265253047741678888899999999-997447-----------------------


Q ss_pred             HHHHHHHHHHHHCCCHHHHHH-------HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             875001344442786899999-------999999-9999999999999999999999999861139
Q gi|254780138|r  236 KINEEIDAIRTMGLDFVRILI-------SPRIWA-LIISLPLLTILANFSAIIGASIVIWKYYDIP  293 (373)
Q Consensus       236 ~v~eeidAL~~~Gi~p~~~Lv-------~PRv~A-~~i~~p~L~~~~~~~~i~gg~~~~~~~~~i~  293 (373)
                        .+-|+|=+.||.+|.+-.-       .|-++. .++..-.|.-|+.+.|..||--..+...-..
T Consensus       122 --~GvIEAA~amGAs~~~II~kVlLpEa~p~li~g~Tvt~I~LIg~SAMAGaIGgGGLGdlAiryG  185 (222)
T COG2011         122 --KGVIEAAQAMGASPWQIIRKVLLPEALPGLVSGITVTLISLIGYSAMAGAIGGGGLGDLAIRYG  185 (222)
T ss_pred             --CCHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             --2589999984998888878732621367899889999999980888830226673369999987


No 60 
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=21.40  E-value=37  Score=12.65  Aligned_cols=13  Identities=15%  Similarity=0.105  Sum_probs=4.7

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             9912699999886
Q gi|254780138|r   74 VSTHIEQLFSLIS   86 (373)
Q Consensus        74 l~~~~~~Ll~Ll~   86 (373)
                      ++|++++|-.+.+
T Consensus       146 FRPeY~~L~~l~~  158 (607)
T TIGR01389       146 FRPEYRRLGELAE  158 (607)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             7565899999998


No 61 
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.65  E-value=45  Score=12.09  Aligned_cols=21  Identities=33%  Similarity=0.506  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999986
Q gi|254780138|r  269 LLTILANFSAIIGASIVIWKY  289 (373)
Q Consensus       269 ~L~~~~~~~~i~gg~~~~~~~  289 (373)
                      ++.+++-++|++||+.++.-.
T Consensus         8 l~ivl~ll~G~~~G~fiark~   28 (71)
T COG3763           8 LLIVLALLAGLIGGFFIARKQ   28 (71)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999


No 62 
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=20.52  E-value=45  Score=12.07  Aligned_cols=33  Identities=18%  Similarity=0.124  Sum_probs=14.5

Q ss_pred             CCCCCCCCCCHHHHH---HHHHHHHHHHHCCCCCCC
Q ss_conf             876431589912699---999886422201124565
Q gi|254780138|r   66 HGKIKLQGVSTHIEQ---LFSLISFTHRKKIKNQKP   98 (373)
Q Consensus        66 ~~~~~~~~l~~~~~~---Ll~Ll~~~~~~~~~~~~~   98 (373)
                      ..+....+.+|-.++   |-.+.+...+...|..+|
T Consensus        25 ~edvi~ldv~pi~Eqi~kLe~~vddl~~sldPstp~   60 (108)
T COG4062          25 FEDVIFLDVDPIEEQIKKLETLVDDLENSLDPSTPP   60 (108)
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             575489964179999999999999999635999998


Done!