Query         gi|254780373|ref|YP_003064786.1| flagellar basal body-associated protein FliL [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 172
No_of_seqs    118 out of 496
Neff          7.8 
Searched_HMMs 39220
Date          Sun May 29 16:49:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780373.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK08455 fliL flagellar basal  100.0 1.9E-40 4.2E-45  239.7  15.0  170    1-171     1-179 (180)
  2 PRK05696 fliL flagellar basal  100.0   1E-37 2.6E-42  224.8  14.6  155    2-171     2-167 (168)
  3 PRK12785 fliL flagellar basal  100.0 3.7E-38 9.4E-43  227.2  11.7  144    7-171    15-166 (167)
  4 PRK07021 fliL flagellar basal  100.0 9.8E-37 2.5E-41  219.5  15.1  143    9-171     5-158 (159)
  5 PRK07718 fliL flagellar basal  100.0 3.3E-31 8.4E-36  189.4  13.4   90   80-171    47-141 (142)
  6 COG1580 FliL Flagellar basal b 100.0 8.5E-30 2.2E-34  181.7  14.7   97   76-172    56-159 (159)
  7 pfam03748 FliL Flagellar basal 100.0 6.8E-30 1.7E-34  182.2  13.7   92   80-171    47-144 (145)
  8 PRK05697 flagellar basal body-  99.9 6.5E-24 1.6E-28  149.7  13.3   92   80-171    31-134 (135)
  9 PRK06654 fliL flagellar basal   99.5   1E-13 2.7E-18   94.1  11.4   88   80-171    79-174 (177)
 10 PRK08455 fliL flagellar basal   96.9 0.00056 1.4E-08   41.2   2.2   43    3-45      7-49  (180)
 11 PRK12785 fliL flagellar basal   95.4   0.004   1E-07   36.5   0.2   35    1-35      1-40  (167)
 12 PRK07021 fliL flagellar basal   94.6   0.039 9.9E-07   31.1   3.5   51    1-52      1-51  (159)
 13 PRK10920 putative uroporphyrin  94.4   0.074 1.9E-06   29.6   4.5   33    7-39     26-58  (389)
 14 TIGR02837 spore_II_R stage II   91.8    0.85 2.2E-05   23.8   6.7   57   96-152    40-96  (172)
 15 PRK05696 fliL flagellar basal   90.7    0.21 5.4E-06   27.1   2.8   42    3-44      6-47  (168)
 16 PRK10270 hypothetical protein;  88.7    0.72 1.8E-05   24.2   4.2   27   16-42      2-28  (340)
 17 pfam04375 HemX HemX. This fami  87.1     1.1 2.8E-05   23.2   4.3   17   10-26     24-40  (372)
 18 pfam12072 DUF3552 Domain of un  83.9     1.3 3.2E-05   22.9   3.4   25   18-42      1-25  (201)
 19 PRK09379 membrane-bound transc  82.9     1.3 3.3E-05   22.9   3.1   23   15-37      2-24  (303)
 20 PRK03598 hypothetical protein;  82.3     1.3 3.4E-05   22.8   3.0   18   17-34      3-20  (331)
 21 cd03400 Band_7_1 A subgroup of  79.3     4.7 0.00012   19.8   9.8   82   88-172    14-113 (124)
 22 COG5353 Uncharacterized protei  78.0     2.8 7.1E-05   21.0   3.4   42   15-56      4-45  (161)
 23 PRK06770 hypothetical protein;  74.3     4.9 0.00013   19.7   3.9   25   16-40      4-28  (185)
 24 TIGR01495 ETRAMP early transcr  74.2     3.7 9.5E-05   20.3   3.2   38    8-45     53-93  (99)
 25 pfam09716 ETRAMP Malarial earl  72.9     2.8 7.2E-05   21.0   2.4   34    8-41     44-77  (84)
 26 PRK01844 hypothetical protein;  71.6     6.4 0.00016   19.1   4.0   23   18-40      5-27  (72)
 27 pfam07423 DUF1510 Protein of u  70.4       4  0.0001   20.2   2.7   12   20-31     18-29  (214)
 28 PRK11636 mrcA peptidoglycan sy  66.2     5.1 0.00013   19.6   2.5   25   17-41      5-29  (850)
 29 COG2959 HemX Uncharacterized e  63.9     8.5 0.00022   18.4   3.3   27   12-38     28-54  (391)
 30 COG3167 PilO Tfp pilus assembl  62.9     6.6 0.00017   19.0   2.6   26   16-45     23-48  (211)
 31 pfam09551 Spore_II_R Stage II   62.7      12  0.0003   17.6   4.5   33   99-131     5-37  (132)
 32 pfam12245 DUF3607 Protein of u  62.3      12  0.0003   17.6   4.1   27   80-106    43-69  (721)
 33 PRK10927 essential cell divisi  61.6     4.5 0.00012   19.9   1.6   12   39-50     51-62  (319)
 34 TIGR00247 TIGR00247 conserved   61.5      11 0.00029   17.7   3.5   21   20-40     16-36  (373)
 35 PRK10559 p-hydroxybenzoic acid  61.0      13 0.00032   17.5   4.0   24   18-41      9-32  (310)
 36 COG5294 Uncharacterized protei  58.7     8.8 0.00022   18.3   2.6   19   88-106    72-90  (113)
 37 COG3197 FixS Uncharacterized p  53.6      14 0.00035   17.2   2.9   34   19-52      5-38  (58)
 38 PRK01294 lipase chaperone; Pro  51.0      19 0.00048   16.5   4.6   15   33-47     19-33  (339)
 39 PRK10361 DNA recombination pro  49.4      20 0.00051   16.4   4.4   31   18-48      3-33  (475)
 40 PRK13481 glycosyltransferase;   49.3      20 0.00051   16.4   4.6   17   10-26     34-50  (269)
 41 cd03401 Band_7_prohibitin Band  46.3      22 0.00057   16.1   5.9   53  116-170    94-149 (196)
 42 pfam06365 CD34_antigen CD34/Po  45.5      15 0.00039   17.0   2.1   22   16-37     99-122 (202)
 43 TIGR00847 ccoS cytochrome oxid  44.9      24  0.0006   16.0   4.3   33   21-53      5-39  (53)
 44 TIGR00998 8a0101 efflux pump m  43.1      25 0.00064   15.8   3.8   23  128-150   115-137 (379)
 45 PRK11556 multidrug efflux syst  42.1      26 0.00066   15.7   6.7   14   12-25      2-15  (415)
 46 PRK10930 FtsH protease regulat  40.8      27  0.0007   15.6   9.5   70   98-168   155-240 (419)
 47 pfam08229 SHR3_chaperone ER me  39.7      29 0.00073   15.5   3.0   14   81-94     98-111 (196)
 48 PRK09783 copper/silver efflux   38.8      28 0.00072   15.6   2.6   29  117-146   155-186 (407)
 49 PRK10833 putative assembly pro  38.6      30 0.00076   15.4   3.4   22   16-37      2-23  (617)
 50 smart00786 SHR3_chaperone ER m  38.2      30 0.00077   15.4   3.0   13   82-94     99-111 (196)
 51 PRK10381 ferric enterobactin t  38.1      30 0.00077   15.4   3.4   11  100-110   170-180 (379)
 52 pfam03264 Cytochrom_NNT NapC/N  37.8      31 0.00078   15.4   3.7   35  119-155    87-122 (174)
 53 COG3763 Uncharacterized protei  37.8      31 0.00078   15.4   4.0   21   18-38      5-25  (71)
 54 PRK00059 prsA peptidylprolyl i  36.6      21 0.00055   16.2   1.7   18   17-34      5-22  (336)
 55 PRK12705 hypothetical protein;  36.5      32 0.00082   15.2   2.7   26   17-42      8-33  (485)
 56 pfam10410 DnaB_bind DnaB-helic  36.2      11 0.00029   17.7   0.3   41  124-166     5-45  (59)
 57 PRK00720 tatA twin arginine tr  36.1      33 0.00083   15.2   3.7   12   19-30      9-20  (71)
 58 PRK09859 multidrug efflux syst  35.7      20 0.00052   16.3   1.5   20   14-33      2-21  (385)
 59 pfam03645 Tctex-1 Tctex-1 fami  34.4      35 0.00089   15.1   6.0   53  115-167     3-58  (101)
 60 TIGR02223 ftsN cell division p  32.4      38 0.00097   14.9   3.2   48   15-63     33-89  (354)
 61 pfam03896 TRAP_alpha Transloco  31.3      40   0.001   14.8   5.5   25   88-112    99-124 (281)
 62 COG3322 Predicted periplasmic   29.5      43  0.0011   14.6   3.8   30   16-45     10-39  (295)
 63 TIGR02898 spore_YhcN_YlaJ spor  28.2      34 0.00088   15.1   1.6   17   18-34      2-18  (185)
 64 TIGR03007 pepcterm_ChnLen poly  28.2      45  0.0011   14.5   3.3   40  121-160    80-120 (510)
 65 PRK06287 cobalt transport prot  28.2      45  0.0011   14.5   2.8   17   16-32      3-19  (105)
 66 PRK00523 hypothetical protein;  27.9      46  0.0012   14.4   3.5   21   18-38      5-26  (73)
 67 pfam09624 DUF2393 Protein of u  27.7      46  0.0012   14.4   3.6   29   79-110    46-75  (119)
 68 pfam08999 SP_C-Propep Surfacta  27.6      46  0.0012   14.4   2.8   20   16-35     34-53  (93)
 69 cd03403 Band_7_stomatin_like B  27.1      47  0.0012   14.3   8.7   71   98-170    57-141 (215)
 70 pfam06796 NapE Periplasmic nit  27.0      47  0.0012   14.3   4.2   23    1-23      1-24  (55)
 71 KOG0860 consensus               26.4      49  0.0012   14.3   2.5   21  117-137    42-63  (116)
 72 PRK11677 cytochrome d ubiquino  26.3      49  0.0012   14.3   3.3   22   22-43      5-26  (134)
 73 cd03404 Band_7_HflK Band_7_Hfl  26.3      49  0.0012   14.3   6.0   70   99-169    87-172 (266)
 74 PRK11901 hypothetical protein;  26.2      49  0.0012   14.3   2.7   18   18-35     39-56  (329)
 75 TIGR03319 YmdA_YtgF conserved   26.1      33 0.00083   15.2   1.2   22   20-41      1-22  (514)
 76 COG1566 EmrA Multidrug resista  25.6      50  0.0013   14.2   4.1   30   12-41      9-38  (352)
 77 TIGR01215 minE cell division t  25.6      50  0.0013   14.2   3.7   40  116-155    15-54  (89)
 78 pfam01145 Band_7 SPFH domain /  25.3      51  0.0013   14.2   6.7   53  116-170    91-146 (177)
 79 pfam09576 COX9 Cytochrome c ox  24.9      52  0.0013   14.1   2.6   36    9-44      4-39  (57)
 80 smart00019 SF_P Pulmonary surf  24.2      15 0.00039   17.0  -0.8   23   14-36     32-54  (191)
 81 COG4640 Predicted membrane pro  24.0      54  0.0014   14.0   2.4   28   14-41     48-75  (465)
 82 pfam03597 CcoS Cytochrome oxid  23.7      55  0.0014   14.0   3.0   28   24-51      9-36  (45)
 83 COG4093 Uncharacterized protei  23.5      49  0.0013   14.2   1.7   26   15-43     14-39  (338)
 84 pfam09680 Tiny_TM_bacill Prote  23.0      57  0.0014   13.9   2.2   17   20-36      8-24  (26)
 85 cd02106 Band_7 The band 7 doma  22.9      57  0.0015   13.9   6.2   54  115-170    52-108 (121)
 86 pfam06160 EzrA Septation ring   22.7      42  0.0011   14.6   1.2   18   20-37      2-19  (559)
 87 pfam06097 DUF945 Bacterial pro  22.4      58  0.0015   13.8   2.4   20   19-38      6-25  (460)
 88 pfam11772 EpuA DNA-directed RN  22.3      30 0.00076   15.4   0.4   23   25-47      6-28  (47)
 89 pfam00155 Aminotran_1_2 Aminot  22.2      59  0.0015   13.8   4.8   11  142-152   262-272 (351)
 90 PRK04778 septation ring format  21.9      60  0.0015   13.8   3.2   16   19-34      5-20  (569)
 91 PRK03002 prsA peptidylprolyl i  21.5      61  0.0016   13.7   2.4   19  115-133    82-100 (285)
 92 COG2268 Uncharacterized protei  21.2      62  0.0016   13.7   2.9   34  119-154   143-176 (548)
 93 pfam03672 UPF0154 Uncharacteri  20.9      63  0.0016   13.7   2.5   16   24-39      4-19  (64)
 94 PRK10905 hypothetical protein;  20.7      33 0.00084   15.2   0.4   18   19-36      2-19  (323)
 95 PRK01833 tatA twin arginine tr  20.6      64  0.0016   13.6   3.7   11   18-28      9-19  (75)
 96 PRK10856 hypothetical protein;  20.5      64  0.0016   13.6   4.0   19   16-34    112-130 (332)
 97 TIGR01411 tatAE twin arginine-  20.3      62  0.0016   13.7   1.7   13   18-30      7-19  (48)
 98 PRK04561 tatA twin arginine tr  20.1      65  0.0017   13.6   3.4   12   19-30      9-20  (75)

No 1  
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=100.00  E-value=1.9e-40  Score=239.69  Aligned_cols=170  Identities=15%  Similarity=0.221  Sum_probs=112.4

Q ss_pred             CCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCC--CCCCCCCCCC
Q ss_conf             9854355323-467632059999999999999999999999706787652012455653101122333--3334444333
Q gi|254780373|r    1 MSYDDTTSQY-IRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEKYQKFILNNFYDNSVR--SVHTGDTISL   77 (172)
Q Consensus         1 ma~~~~~~~~-~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~   77 (172)
                      |||+++.+++ +|+++++++||++++++|+++|||+++| +++++..+...++.+........+.+..  ..........
T Consensus         1 MAee~e~~e~~~kkk~k~lliIii~vvvlll~~gG~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (180)
T PRK08455          1 MAEEQENTETKPKKKSKALLIIIIGVVVLLLLIGGVIAF-LLMGSSEEEKENAEQPAEEVQANPPANSAQEAKQRSNDFL   79 (180)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHH-HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             986543555578887875887349999999999999998-7617898642222345421235677655444444443212


Q ss_pred             CCCEEECCCCEEEEECC-CCCEEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf             35302103320242058-983389999998504402----4542189999999998418988950889999999999999
Q gi|254780373|r   78 KKLQIFSLQPIITNFDS-SPKDWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEER  152 (172)
Q Consensus        78 ~~~~~~~l~~fvvNL~~-~~~r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~  152 (172)
                      ....+++++||||||.+ +++||||++++|++++++    .+.|+|.|||.|+.+||+++++||++++||++||++|+++
T Consensus        80 ~~~~~~~l~~f~vNl~~~~~~rylq~~i~l~~~~~~~~~~~~~~~p~ird~ii~~ls~~~~~~l~~~~Gk~~Lr~ei~~~  159 (180)
T PRK08455         80 NIGPMYPLDPFTVNLLSQSGRRYLKTSISLELSNELLKPELDKKDPVIRDTIIRILSSKTVEEVSTNKGKERLKDEIVGK  159 (180)
T ss_pred             CCCCCCCCCCEEEECCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
T ss_conf             44565456777997778998638999999998688889999986699999999999649998950977899999999999


Q ss_pred             HH-HHCCCCEEEEEEEEEEC
Q ss_conf             85-42356312576432201
Q gi|254780373|r  153 VK-LRSQGFVSSVIFRTFII  171 (172)
Q Consensus       153 in-~~~~g~V~~V~Ft~fVv  171 (172)
                      +| ++.+|+|++||||+|||
T Consensus       160 in~~l~~~~V~~V~Ft~fV~  179 (180)
T PRK08455        160 LNEFLIDGFIKNVFFTDFVV  179 (180)
T ss_pred             HHHHHCCCCEEEEEEEEEEE
T ss_conf             99873679557998424176


No 2  
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=100.00  E-value=1e-37  Score=224.85  Aligned_cols=155  Identities=10%  Similarity=0.144  Sum_probs=108.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             85435532346763205999999999999999999999970678765201245565310112233333344443333530
Q gi|254780373|r    2 SYDDTTSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEKYQKFILNNFYDNSVRSVHTGDTISLKKLQ   81 (172)
Q Consensus         2 a~~~~~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (172)
                      |+++...++.+++|+|++||++++++++++|+|+ +| ++++...+.+....+....             ....+..+..
T Consensus         2 a~e~~e~e~~~k~KkKLiiii~~~vlll~ggggg-~~-~~lg~~~~~~~~~~~~~~~-------------~~~~~~~~~~   66 (168)
T PRK05696          2 ASEELEKDEAPKSKKKLIIIIVVGVLLALGGGGA-AW-FFMGSSDPAEAAAAEAAAA-------------AAAAPVPPAL   66 (168)
T ss_pred             CCHHHHCCCCCCCCCEEEHHHHHHHHHHHHHHHH-HH-HHHCCCCCCCCCCCCCCCC-------------CCCCCCCCCC
T ss_conf             0023113467888633204799999999999999-99-9955887544444444556-------------6778877752


Q ss_pred             EECC-CCEEEEECCCCC-EEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             2103-320242058983-389999998504402----4542189999999998418988950889999999999999854
Q gi|254780373|r   82 IFSL-QPIITNFDSSPK-DWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKL  155 (172)
Q Consensus        82 ~~~l-~~fvvNL~~~~~-r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~  155 (172)
                      |+++ +||||||.++++ ||||++++|++++++    ++.|+|.|||+++.+||+++++||+|++||++||+++++++|.
T Consensus        67 y~~l~~~F~VNL~~~~~~ryLqv~i~L~~~d~~~~~~i~~~~P~IR~~ll~lls~~~~~~l~t~eGk~~Lr~e~~~~in~  146 (168)
T PRK05696         67 YVPMPRPFVFNVPGNGRDRLVQIKVQLMVRGSADEELAKKHIPLIENALLMTFSGADVDQLSTPAGKEELRQKALASVQE  146 (168)
T ss_pred             CCCCCCCEEEECCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCHHHHHHHHHHHHHHHHH
T ss_conf             13578663886168997469999999998887689999875588999999999628998960987899999999999999


Q ss_pred             -H----CCCCEEEEEEEEEEC
Q ss_conf             -2----356312576432201
Q gi|254780373|r  156 -R----SQGFVSSVIFRTFII  171 (172)
Q Consensus       156 -~----~~g~V~~V~Ft~fVv  171 (172)
                       +    +++.|++||||+|||
T Consensus       147 ~l~~~~g~~~V~~VlFT~FVv  167 (168)
T PRK05696        147 TLQKVTGKPVVEKVLFTGFVM  167 (168)
T ss_pred             HHHHCCCCCCEEEEEECCCEE
T ss_conf             976313887512785302364


No 3  
>PRK12785 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=100.00  E-value=3.7e-38  Score=227.22  Aligned_cols=144  Identities=16%  Similarity=0.256  Sum_probs=105.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53234676320599999999999999999999997067876520124556531011223333334444333353021033
Q gi|254780373|r    7 TSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEKYQKFILNNFYDNSVRSVHTGDTISLKKLQIFSLQ   86 (172)
Q Consensus         7 ~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   86 (172)
                      ..+++|++|+|++||++++++++++|+|++| + +.+...+.+...                   .......++.|++++
T Consensus        15 e~~~~kkkkkkliIii~~~vlll~gggg~~f-~-~~~~~~~~~~~~-------------------~~~~~~~~~~f~~l~   73 (167)
T PRK12785         15 EGAAPPKKKKKLIIIAAAAVLLLGGGGGGWF-F-FFRGHGADEHHA-------------------EAAPKVKPPVFVDVP   73 (167)
T ss_pred             CCCCCCCCCCEEEEEHHHHHHHHHHHHHHEE-E-EECCCCCCCCCC-------------------CCCCCCCCCEEEECC
T ss_conf             5677877773587619999999973114014-6-642688765555-------------------667778986376148


Q ss_pred             CEEEEECC-CC-C-EEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH-HHCC
Q ss_conf             20242058-98-3-389999998504402----454218999999999841898895088999999999999985-4235
Q gi|254780373|r   87 PIITNFDS-SP-K-DWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK-LRSQ  158 (172)
Q Consensus        87 ~fvvNL~~-~~-~-r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in-~~~~  158 (172)
                      +|+|||++ ++ + ||||++++|+++++.    ++.++|+|||.|+.+||+++++||++++|+++||++|++|+| .+++
T Consensus        74 ~fvVNL~~~~g~r~ryLk~~i~Lev~~~~~~~~~~~~~P~IrD~i~~~L~~~~~~dL~~~~Gk~~Lr~ell~rin~~l~~  153 (167)
T PRK12785         74 DMLVNLAGDPGERVQYLKVKVVLEVKDEKQVEQIKPLMPRVTDLFQTYLRELRSSDLNGSAGLFRLKEELTRRVNVALAP  153 (167)
T ss_pred             CEEEECCCCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             85998789999853599999999988887899998753679999999997189989709377999999999999854178


Q ss_pred             CCEEEEEEEEEEC
Q ss_conf             6312576432201
Q gi|254780373|r  159 GFVSSVIFRTFII  171 (172)
Q Consensus       159 g~V~~V~Ft~fVv  171 (172)
                      ++|++||||+|||
T Consensus       154 ~~V~~VlFtefVv  166 (167)
T PRK12785        154 AQVNAVLFKEVVI  166 (167)
T ss_pred             CCEEEEEEEEEEE
T ss_conf             8235998986387


No 4  
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=100.00  E-value=9.8e-37  Score=219.46  Aligned_cols=143  Identities=13%  Similarity=0.200  Sum_probs=106.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCE
Q ss_conf             23467632059999999999999999999999706787652012455653101122333333444433335302103320
Q gi|254780373|r    9 QYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEKYQKFILNNFYDNSVRSVHTGDTISLKKLQIFSLQPI   88 (172)
Q Consensus         9 ~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~f   88 (172)
                      +.++|+++|++||++++++++++|+|++|+|+ +....... ++..                  +..+..++.|++|+||
T Consensus         5 ~~~~~~kkkl~iii~~~~lll~~~g~g~~~~~-~~~~~~~~-~~~~------------------~~~~~~~pvf~~l~~f   64 (159)
T PRK07021          5 AASKKKKKSIWLILLILITLAAAAGAGYSYWL-SKQGAAHA-AAKA------------------EPAPPPAPVFFPLETF   64 (159)
T ss_pred             CCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHH-CCCCCCCC-CCCC------------------CCCCCCCCEEEECCCE
T ss_conf             77788876040589999999999999999995-47766666-6666------------------6778898757734751


Q ss_pred             EEEEC-CCC-CEEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH-HHCC---
Q ss_conf             24205-898-3389999998504402----454218999999999841898895088999999999999985-4235---
Q gi|254780373|r   89 ITNFD-SSP-KDWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK-LRSQ---  158 (172)
Q Consensus        89 vvNL~-~~~-~r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in-~~~~---  158 (172)
                      ||||. +++ +||||++++|++++++    ++.++|.|||+++.+||+++++||++++||++||++|++++| .+.+   
T Consensus        65 ~VNL~~~~~~~ryLqv~i~L~~~d~~~~~~l~~~~P~Ird~ll~lls~~~~~dL~t~eGk~~L~~ei~~~vn~~l~~~~~  144 (159)
T PRK07021         65 TVNLQPDDDADRVLYIGLTLRLKDEATRERLKEYLPEVRSRLLLLLSRKHAAELATEEGKQKLAAEIKETLEQPLVPGQP  144 (159)
T ss_pred             EEECCCCCCCCEEEEEEEEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             79713899864599999999976877898998607478999999985499889649889999999999999998745688


Q ss_pred             -CCEEEEEEEEEEC
Q ss_conf             -6312576432201
Q gi|254780373|r  159 -GFVSSVIFRTFII  171 (172)
Q Consensus       159 -g~V~~V~Ft~fVv  171 (172)
                       ..|++||||+|||
T Consensus       145 ~~~V~~VlFT~FVv  158 (159)
T PRK07021        145 KQVVTDVLFTAFIL  158 (159)
T ss_pred             CCCEEEEEEEEEEE
T ss_conf             88345892144064


No 5  
>PRK07718 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=99.97  E-value=3.3e-31  Score=189.37  Aligned_cols=90  Identities=19%  Similarity=0.339  Sum_probs=82.9

Q ss_pred             CEEECCCCEEEEECCCCCEEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH-
Q ss_conf             302103320242058983389999998504402----454218999999999841898895088999999999999985-
Q gi|254780373|r   80 LQIFSLQPIITNFDSSPKDWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK-  154 (172)
Q Consensus        80 ~~~~~l~~fvvNL~~~~~r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in-  154 (172)
                      ...+++|+|+|||.+  +||+|+++.++++++.    .+.+.|+|||.|+.+||+++++||++++|+++||++|++++| 
T Consensus        47 ~~~~~~~e~~tNL~~--~rylkv~i~le~~~~~~~~El~~r~pqIrD~Ii~~Ls~kt~~dl~~~~Gk~~Lk~ei~~~iN~  124 (142)
T PRK07718         47 ESSVEVPEITTNLKS--GNFIRISFKIETDSKKAKEELEKRDFQVKDIIISELAEMNAEDLEGKKGLEKLKEQLKEKINN  124 (142)
T ss_pred             CCCCCCCCEEEECCC--CCEEEEEEEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             554015851687599--967999999998898899776651425699999999749997945977899999999999986


Q ss_pred             HHCCCCEEEEEEEEEEC
Q ss_conf             42356312576432201
Q gi|254780373|r  155 LRSQGFVSSVIFRTFII  171 (172)
Q Consensus       155 ~~~~g~V~~V~Ft~fVv  171 (172)
                      .+.+|+|++||||+|||
T Consensus       125 ~l~~G~V~~VyfT~fVi  141 (142)
T PRK07718        125 LMQEGKVKKVYITSFIL  141 (142)
T ss_pred             HCCCCCEEEEEEEEEEE
T ss_conf             46789469999887661


No 6  
>COG1580 FliL Flagellar basal body-associated protein [Cell motility and secretion]
Probab=99.97  E-value=8.5e-30  Score=181.69  Aligned_cols=97  Identities=16%  Similarity=0.312  Sum_probs=87.1

Q ss_pred             CCCCCEEECCCCEEEEECC-CCCEEEEEEEEEEECCC----HHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHH
Q ss_conf             3335302103320242058-98338999999850440----245421899999999984189889508899999999999
Q gi|254780373|r   76 SLKKLQIFSLQPIITNFDS-SPKDWLRLDIALICKDI----PDKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIE  150 (172)
Q Consensus        76 ~~~~~~~~~l~~fvvNL~~-~~~r~lk~~i~l~~~~~----~~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~  150 (172)
                      .....+|+.+++|++||.+ ++.||+++.++++..+.    +.+.+.|+|||.++.+|++++.++|++++|+++||.+|+
T Consensus        56 ~~~~~~~~~~~~~t~Nl~~~~~~~~v~i~i~l~~~n~~~~~el~~~~p~vrd~li~lfsskt~~eL~t~~Gke~Lk~ei~  135 (159)
T COG1580          56 VEILAYYYLLEEFTTNLLDGPKDRYVKIAITLEVANKALLEELEEKKPEVRDALLMLFSSKTAAELSTPEGKEKLKAEIK  135 (159)
T ss_pred             CCCCCEEEECCCEEEECCCCCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHHHHHHHHHH
T ss_conf             87554465225504562668874799999988608888999999756899999999997178988368221899999999


Q ss_pred             HHHH-HHCCC-CEEEEEEEEEECC
Q ss_conf             9985-42356-3125764322019
Q gi|254780373|r  151 ERVK-LRSQG-FVSSVIFRTFIIA  172 (172)
Q Consensus       151 ~~in-~~~~g-~V~~V~Ft~fVv~  172 (172)
                      +++| .+..| .|.+||||+|||.
T Consensus       136 ~~in~~L~~g~~V~dV~fT~fiiq  159 (159)
T COG1580         136 DRINTILKEGQVVKDVLFTNFIIQ  159 (159)
T ss_pred             HHHHHHHHCCCEEEEEEEEHHHCC
T ss_conf             999899845872677855513119


No 7  
>pfam03748 FliL Flagellar basal body-associated protein FliL. This FliL protein controls the rotational direction of the flagella during chemotaxis. FliL is a cytoplasmic membrane protein associated with the basal body.
Probab=99.97  E-value=6.8e-30  Score=182.21  Aligned_cols=92  Identities=22%  Similarity=0.443  Sum_probs=85.3

Q ss_pred             CEEECCCCEEEEECCCCC-EEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             302103320242058983-389999998504402----454218999999999841898895088999999999999985
Q gi|254780373|r   80 LQIFSLQPIITNFDSSPK-DWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK  154 (172)
Q Consensus        80 ~~~~~l~~fvvNL~~~~~-r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in  154 (172)
                      ..|++++||||||.++++ ||+|++++++++++.    .+.++|.|||.++.+||+++++||++++|+++||++|++++|
T Consensus        47 ~~~~~l~~~~vNl~~~~~~r~l~~~i~l~~~~~~~~~~~~~~~p~Ird~ii~~l~~~~~~dl~~~~g~~~Lk~~l~~~in  126 (145)
T pfam03748        47 AAYVPLEPFVVNLADDGGTRYLKISIALEVRDPKAAEELEKHMPLIRDAILMLLSSKTAEDLSTPEGKEKLKEELLERIN  126 (145)
T ss_pred             CEEEECCCEEEECCCCCCCEEEEEEEEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCCHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             64886498899826899636999999999768878998886263337999999865882121493379999999999999


Q ss_pred             -HHCCCCEEEEEEEEEEC
Q ss_conf             -42356312576432201
Q gi|254780373|r  155 -LRSQGFVSSVIFRTFII  171 (172)
Q Consensus       155 -~~~~g~V~~V~Ft~fVv  171 (172)
                       .+.+++|++||||+|||
T Consensus       127 ~~l~~~~V~~V~ft~fVv  144 (145)
T pfam03748       127 EVLLEGEVEDVLFTSFVI  144 (145)
T ss_pred             HHHCCCCEEEEEEEEEEE
T ss_conf             873758546998885086


No 8  
>PRK05697 flagellar basal body-associated protein FliL-like protein; Validated
Probab=99.92  E-value=6.5e-24  Score=149.68  Aligned_cols=92  Identities=16%  Similarity=0.353  Sum_probs=80.4

Q ss_pred             CEEECC-CCEEEEECCCC-C-EEEEEEEEEEECCCH----HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf             302103-32024205898-3-389999998504402----4542189999999998418988950889999999999999
Q gi|254780373|r   80 LQIFSL-QPIITNFDSSP-K-DWLRLDIALICKDIP----DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEER  152 (172)
Q Consensus        80 ~~~~~l-~~fvvNL~~~~-~-r~lk~~i~l~~~~~~----~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~  152 (172)
                      ..|+.+ |+||||+.+++ + ||+|+++++++++++    ++.|+|.|||.|+.+|+++++++|+|++||+.||++++++
T Consensus        31 ~~Y~~l~P~fV~N~~~~g~rlrylqv~v~Lmv~d~~~~~~le~H~PlIR~~li~lls~qt~~~l~t~eGre~Lr~e~l~~  110 (135)
T PRK05697         31 YAYYGLEPDIVTNYISDGKKLGYVKIDVELMVKDPDDLAAVEHHDPLIRNALVELLGQQTEDKVKSLTGREEIRQECLKQ  110 (135)
T ss_pred             EEEEECCCCEEEECCCCCCCEEEEEEEEEEEECCHHHHHHHHHHCHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
T ss_conf             58996589979965789860469999999998787568999970768999999998549987965987899999999999


Q ss_pred             HH-HH----CCCCEEEEEEEEEEC
Q ss_conf             85-42----356312576432201
Q gi|254780373|r  153 VK-LR----SQGFVSSVIFRTFII  171 (172)
Q Consensus       153 in-~~----~~g~V~~V~Ft~fVv  171 (172)
                      +| ++    +++.|++||||+||+
T Consensus       111 vn~~l~~etG~~~Ve~VlFT~fV~  134 (135)
T PRK05697        111 VNELLEQETGKPLVVDLLFTKYLY  134 (135)
T ss_pred             HHHHHHHHHCCCCEEEEEEECCEE
T ss_conf             999998631866434675000344


No 9  
>PRK06654 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=99.54  E-value=1e-13  Score=94.12  Aligned_cols=88  Identities=18%  Similarity=0.208  Sum_probs=73.8

Q ss_pred             CEEECCCCEEEEECCC-CCEEEEEEEEEEECCCH------HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf             3021033202420589-83389999998504402------4542189999999998418988950889999999999999
Q gi|254780373|r   80 LQIFSLQPIITNFDSS-PKDWLRLDIALICKDIP------DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEER  152 (172)
Q Consensus        80 ~~~~~l~~fvvNL~~~-~~r~lk~~i~l~~~~~~------~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~  152 (172)
                      .+|-..++|-+|-+|. +.+|+ ++++|.+....      ...+.-++||.|..|+++++.++|..   .+++|.||+++
T Consensus        79 ~~Y~~~~e~r~nTaD~~~at~V-v~~aLGY~~n~k~l~~EL~~R~v~lkD~i~~yfs~kT~~ELrn---e~qiK~EIk~~  154 (177)
T PRK06654         79 IWYESIDEIRGNTADAPPKTFV-VKLALGYAENNVNILQELGRQKVRLKDIIREYFSQRTGQEIKN---ESQIKAEIKAR  154 (177)
T ss_pred             HHHHHCCHHCCCCCCCCCCEEE-EEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
T ss_conf             5543113310455667872189-9987424678877999997648589999999984510998751---89999999999


Q ss_pred             HH-HHCCCCEEEEEEEEEEC
Q ss_conf             85-42356312576432201
Q gi|254780373|r  153 VK-LRSQGFVSSVIFRTFII  171 (172)
Q Consensus       153 in-~~~~g~V~~V~Ft~fVv  171 (172)
                      +| ++..|+|.+|+||.|=|
T Consensus       155 IN~IL~~gkIkdI~FTq~di  174 (177)
T PRK06654        155 INSILRNGEIKEIALTQIDI  174 (177)
T ss_pred             HHHHHHCCCEEEEEEEEEEE
T ss_conf             99887428600698766543


No 10 
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=96.89  E-value=0.00056  Score=41.17  Aligned_cols=43  Identities=12%  Similarity=-0.081  Sum_probs=34.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             5435532346763205999999999999999999999970678
Q gi|254780373|r    3 YDDTTSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLF   45 (172)
Q Consensus         3 ~~~~~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~   45 (172)
                      +.++.++++++....++|.+++++++.+++++|++...-....
T Consensus         7 ~~e~~~kkk~k~lliIii~vvvlll~~gG~~~~~l~~~~~~~~   49 (180)
T PRK08455          7 NTETKPKKKSKALLIIIIGVVVLLLLIGGVIAFLLMGSSEEEK   49 (180)
T ss_pred             CCCCCCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             5555788878758873499999999999999987617898642


No 11 
>PRK12785 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=95.36  E-value=0.004  Score=36.48  Aligned_cols=35  Identities=9%  Similarity=-0.013  Sum_probs=21.0

Q ss_pred             CCCCCCC-----CCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9854355-----3234676320599999999999999999
Q gi|254780373|r    1 MSYDDTT-----SQYIRGNQHKLFVTWFVVYTFIGIFCGW   35 (172)
Q Consensus         1 ma~~~~~-----~~~~kG~~~kl~Iii~~vv~ll~~g~g~   35 (172)
                      ||++|+.     .++....++|...+++++++++.+.+|+
T Consensus         1 ma~~~~~~~~~e~ee~~~~kkkkkkliIii~~~vlll~gg   40 (167)
T PRK12785          1 MAKKEKKAEAAEGEEGAAPPKKKKKLIIIAAAAVLLLGGG   40 (167)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHH
T ss_conf             9987666765445456778777735876199999999731


No 12 
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=94.62  E-value=0.039  Score=31.12  Aligned_cols=51  Identities=10%  Similarity=-0.019  Sum_probs=38.6

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf             9854355323467632059999999999999999999999706787652012
Q gi|254780373|r    1 MSYDDTTSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEK   52 (172)
Q Consensus         1 ma~~~~~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~   52 (172)
                      ||++ ..++++|.+...+++++++++++.++|+.|+.+.--........++.
T Consensus         1 ma~~-~~~~~~kkkl~iii~~~~lll~~~g~g~~~~~~~~~~~~~~~~~~~~   51 (159)
T PRK07021          1 MADK-AASKKKKKSIWLILLILITLAAAAGAGYSYWLSKQGAAHAAAKAEPA   51 (159)
T ss_pred             CCCC-CCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             9988-77788876040589999999999999999995477666666666677


No 13 
>PRK10920 putative uroporphyrinogen III C-methyltransferase; Provisional
Probab=94.39  E-value=0.074  Score=29.62  Aligned_cols=33  Identities=12%  Similarity=0.079  Sum_probs=22.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             532346763205999999999999999999999
Q gi|254780373|r    7 TSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGI   39 (172)
Q Consensus         7 ~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~   39 (172)
                      .+++.++++..+++.++++++++++|+|++++.
T Consensus        26 ~~~~~~~~~~g~~l~~lai~l~la~g~g~y~~~   58 (389)
T PRK10920         26 ATEKKSKNRTALILSAVAIAIALAAGAGLYGWG   58 (389)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             988999887419999999999999999999999


No 14 
>TIGR02837 spore_II_R stage II sporulation protein R; InterPro: IPR014202    This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation , ..
Probab=91.84  E-value=0.85  Score=23.84  Aligned_cols=57  Identities=12%  Similarity=0.117  Sum_probs=44.3

Q ss_pred             CCEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf             833899999985044024542189999999998418988950889999999999999
Q gi|254780373|r   96 PKDWLRLDIALICKDIPDKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEER  152 (172)
Q Consensus        96 ~~r~lk~~i~l~~~~~~~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~  152 (172)
                      ...-+|+.+=.-.+.+++..++-.|||+++.+|+..=-+-=+-.+.+..||+.+.+-
T Consensus        40 ~~~lIR~hvlANSDS~~DQ~LKl~vRDaVl~~i~p~l~g~~s~~ea~~~i~~~l~eI   96 (172)
T TIGR02837        40 SEKLIRFHVLANSDSDEDQELKLKVRDAVLKEITPKLKGLKSLEEARRVIKENLPEI   96 (172)
T ss_pred             CCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCH
T ss_conf             577167776524898467777777678888767787517878889999998518127


No 15 
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=90.72  E-value=0.21  Score=27.10  Aligned_cols=42  Identities=7%  Similarity=-0.139  Sum_probs=35.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             543553234676320599999999999999999999997067
Q gi|254780373|r    3 YDDTTSQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFL   44 (172)
Q Consensus         3 ~~~~~~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~   44 (172)
                      .|.+..+++|.+...++++++++++..++|+.++.+......
T Consensus         6 ~e~e~~~k~KkKLiiii~~~vlll~ggggg~~~~lg~~~~~~   47 (168)
T PRK05696          6 LEKDEAPKSKKKLIIIIVVGVLLALGGGGAAWFFMGSSDPAE   47 (168)
T ss_pred             HHCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             113467888633204799999999999999999955887544


No 16 
>PRK10270 hypothetical protein; Provisional
Probab=88.68  E-value=0.72  Score=24.21  Aligned_cols=27  Identities=19%  Similarity=0.178  Sum_probs=15.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             205999999999999999999999970
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGWLGGIVML   42 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~~~~~~~~   42 (172)
                      +|.+++++++++++++++|++++.+..
T Consensus         2 kk~~~~~~~l~~~l~i~~g~~~~~~~~   28 (340)
T PRK10270          2 KKVLLIILLLLVVLGIAAGVGVWKVRH   28 (340)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             028999999999999999999987410


No 17 
>pfam04375 HemX HemX. This family consists of several bacterial HemX proteins. The hemX gene is not essential for haem synthesis in B. subtilis. HemX is a polytopic membrane protein which by an unknown mechanism down-regulates the level of HemA.
Probab=87.06  E-value=1.1  Score=23.19  Aligned_cols=17  Identities=18%  Similarity=0.057  Sum_probs=6.4

Q ss_pred             CCCCCCCHHHHHHHHHH
Q ss_conf             34676320599999999
Q gi|254780373|r   10 YIRGNQHKLFVTWFVVY   26 (172)
Q Consensus        10 ~~kG~~~kl~Iii~~vv   26 (172)
                      .++|+...+..+.+++.
T Consensus        24 ~~~g~~~~l~~~allla   40 (372)
T pfam04375        24 AKSGGATGLAALALLVA   40 (372)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             55775279999999999


No 18 
>pfam12072 DUF3552 Domain of unknown function (DUF3552). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with pfam00013, pfam01966. This domain has a single completely conserved residue A that may be functionally important.
Probab=83.85  E-value=1.3  Score=22.89  Aligned_cols=25  Identities=12%  Similarity=0.284  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5999999999999999999999970
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGWLGGIVML   42 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~~~~~~~~   42 (172)
                      ++|++.++.+++|++.||++..+..
T Consensus         1 ~~Ii~~i~~~~iG~~~G~~~~~~~~   25 (201)
T pfam12072         1 LIIILAIIALVVGFAIGYFVRKSIA   25 (201)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9239999999999999999999999


No 19 
>PRK09379 membrane-bound transcriptional regulator LytR; Provisional
Probab=82.94  E-value=1.3  Score=22.87  Aligned_cols=23  Identities=13%  Similarity=0.081  Sum_probs=8.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             32059999999999999999999
Q gi|254780373|r   15 QHKLFVTWFVVYTFIGIFCGWLG   37 (172)
Q Consensus        15 ~~kl~Iii~~vv~ll~~g~g~~~   37 (172)
                      |+|++++++.+++++.+++|+++
T Consensus         2 KKkil~~i~~v~~vlll~~g~~~   24 (303)
T PRK09379          2 KKKILFWILGIIGVLIIGGGIYA   24 (303)
T ss_pred             CCEEEHHHHHHHHHHHHHHHHHH
T ss_conf             82660369999999999999999


No 20 
>PRK03598 hypothetical protein; Provisional
Probab=82.31  E-value=1.3  Score=22.77  Aligned_cols=18  Identities=22%  Similarity=0.287  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             059999999999999999
Q gi|254780373|r   17 KLFVTWFVVYTFIGIFCG   34 (172)
Q Consensus        17 kl~Iii~~vv~ll~~g~g   34 (172)
                      |-++++++++++++++++
T Consensus         3 k~~~~~~~~~~~~~~~~~   20 (331)
T PRK03598          3 KPVVIGLAVVALVAVGAG   20 (331)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             338999999999999999


No 21 
>cd03400 Band_7_1 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes.  Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic H
Probab=79.27  E-value=4.7  Score=19.80  Aligned_cols=82  Identities=13%  Similarity=0.153  Sum_probs=56.5

Q ss_pred             EEEEECCCCCEEEEEEEEEEECCCHH---------------HHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHH
Q ss_conf             02420589833899999985044024---------------542189999999998418988950889999999999999
Q gi|254780373|r   88 IITNFDSSPKDWLRLDIALICKDIPD---------------KVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEER  152 (172)
Q Consensus        88 fvvNL~~~~~r~lk~~i~l~~~~~~~---------------e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~  152 (172)
                      +.|.-.++  --+.+++++.++-...               .-..|.+|+.+-...+..++++|=+ ..|..+..+|.+.
T Consensus        14 ~~vlskdg--l~v~~dvtV~Y~v~~~~~~~l~~~~G~~y~~~iI~p~vrs~~R~v~~~y~a~elys-~kR~~i~~~I~~~   90 (124)
T cd03400          14 IDVLSKEG--LSINADVSVQYRINPNKAAAVHSKLGTDYARKIVRPTFRSLVREVTGRYTAEQIYS-TKRKEIESAIKKE   90 (124)
T ss_pred             EEEECCCC--CEEEEEEEEEEEECHHHHHHHHHHHCCCHHHEEECHHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHH
T ss_conf             88787899--78999999999998888999999849777773521789999999973378999988-5799999999999


Q ss_pred             HHHHC-C-C-CEEEEEEEEEECC
Q ss_conf             85423-5-6-3125764322019
Q gi|254780373|r  153 VKLRS-Q-G-FVSSVIFRTFIIA  172 (172)
Q Consensus       153 in~~~-~-g-~V~~V~Ft~fVv~  172 (172)
                      ++... + | .|++|+++++..+
T Consensus        91 l~~~l~~~gi~ve~VlIr~I~lP  113 (124)
T cd03400          91 LIEEFVGDGLILEEVLLRNIKLP  113 (124)
T ss_pred             HHHHHHHCCEEEEEEEEEEEECC
T ss_conf             99988638959999999975289


No 22 
>COG5353 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.00  E-value=2.8  Score=21.03  Aligned_cols=42  Identities=12%  Similarity=-0.006  Sum_probs=19.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf             320599999999999999999999997067876520124556
Q gi|254780373|r   15 QHKLFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEKYQKF   56 (172)
Q Consensus        15 ~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~~~~~   56 (172)
                      +...+|+|++++.++..+.+++++..-+.+.....+++....
T Consensus         4 k~~~~i~ii~viflai~~s~~~~~~~s~~P~~~~~~qA~~~a   45 (161)
T COG5353           4 KHLIIIIIILVIFLAIILSIALFFWKSMKPYHEAEEQAIDLA   45 (161)
T ss_pred             EEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             476622468899999999999987575184421688999987


No 23 
>PRK06770 hypothetical protein; Provisional
Probab=74.35  E-value=4.9  Score=19.69  Aligned_cols=25  Identities=8%  Similarity=-0.105  Sum_probs=12.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2059999999999999999999999
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGWLGGIV   40 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~~~~~~   40 (172)
                      ...++.+++.++++++|.++...++
T Consensus         4 ~~kwi~ii~~~~Vl~ig~tygml~y   28 (185)
T PRK06770          4 LFKWIGIIAGMAVLGIGVTYGMLYY   28 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999888777887


No 24 
>TIGR01495 ETRAMP early transcribed membrane protein (ETRAMP) family; InterPro: IPR006389   These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii . A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane . Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes..
Probab=74.17  E-value=3.7  Score=20.34  Aligned_cols=38  Identities=8%  Similarity=-0.133  Sum_probs=18.1

Q ss_pred             CCCCC--CCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             32346--763205999-999999999999999999970678
Q gi|254780373|r    8 SQYIR--GNQHKLFVT-WFVVYTFIGIFCGWLGGIVMLFLF   45 (172)
Q Consensus         8 ~~~~k--G~~~kl~Ii-i~~vv~ll~~g~g~~~~~~~~~~~   45 (172)
                      .+.+|  -+++.+++= .++..+.+.+|.|.++|+++-...
T Consensus        53 ~~~~KkNr~~k~ilySl~~as~lAlL~g~~~GlG~y~~~K~   93 (99)
T TIGR01495        53 AEKKKKNRNKKIILYSLSIASGLALLVGAGVGLGYYYKKKN   93 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99987777522799989999999999999999999875236


No 25 
>pfam09716 ETRAMP Malarial early transcribed membrane protein (ETRAMP). These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii. A homologue from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane. Members have an initial hydrophobic, Phe/Tyr-rich, stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes.
Probab=72.89  E-value=2.8  Score=21.01  Aligned_cols=34  Identities=12%  Similarity=-0.048  Sum_probs=17.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3234676320599999999999999999999997
Q gi|254780373|r    8 SQYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus         8 ~~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      -+.++.++++++|..+...+.+++|.+++++++.
T Consensus        44 ~~kKkk~kK~~iiSsias~lalli~~~~G~g~y~   77 (84)
T pfam09716        44 LEKKKKNKKKIIISSIASGLALLIGTALGLGYYK   77 (84)
T ss_pred             HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998863412008999999999999888876541


No 26 
>PRK01844 hypothetical protein; Provisional
Probab=71.59  E-value=6.4  Score=19.06  Aligned_cols=23  Identities=22%  Similarity=0.080  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             59999999999999999999999
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGWLGGIV   40 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~~~~~~   40 (172)
                      ++|+++++.+++|+.+|+|..-.
T Consensus         5 ~~Ili~i~~li~G~~~GffiaRk   27 (72)
T PRK01844          5 LGILVGVVALVAGVALGFFIARK   27 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999


No 27 
>pfam07423 DUF1510 Protein of unknown function (DUF1510). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=70.38  E-value=4  Score=20.19  Aligned_cols=12  Identities=25%  Similarity=0.213  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780373|r   20 VTWFVVYTFIGI   31 (172)
Q Consensus        20 Iii~~vv~ll~~   31 (172)
                      |+|.+|++|+++
T Consensus        18 iaI~iV~llIii   29 (214)
T pfam07423        18 IAIGIVVVLIII   29 (214)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 28 
>PRK11636 mrcA peptidoglycan synthetase; Provisional
Probab=66.24  E-value=5.1  Score=19.61  Aligned_cols=25  Identities=16%  Similarity=0.029  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0599999999999999999999997
Q gi|254780373|r   17 KLFVTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus        17 kl~Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      |.+++++++++++++++++++++++
T Consensus         5 k~~~~~~~~~~~~~~~~~~~~~~~~   29 (850)
T PRK11636          5 KYFLILAVCCILLGAGSIYGLYRYI   29 (850)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999987


No 29 
>COG2959 HemX Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=63.95  E-value=8.5  Score=18.39  Aligned_cols=27  Identities=11%  Similarity=-0.020  Sum_probs=10.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             676320599999999999999999999
Q gi|254780373|r   12 RGNQHKLFVTWFVVYTFIGIFCGWLGG   38 (172)
Q Consensus        12 kG~~~kl~Iii~~vv~ll~~g~g~~~~   38 (172)
                      |++...++..+.++++|..++|||+++
T Consensus        28 k~g~g~~l~~~all~aLgLGagg~~f~   54 (391)
T COG2959          28 KNGAGLLLSLAALLLALGLGAGGYYFG   54 (391)
T ss_pred             CCCCHHHHHHHHHHHHHHHCHHHHHHH
T ss_conf             788426889999999998440578888


No 30 
>COG3167 PilO Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=62.85  E-value=6.6  Score=18.97  Aligned_cols=26  Identities=12%  Similarity=0.097  Sum_probs=13.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             205999999999999999999999970678
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGWLGGIVMLFLF   45 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~   45 (172)
                      .++++++++++++++.|    |++++++..
T Consensus        23 ~rlv~~lL~~~~V~~lG----y~f~~s~k~   48 (211)
T COG3167          23 PRLVFCLLAVAAVLGLG----YAFYLSGKL   48 (211)
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHCCHH
T ss_conf             79999999999999999----999854078


No 31 
>pfam09551 Spore_II_R Stage II sporulation protein R (spore_II_R). SpoIIR is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation.
Probab=62.69  E-value=12  Score=17.64  Aligned_cols=33  Identities=9%  Similarity=0.297  Sum_probs=26.3

Q ss_pred             EEEEEEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             899999985044024542189999999998418
Q gi|254780373|r   99 WLRLDIALICKDIPDKVFLETLHQDIMAYIRTV  131 (172)
Q Consensus        99 ~lk~~i~l~~~~~~~e~~~p~Ird~il~~L~~~  131 (172)
                      -+|+-+-.-.+.+++..++-.+||.++.+|+..
T Consensus         5 ~iRfHVlANSDs~~DQ~lKl~VRD~Vl~~~~~~   37 (132)
T pfam09551         5 LIRFHVLANSDSPEDQALKLKVRDEVLEYLTPK   37 (132)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             189999827999899999999899999999998


No 32 
>pfam12245 DUF3607 Protein of unknown function (DUF3607). This family of proteins is found in bacteria. Proteins in this family are typically between 202 and 818 amino acids in length. There are two conserved sequence motifs: AGN and GMT.
Probab=62.27  E-value=12  Score=17.60  Aligned_cols=27  Identities=15%  Similarity=0.115  Sum_probs=21.1

Q ss_pred             CEEECCCCEEEEECCCCCEEEEEEEEE
Q ss_conf             302103320242058983389999998
Q gi|254780373|r   80 LQIFSLQPIITNFDSSPKDWLRLDIAL  106 (172)
Q Consensus        80 ~~~~~l~~fvvNL~~~~~r~lk~~i~l  106 (172)
                      .++-+-..+++||..+=+||+|+.+.-
T Consensus        43 ~yiNP~~~it~~LssGLDRk~kvsV~r   69 (721)
T pfam12245        43 NYINPVGSITVALSSGLDRKVKLSVLR   69 (721)
T ss_pred             CEECCCCCEEEEEECCCCCEEEEEEEE
T ss_conf             300788747999841655307999995


No 33 
>PRK10927 essential cell division protein; Provisional
Probab=61.61  E-value=4.5  Score=19.88  Aligned_cols=12  Identities=0%  Similarity=0.099  Sum_probs=4.7

Q ss_pred             HHHHCCCCCCCC
Q ss_conf             997067876520
Q gi|254780373|r   39 IVMLFLFAGQKE   50 (172)
Q Consensus        39 ~~~~~~~~~~~~   50 (172)
                      +||+....++..
T Consensus        51 LyFith~K~e~~   62 (319)
T PRK10927         51 LYFITHHKKEES   62 (319)
T ss_pred             EEEEECCCCCCC
T ss_conf             478870587667


No 34 
>TIGR00247 TIGR00247 conserved hypothetical protein TIGR00247; InterPro: IPR003770    This family contains several aminodeoxychorismate lyase proteins. Aminodeoxychorismate lyase is a pyridoxal 5'-phosphate-dependent enzyme that converts 4-aminodeoxychorismate to pyruvate and p-aminobenzoate, a precursor of folic acid in bacteria .  .
Probab=61.48  E-value=11  Score=17.74  Aligned_cols=21  Identities=10%  Similarity=0.080  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999
Q gi|254780373|r   20 VTWFVVYTFIGIFCGWLGGIV   40 (172)
Q Consensus        20 Iii~~vv~ll~~g~g~~~~~~   40 (172)
                      |+|..+++|+++.||++.+.+
T Consensus        16 i~i~~~~vll~~~gs~~~y~~   36 (373)
T TIGR00247        16 IIILLLLVLLLIIGSILLYKI   36 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999988998877


No 35 
>PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional
Probab=60.96  E-value=13  Score=17.46  Aligned_cols=24  Identities=8%  Similarity=-0.007  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             599999999999999999999997
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      +.+.+.++++++++.+++++|++.
T Consensus         9 ~r~~i~i~~v~~~~~~~~~~w~~~   32 (310)
T PRK10559          9 SRTAITVVLVILAFIAIFNAWVYY   32 (310)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999862


No 36 
>COG5294 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.67  E-value=8.8  Score=18.32  Aligned_cols=19  Identities=11%  Similarity=0.167  Sum_probs=11.3

Q ss_pred             EEEEECCCCCEEEEEEEEE
Q ss_conf             0242058983389999998
Q gi|254780373|r   88 IITNFDSSPKDWLRLDIAL  106 (172)
Q Consensus        88 fvvNL~~~~~r~lk~~i~l  106 (172)
                      |+.+-..+.++||+++..=
T Consensus        72 f~a~~~lr~~aYLKlt~kg   90 (113)
T COG5294          72 FTATHNLRKEAYLKLTHKG   90 (113)
T ss_pred             EEECCCCCCCCEEEEEECC
T ss_conf             9714767876379999547


No 37 
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=53.61  E-value=14  Score=17.22  Aligned_cols=34  Identities=9%  Similarity=-0.124  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf             9999999999999999999999706787652012
Q gi|254780373|r   19 FVTWFVVYTFIGIFCGWLGGIVMLFLFAGQKEEK   52 (172)
Q Consensus        19 ~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~~~~~   52 (172)
                      .+.+-+.+++.++|.++|+|.+-.++.++...++
T Consensus         5 ~~Lipvsi~l~~v~l~~flWavksgQyDDl~g~a   38 (58)
T COG3197           5 YILIPVSILLGAVGLGAFLWAVKSGQYDDLDGPA   38 (58)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCH
T ss_conf             2179999999999999999851357755654638


No 38 
>PRK01294 lipase chaperone; Provisional
Probab=51.00  E-value=19  Score=16.53  Aligned_cols=15  Identities=0%  Similarity=-0.494  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHCCCCC
Q ss_conf             999999997067876
Q gi|254780373|r   33 CGWLGGIVMLFLFAG   47 (172)
Q Consensus        33 ~g~~~~~~~~~~~~~   47 (172)
                      +++.++++..+....
T Consensus        19 ~~~~~~~~~~~~~~~   33 (339)
T PRK01294         19 LAVWYWLGLPPSSDT   33 (339)
T ss_pred             HHHHHHHCCCCCCCC
T ss_conf             999998065667887


No 39 
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=49.43  E-value=20  Score=16.39  Aligned_cols=31  Identities=16%  Similarity=0.309  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             5999999999999999999999970678765
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGWLGGIVMLFLFAGQ   48 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~~~~~~~~~~~~~~   48 (172)
                      +-|++.++++|+|+..||++...-.+.....
T Consensus         3 ~~~~i~~i~al~G~~igwl~~~~~~~~~~a~   33 (475)
T PRK10361          3 FSIMVYAVIALVGVAIGWLFASYQHAQQKAE   33 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             7799999999999999999999873451446


No 40 
>PRK13481 glycosyltransferase; Provisional
Probab=49.30  E-value=20  Score=16.37  Aligned_cols=17  Identities=0%  Similarity=0.172  Sum_probs=6.4

Q ss_pred             CCCCCCCHHHHHHHHHH
Q ss_conf             34676320599999999
Q gi|254780373|r   10 YIRGNQHKLFVTWFVVY   26 (172)
Q Consensus        10 ~~kG~~~kl~Iii~~vv   26 (172)
                      ++|.+.+++++.+++.+
T Consensus        34 ~k~k~~~~~~~~~~l~~   50 (269)
T PRK13481         34 PKKKKSKRILLKILLTI   50 (269)
T ss_pred             CCCHHHHHHHHHHHHHH
T ss_conf             64225688899999999


No 41 
>cd03401 Band_7_prohibitin Band_7_prohibitin. A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup group includes proteins similar to prohibitin (a lipid raft-associated integral membrane protein).  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains in addition to being stable scaffolds may also be also dynamic units with their own regulatory functions.  Prohibitin is a mitochondrial inner-membrane protein which may act as a chaperone for the stabilization of mitochondrial proteins.  Human prohibitin forms a heter-oligomeric complex with Bap-37 (prohibitin 2, a band 7 domain carrying homologue). This complex may protect non-assembled membrane proteins against proteolysis by the m-AAA protease. Prohibitin and Bap-37 yeast homologues have been implicated in yeast longevity and, in the maintenance of mitochondrial morphology.
Probab=46.34  E-value=22  Score=16.11  Aligned_cols=53  Identities=9%  Similarity=0.118  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHCC---CCEEEEEEEEEE
Q ss_conf             2189999999998418988950889999999999999854235---631257643220
Q gi|254780373|r  116 FLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRSQ---GFVSSVIFRTFI  170 (172)
Q Consensus       116 ~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~~---g~V~~V~Ft~fV  170 (172)
                      ..|.+++.+=..++..+.+++-+  -|..|..+|.++++....   =.|.+|.+++.-
T Consensus        94 l~~~~~~~lR~v~g~~~~~ei~s--~R~~i~~~i~~~l~~~~~~~GI~v~~V~i~~i~  149 (196)
T cd03401          94 LPSIINEVLKAVVAQFTAEELIT--QREEVSALIREALTERAKDFGIILDDVSITHLT  149 (196)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHCCEEEEEEEEEECC
T ss_conf             99999998898845755999986--599999999999998887289499999998548


No 42 
>pfam06365 CD34_antigen CD34/Podocalyxin family. This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion.
Probab=45.51  E-value=15  Score=17.02  Aligned_cols=22  Identities=0%  Similarity=-0.377  Sum_probs=8.8

Q ss_pred             CHHHHHHHHHH--HHHHHHHHHHH
Q ss_conf             20599999999--99999999999
Q gi|254780373|r   16 HKLFVTWFVVY--TFIGIFCGWLG   37 (172)
Q Consensus        16 ~kl~Iii~~vv--~ll~~g~g~~~   37 (172)
                      .+++|.++...  +||++.+++.|
T Consensus        99 ~~llIaLV~~gs~llLi~~~~~~Y  122 (202)
T pfam06365        99 YPTLIALVTSGGFLLLIAAIYTGY  122 (202)
T ss_pred             CCEEEEHHHHHHHHHHHHHHHHHH
T ss_conf             454765287647999999998778


No 43 
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type; InterPro: IPR004714   Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation .  Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase. .
Probab=44.89  E-value=24  Score=15.99  Aligned_cols=33  Identities=6%  Similarity=-0.175  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHCCCCCCCCHHH
Q ss_conf             99999999999999--9999997067876520124
Q gi|254780373|r   21 TWFVVYTFIGIFCG--WLGGIVMLFLFAGQKEEKY   53 (172)
Q Consensus        21 ii~~vv~ll~~g~g--~~~~~~~~~~~~~~~~~~~   53 (172)
                      ++++++.++.++.|  +|.+-.-.++.++.+-++.
T Consensus         5 ~~L~Pisl~lG~~GL~AFlWslksGQyDD~~G~a~   39 (53)
T TIGR00847         5 TILIPISLLLGGVGLVAFLWSLKSGQYDDLEGAAE   39 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH
T ss_conf             77889999999999999998531147888642067


No 44 
>TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694    emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=43.06  E-value=25  Score=15.82  Aligned_cols=23  Identities=9%  Similarity=0.094  Sum_probs=10.9

Q ss_pred             HHCCCHHHHCCHHHHHHHHHHHH
Q ss_conf             84189889508899999999999
Q gi|254780373|r  128 IRTVSIKQITGAQGFRYFKEDIE  150 (172)
Q Consensus       128 L~~~~~~dl~~~~Gk~~Lk~el~  150 (172)
                      ||.+...==+.....+++|+.++
T Consensus       115 LsakkL~v~s~~~~~~qar~~l~  137 (379)
T TIGR00998       115 LSAKKLKVESLKIKLEQAREKLK  137 (379)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             24567889999999999999987


No 45 
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=42.14  E-value=26  Score=15.74  Aligned_cols=14  Identities=29%  Similarity=0.363  Sum_probs=5.8

Q ss_pred             CCCCCHHHHHHHHH
Q ss_conf             67632059999999
Q gi|254780373|r   12 RGNQHKLFVTWFVV   25 (172)
Q Consensus        12 kG~~~kl~Iii~~v   25 (172)
                      |++.+.-|++++++
T Consensus         2 ~~~~~~~~~~~~~~   15 (415)
T PRK11556          2 KGSYKFRWVIVIVV   15 (415)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             84115589999999


No 46 
>PRK10930 FtsH protease regulator HflK; Provisional
Probab=40.85  E-value=27  Score=15.63  Aligned_cols=70  Identities=11%  Similarity=0.195  Sum_probs=46.3

Q ss_pred             EEEEEEEEEEECCCH-----------HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH-HH----CCCCE
Q ss_conf             389999998504402-----------454218999999999841898895088999999999999985-42----35631
Q gi|254780373|r   98 DWLRLDIALICKDIP-----------DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK-LR----SQGFV  161 (172)
Q Consensus        98 r~lk~~i~l~~~~~~-----------~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in-~~----~~g~V  161 (172)
                      ..+.+++.+.++-..           .........+++=.+..+.+.+++-| +||..++.+.++++. ++    ..=.|
T Consensus       155 NIVdV~~~VQYrI~dp~~yLFnv~dPe~tlr~aaESAmReVVG~~~~d~vLT-~gR~~Ia~~v~~~lQ~~Ld~Y~~GI~I  233 (419)
T PRK10930        155 NVVRVEMNVQYRVTDPEKYLFSVTSPDDSLRQATDSALRGVIGKYTMDRILT-EGRTVIRSDTQRELEETIRPYDMGITL  233 (419)
T ss_pred             CEEEEEEEEEEEECCHHHHEEECCCHHHHHHHHHHHHHHHHHCCCCHHHHHC-CCHHHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             7698778999995685781364578768999999999999976364899964-888999999999999999850899789


Q ss_pred             EEEEEEE
Q ss_conf             2576432
Q gi|254780373|r  162 SSVIFRT  168 (172)
Q Consensus       162 ~~V~Ft~  168 (172)
                      .+|-|.+
T Consensus       234 ~~V~lq~  240 (419)
T PRK10930        234 LDVNFQA  240 (419)
T ss_pred             EEEEECC
T ss_conf             9988467


No 47 
>pfam08229 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localized chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER.
Probab=39.72  E-value=29  Score=15.53  Aligned_cols=14  Identities=14%  Similarity=0.192  Sum_probs=6.6

Q ss_pred             EEECCCCEEEEECC
Q ss_conf             02103320242058
Q gi|254780373|r   81 QIFSLQPIITNFDS   94 (172)
Q Consensus        81 ~~~~l~~fvvNL~~   94 (172)
                      ++..+--+++|+..
T Consensus        98 y~~~i~vYltNi~~  111 (196)
T pfam08229        98 YVVGVIVYLTNIVT  111 (196)
T ss_pred             HHHHHEEEEEECCC
T ss_conf             98867035563024


No 48 
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=38.77  E-value=28  Score=15.57  Aligned_cols=29  Identities=3%  Similarity=0.002  Sum_probs=11.5

Q ss_pred             HHHH---HHHHHHHHHCCCHHHHCCHHHHHHHH
Q ss_conf             1899---99999998418988950889999999
Q gi|254780373|r  117 LETL---HQDIMAYIRTVSIKQITGAQGFRYFK  146 (172)
Q Consensus       117 ~p~I---rd~il~~L~~~~~~dl~~~~Gk~~Lk  146 (172)
                      -|.+   +..+|..........+ ...-+++||
T Consensus       155 SPel~~AQ~EyL~~~~~~~~~~~-~~aa~~rL~  186 (407)
T PRK09783        155 IPDWVEAQSEYLLLRETGGTATQ-TEGILERLR  186 (407)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHH-HHHHHHHHH
T ss_conf             88899999999999872797268-899999999


No 49 
>PRK10833 putative assembly protein; Provisional
Probab=38.62  E-value=30  Score=15.43  Aligned_cols=22  Identities=9%  Similarity=0.081  Sum_probs=9.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2059999999999999999999
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGWLG   37 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~~~   37 (172)
                      |+++++++++++++.+|..++.
T Consensus         2 Krll~~l~illvvvv~gl~aLv   23 (617)
T PRK10833          2 RRFLTTLMILLVVLVAGLSALV   23 (617)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4189999999999999999881


No 50 
>smart00786 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) PUBMED:15623581. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=38.18  E-value=30  Score=15.39  Aligned_cols=13  Identities=15%  Similarity=0.250  Sum_probs=5.7

Q ss_pred             EECCCCEEEEECC
Q ss_conf             2103320242058
Q gi|254780373|r   82 IFSLQPIITNFDS   94 (172)
Q Consensus        82 ~~~l~~fvvNL~~   94 (172)
                      +..+--+++|+..
T Consensus        99 ~~~i~vYltNi~~  111 (196)
T smart00786       99 VLGVCVYLTNIVK  111 (196)
T ss_pred             HHHHHEEEEECCC
T ss_conf             9867035563024


No 51 
>PRK10381 ferric enterobactin transport protein FepE; Provisional
Probab=38.05  E-value=30  Score=15.38  Aligned_cols=11  Identities=0%  Similarity=0.093  Sum_probs=4.2

Q ss_pred             EEEEEEEEECC
Q ss_conf             99999985044
Q gi|254780373|r  100 LRLDIALICKD  110 (172)
Q Consensus       100 lk~~i~l~~~~  110 (172)
                      ...++......
T Consensus       170 ~~~~ls~~a~t  180 (379)
T PRK10381        170 TSWTLSFTAPT  180 (379)
T ss_pred             CCEEEEEECCC
T ss_conf             33489872598


No 52 
>pfam03264 Cytochrom_NNT NapC/NirT cytochrome c family, N-terminal region. Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC and NirT, bind four haem groups, while others, such as TorC, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.
Probab=37.84  E-value=31  Score=15.36  Aligned_cols=35  Identities=11%  Similarity=0.040  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHHCCC-HHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999984189-88950889999999999999854
Q gi|254780373|r  119 TLHQDIMAYIRTVS-IKQITGAQGFRYFKEDIEERVKL  155 (172)
Q Consensus       119 ~Ird~il~~L~~~~-~~dl~~~~Gk~~Lk~el~~~in~  155 (172)
                      -++|....++...+ ++-+.  +-+.++.+.-.++++.
T Consensus        87 g~~d~~~~~~g~~~~p~k~e--~~r~~~a~~~~~~~~~  122 (174)
T pfam03264        87 ASKEVYAELTGTIDTPEKFE--AHRLEMAERVWARMKA  122 (174)
T ss_pred             HHHHHHHHHHCCCCCHHHHH--HHHHHHHHHHHHHHHC
T ss_conf             69999999962789577887--8789999999999860


No 53 
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.79  E-value=31  Score=15.36  Aligned_cols=21  Identities=19%  Similarity=0.371  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             599999999999999999999
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGWLGG   38 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~~~~   38 (172)
                      +.|+++++.+++|+.+|+|..
T Consensus         5 lail~ivl~ll~G~~~G~fia   25 (71)
T COG3763           5 LAILLIVLALLAGLIGGFFIA   25 (71)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999


No 54 
>PRK00059 prsA peptidylprolyl isomerase; Provisional
Probab=36.63  E-value=21  Score=16.21  Aligned_cols=18  Identities=33%  Similarity=0.266  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             059999999999999999
Q gi|254780373|r   17 KLFVTWFVVYTFIGIFCG   34 (172)
Q Consensus        17 kl~Iii~~vv~ll~~g~g   34 (172)
                      |.+|+.+++++++..++|
T Consensus         5 ~ki~~~~ii~~~~~~~vg   22 (336)
T PRK00059          5 KKIVASLLVGVFIFSAVG   22 (336)
T ss_pred             HHHHHHHHHHHHHHHHHC
T ss_conf             999999999999999830


No 55 
>PRK12705 hypothetical protein; Provisional
Probab=36.55  E-value=32  Score=15.24  Aligned_cols=26  Identities=15%  Similarity=0.319  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             05999999999999999999999970
Q gi|254780373|r   17 KLFVTWFVVYTFIGIFCGWLGGIVML   42 (172)
Q Consensus        17 kl~Iii~~vv~ll~~g~g~~~~~~~~   42 (172)
                      .+++++++++++++.+.|+++.+...
T Consensus         8 ~~~~i~~l~~~~ig~~lg~~~~~~~~   33 (485)
T PRK12705          8 LTILVLFLILVLIGLVLGVFIRYLYA   33 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999


No 56 
>pfam10410 DnaB_bind DnaB-helicase binding domain of primase. This domain is the C-terminal region three-helical domain of primase. Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase. It is associated with the Toprim domain (pfam01751) which is the central catalytic core.
Probab=36.24  E-value=11  Score=17.70  Aligned_cols=41  Identities=2%  Similarity=0.020  Sum_probs=27.7

Q ss_pred             HHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             9999841898895088999999999999985423563125764
Q gi|254780373|r  124 IMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRSQGFVSSVIF  166 (172)
Q Consensus       124 il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~~g~V~~V~F  166 (172)
                      ++..++..-  |+++++||.++.+++..-++.+..+-.++.|.
T Consensus         5 ~~~~l~~~~--dl~~~egk~~~~~~~~pli~~i~~~~~r~~y~   45 (59)
T pfam10410         5 LFRRLLEGY--DLDTPEGRAALLREALPLIAKIPDPVLRELYL   45 (59)
T ss_pred             HHHHHHHCC--CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             999987358--99998899999999707875598388999999


No 57 
>PRK00720 tatA twin arginine translocase protein A; Provisional
Probab=36.14  E-value=33  Score=15.21  Aligned_cols=12  Identities=8%  Similarity=0.138  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780373|r   19 FVTWFVVYTFIG   30 (172)
Q Consensus        19 ~Iii~~vv~ll~   30 (172)
                      |+||++|++||.
T Consensus         9 ~lIi~~vVllLF   20 (71)
T PRK00720          9 WLIVLAVVLLLF   20 (71)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999995


No 58 
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=35.67  E-value=20  Score=16.33  Aligned_cols=20  Identities=10%  Similarity=0.192  Sum_probs=10.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHH
Q ss_conf             63205999999999999999
Q gi|254780373|r   14 NQHKLFVTWFVVYTFIGIFC   33 (172)
Q Consensus        14 ~~~kl~Iii~~vv~ll~~g~   33 (172)
                      +++|.+++.+++++++..||
T Consensus         2 ~~k~~~li~ll~~~~lL~gC   21 (385)
T PRK09859          2 NRRRKLLIPLLFCGAMLTAC   21 (385)
T ss_pred             CCHHHHHHHHHHHHHHHHCC
T ss_conf             82067899999999999537


No 59 
>pfam03645 Tctex-1 Tctex-1 family. Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Probab=34.43  E-value=35  Score=15.05  Aligned_cols=53  Identities=17%  Similarity=0.049  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHCCCC---EEEEEEE
Q ss_conf             4218999999999841898895088999999999999985423563---1257643
Q gi|254780373|r  115 VFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRSQGF---VSSVIFR  167 (172)
Q Consensus       115 ~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~~g~---V~~V~Ft  167 (172)
                      .....|++.+-..|.+.+|+.-....--..|.++|++++..+...+   |-.+++.
T Consensus         3 ~v~~ii~~~l~~~L~~~~Y~~~~~~~~~~~i~~~I~~~lk~l~~~ryK~vv~v~I~   58 (101)
T pfam03645         3 EVKEIIKEVLEEKLGGVEYDHEKVQQWSKEISETILKRLKELGGKRYKYVVQVTIG   58 (101)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEE
T ss_conf             89999999999987899518699999999999999999984279871799999998


No 60 
>TIGR02223 ftsN cell division protein FtsN; InterPro: IPR011930    FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis ..
Probab=32.37  E-value=38  Score=14.86  Aligned_cols=48  Identities=8%  Similarity=-0.105  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH---------HHHHHHHCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             320599999999999999999---------9999970678765201245565310112
Q gi|254780373|r   15 QHKLFVTWFVVYTFIGIFCGW---------LGGIVMLFLFAGQKEEKYQKFILNNFYD   63 (172)
Q Consensus        15 ~~kl~Iii~~vv~ll~~g~g~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (172)
                      ...+++|.+++++|+. |++.         -+|+|++..+.................+
T Consensus        33 ~~a~~~ia~~~i~l~~-g~~~DPaDsnPaPqagl~~~~~~~~~~~~~~~~~k~~~~~~   89 (354)
T TIGR02223        33 VRATVLIAVILILLFI-GGSSDPADSNPAPQAGLYLLTESKQAKEPEVLQPKNQTENG   89 (354)
T ss_pred             CHHHHHHHHHHHHHHH-HCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             2489999999999986-12567434663236663433057788887666555546777


No 61 
>pfam03896 TRAP_alpha Translocon-associated protein (TRAP), alpha subunit. The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane.
Probab=31.26  E-value=40  Score=14.75  Aligned_cols=25  Identities=8%  Similarity=0.211  Sum_probs=13.2

Q ss_pred             EEEEECCC-CCEEEEEEEEEEECCCH
Q ss_conf             02420589-83389999998504402
Q gi|254780373|r   88 IITNFDSS-PKDWLRLDIALICKDIP  112 (172)
Q Consensus        88 fvvNL~~~-~~r~lk~~i~l~~~~~~  112 (172)
                      |+|-+.+. ...|+-..+...+++|.
T Consensus        99 fLVGF~NkG~~df~Vesi~ASfryP~  124 (281)
T pfam03896        99 FLVGFTNKGSEDFVVESLEASFRYPQ  124 (281)
T ss_pred             EEEEECCCCCCCEEEEEEEEEECCCC
T ss_conf             99974247863258998643340675


No 62 
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=29.48  E-value=43  Score=14.58  Aligned_cols=30  Identities=13%  Similarity=0.247  Sum_probs=14.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             205999999999999999999999970678
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGWLGGIVMLFLF   45 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~~~~~~~~~~~   45 (172)
                      +|.++++..+++++.++.+++...++....
T Consensus        10 ~kvl~~~~~i~aal~~~~~~~~~~il~s~f   39 (295)
T COG3322          10 KKVLIILLAIFAALTAALGGASYNILLSSF   39 (295)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999999999999854


No 63 
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein,  YhcN/YlaJ family; InterPro: IPR014247   This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. .
Probab=28.24  E-value=34  Score=15.08  Aligned_cols=17  Identities=18%  Similarity=0.530  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             59999999999999999
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCG   34 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g   34 (172)
                      |++++++.++|++.||+
T Consensus         2 l~~~ll~~~~l~~tgC~   18 (185)
T TIGR02898         2 LFIILLLLLLLLATGCT   18 (185)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             68899999999873134


No 64 
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345   Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene..
Probab=28.23  E-value=45  Score=14.46  Aligned_cols=40  Identities=8%  Similarity=0.225  Sum_probs=31.4

Q ss_pred             HHHHHHHHHCCCHH-HHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999998418988-95088999999999999985423563
Q gi|254780373|r  121 HQDIMAYIRTVSIK-QITGAQGFRYFKEDIEERVKLRSQGF  160 (172)
Q Consensus       121 rd~il~~L~~~~~~-dl~~~~Gk~~Lk~el~~~in~~~~g~  160 (172)
                      |-.+..+++..+.| .+++++-++.|=++|.+.|.+...|+
T Consensus        80 Rp~l~~V~r~~DlD~~~~~pa~~E~li~~l~~~i~i~~~gr  120 (510)
T TIGR03007        80 RPNLEKVIRMLDLDVGAKSPAQLEALITKLQKNISISLAGR  120 (510)
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCEEEECCC
T ss_conf             45789999885267776998999999998761434611167


No 65 
>PRK06287 cobalt transport protein CbiN; Validated
Probab=28.18  E-value=45  Score=14.45  Aligned_cols=17  Identities=12%  Similarity=0.067  Sum_probs=7.9

Q ss_pred             CHHHHHHHHHHHHHHHH
Q ss_conf             20599999999999999
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIF   32 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g   32 (172)
                      .|.+++..++++|+.++
T Consensus         3 nkkfli~g~~iALlia~   19 (105)
T PRK06287          3 NKKFLIAGLIIALLIGI   19 (105)
T ss_pred             CCEEEHHHHHHHHHHHH
T ss_conf             73765679999999998


No 66 
>PRK00523 hypothetical protein; Provisional
Probab=27.88  E-value=46  Score=14.42  Aligned_cols=21  Identities=14%  Similarity=0.070  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHH
Q ss_conf             599999999999999-999999
Q gi|254780373|r   18 LFVTWFVVYTFIGIF-CGWLGG   38 (172)
Q Consensus        18 l~Iii~~vv~ll~~g-~g~~~~   38 (172)
                      +.|.+.+++++++++ +|+|+.
T Consensus         5 l~iglgiil~li~G~~~Gff~a   26 (73)
T PRK00523          5 LILGLGIPLSLIVGGIIGYFVS   26 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7659989999999999999999


No 67 
>pfam09624 DUF2393 Protein of unknown function (DUF2393). The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.
Probab=27.68  E-value=46  Score=14.40  Aligned_cols=29  Identities=10%  Similarity=-0.101  Sum_probs=14.4

Q ss_pred             CCEEECCCCEEE-EECCCCCEEEEEEEEEEECC
Q ss_conf             530210332024-20589833899999985044
Q gi|254780373|r   79 KLQIFSLQPIIT-NFDSSPKDWLRLDIALICKD  110 (172)
Q Consensus        79 ~~~~~~l~~fvv-NL~~~~~r~lk~~i~l~~~~  110 (172)
                      ..||+   ||.+ |.++....-+++.-.|...+
T Consensus        46 ~qyyV---pF~v~N~Gg~TAa~V~V~geL~~~~   75 (119)
T pfam09624        46 GQFYV---PFAVRNDGGQTAAAVTVIGELRQGG   75 (119)
T ss_pred             CEEEE---EEEEEECCCCEEEEEEEEEEECCCC
T ss_conf             87899---9999968866777999999997699


No 68 
>pfam08999 SP_C-Propep Surfactant protein C, N terminal propeptide. The N-terminal propeptide of surfactant protein C adopts an alpha-helical structure, with turn and extended regions. It's main function is the stabilisation of metastable surfactant protein C (SP-C), since the latter can irreversibly transform from its native alpha-helical structure to beta-sheet aggregates and form amyloid-like fibrils. The correct intracellular trafficking of proSP-C has also been reported to depend on the propeptide.
Probab=27.57  E-value=46  Score=14.39  Aligned_cols=20  Identities=20%  Similarity=0.356  Sum_probs=8.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             20599999999999999999
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCGW   35 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g~   35 (172)
                      +.++|+++++++++.+..|+
T Consensus        34 krlli~vvvvvlvvvvivga   53 (93)
T pfam08999        34 KRLLIVVVVVVLVVVVIVGA   53 (93)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             65131023346789999999


No 69 
>cd03403 Band_7_stomatin_like Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Stomatin is widely expressed and, highly expressed in red blood cells. It localizes predominantly to the plasma membrane and to intracellular vesicles of the endocytic pathway, where it is present in higher order homo-oligomeric complexes (of between 9 and 12 monomers).  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and, is implicated in trafficking of Glut1 glucose transporters. Prohibitin is a mitochondrial inner-membrane protein hypothesized to act as a chaperone for the stabilization of mitochondrial proteins. Podicin local
Probab=27.14  E-value=47  Score=14.35  Aligned_cols=71  Identities=13%  Similarity=0.140  Sum_probs=49.3

Q ss_pred             EEEEEEEEEEEC--CCH---------HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHCC---CCEEE
Q ss_conf             389999998504--402---------4542189999999998418988950889999999999999854235---63125
Q gi|254780373|r   98 DWLRLDIALICK--DIP---------DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRSQ---GFVSS  163 (172)
Q Consensus        98 r~lk~~i~l~~~--~~~---------~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~~---g~V~~  163 (172)
                      ..+.+++.+.++  ++.         .....+.+++.+-..+++.+.+++-+  .|+.|.++|.+.++....   =.|.+
T Consensus        57 ~~v~v~~~v~yrI~dp~~~~~~v~~~~~~l~~~~~~~lR~~i~~~~~~~i~~--~R~~i~~~i~~~l~~~l~~~Gi~v~~  134 (215)
T cd03403          57 VTVRVDAVLYYRVVDPVKAVYGVEDYRYAISQLAQTTLRSVIGKMELDELLS--EREEINAELVEILDEATDPWGVKVER  134 (215)
T ss_pred             CEEEEEEEEEEEECCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCHHHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             7899999999995788999973289999999999999998853233899985--49999999999999872128859999


Q ss_pred             EEEEEEE
Q ss_conf             7643220
Q gi|254780373|r  164 VIFRTFI  170 (172)
Q Consensus       164 V~Ft~fV  170 (172)
                      |.++++.
T Consensus       135 v~i~~i~  141 (215)
T cd03403         135 VEIKDII  141 (215)
T ss_pred             EEEEECC
T ss_conf             9997538


No 70 
>pfam06796 NapE Periplasmic nitrate reductase protein NapE. This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans IL106. NapE is thought to be a transmembrane protein.
Probab=27.01  E-value=47  Score=14.33  Aligned_cols=23  Identities=17%  Similarity=0.189  Sum_probs=10.7

Q ss_pred             CCCCCCCC-CCCCCCCCHHHHHHH
Q ss_conf             98543553-234676320599999
Q gi|254780373|r    1 MSYDDTTS-QYIRGNQHKLFVTWF   23 (172)
Q Consensus         1 ma~~~~~~-~~~kG~~~kl~Iii~   23 (172)
                      |+++..++ +..|+.-.|.++++.
T Consensus         1 Ms~~~~~~~~~~k~~El~~f~fl~   24 (55)
T pfam06796         1 MSEQPSSTEKERKRKELKAFLFLT   24 (55)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             987899998103479999999999


No 71 
>KOG0860 consensus
Probab=26.38  E-value=49  Score=14.27  Aligned_cols=21  Identities=5%  Similarity=0.370  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHH-HCCCHHHHC
Q ss_conf             189999999998-418988950
Q gi|254780373|r  117 LETLHQDIMAYI-RTVSIKQIT  137 (172)
Q Consensus       117 ~p~Ird~il~~L-~~~~~~dl~  137 (172)
                      ...+|+.+--+| |....++|.
T Consensus        42 v~IMr~NV~KVlER~ekL~~L~   63 (116)
T KOG0860          42 VDIMRENVEKVLERGEKLDELD   63 (116)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHH
T ss_conf             9999991999998202087899


No 72 
>PRK11677 cytochrome d ubiquinol oxidase subunit III; Provisional
Probab=26.33  E-value=49  Score=14.26  Aligned_cols=22  Identities=14%  Similarity=0.076  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999706
Q gi|254780373|r   22 WFVVYTFIGIFCGWLGGIVMLF   43 (172)
Q Consensus        22 i~~vv~ll~~g~g~~~~~~~~~   43 (172)
                      +.++.+++|+.+|++++.+..+
T Consensus         5 ~ali~lvvGiiIG~~~~R~~~~   26 (134)
T PRK11677          5 YALIGLVVGIIIGAVAMRFGNR   26 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999999998175


No 73 
>cd03404 Band_7_HflK Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another band 7 family member (HflC) to form an HflKC complex.  HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins.  HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during la
Probab=26.32  E-value=49  Score=14.26  Aligned_cols=70  Identities=9%  Similarity=0.124  Sum_probs=48.4

Q ss_pred             EEEEEEEEEEC--CCH---------HHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHC-----CCCEE
Q ss_conf             89999998504--402---------454218999999999841898895088999999999999985423-----56312
Q gi|254780373|r   99 WLRLDIALICK--DIP---------DKVFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRS-----QGFVS  162 (172)
Q Consensus        99 ~lk~~i~l~~~--~~~---------~e~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~-----~g~V~  162 (172)
                      .+.+...+.++  ++.         .....+.+++.+-..+++.+.+++-+ .++..+.++++++++...     +=.|.
T Consensus        87 ~v~vd~~v~yrI~dp~~~~~~~~~~~~~l~~~~~~~lR~~ig~~~lde~l~-~~R~~i~~~i~~~l~~~~~~~~~GI~v~  165 (266)
T cd03404          87 IVDVEFAVQYRISDPYDYLFNVRDPEGTLRQAAESAMREVVGRSTLDDVLT-EGREEIAQDVRELLQAILDAYKAGIEIV  165 (266)
T ss_pred             EEEEEEEEEEEECCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCHHHHHH-CCHHHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             899999999998868998886258999999999999999972660688864-3799999999999999873456867999


Q ss_pred             EEEEEEE
Q ss_conf             5764322
Q gi|254780373|r  163 SVIFRTF  169 (172)
Q Consensus       163 ~V~Ft~f  169 (172)
                      +|-+++.
T Consensus       166 ~V~i~~i  172 (266)
T cd03404         166 GVNLQDA  172 (266)
T ss_pred             EEEEEEC
T ss_conf             9997526


No 74 
>PRK11901 hypothetical protein; Reviewed
Probab=26.24  E-value=49  Score=14.25  Aligned_cols=18  Identities=17%  Similarity=0.095  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             599999999999999999
Q gi|254780373|r   18 LFVTWFVVYTFIGIFCGW   35 (172)
Q Consensus        18 l~Iii~~vv~ll~~g~g~   35 (172)
                      |+-+-++|++||.+|+|-
T Consensus        39 MiGiGILVLLLLIIgIgS   56 (329)
T PRK11901         39 MIGIGILVLLLLIIAIGS   56 (329)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999998656


No 75 
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=26.14  E-value=33  Score=15.22  Aligned_cols=22  Identities=18%  Similarity=0.329  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999997
Q gi|254780373|r   20 VTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus        20 Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      |+++++.+++|++.||++..+.
T Consensus         1 Ii~~ii~lviG~~iGy~l~k~~   22 (514)
T TIGR03319         1 ILLALVALIVGLIIGYLLRKRI   22 (514)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9068999999999999999999


No 76 
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=25.64  E-value=50  Score=14.19  Aligned_cols=30  Identities=7%  Similarity=0.167  Sum_probs=12.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             676320599999999999999999999997
Q gi|254780373|r   12 RGNQHKLFVTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus        12 kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      +.+.++.++.+.+++++.++..||+++.+.
T Consensus         9 ~~~~k~~~~~~~~~~~~~a~~~~~~~~~~~   38 (352)
T COG1566           9 KAKRKRFKLPLTLLVVLAAVLYGGLIWLYY   38 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             445567788999999999999999999972


No 77 
>TIGR01215 minE cell division topological specificity factor MinE; InterPro: IPR005527    Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerization, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD .     MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for 'topological specificity' - that is, the ability of MinE to antagonize MinCD inhibition of Z rings at the midcell position but not at the poles..
Probab=25.57  E-value=50  Score=14.18  Aligned_cols=40  Identities=10%  Similarity=0.086  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             2189999999998418988950889999999999999854
Q gi|254780373|r  116 FLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKL  155 (172)
Q Consensus       116 ~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~  155 (172)
                      -....||++..++..-+...-..|+=.+.||.||++-|.-
T Consensus        15 Sa~~Ak~RL~li~A~~R~~~~~~P~yle~lR~dileVi~K   54 (89)
T TIGR01215        15 SAEVAKDRLQLIVAEERAQSGAAPDYLEELRKDILEVIQK   54 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             1789999998876644422678871238889999988773


No 78 
>pfam01145 Band_7 SPFH domain / Band 7 family. This family has been called SPFH, Band 7 or PHB domain.
Probab=25.31  E-value=51  Score=14.15  Aligned_cols=53  Identities=8%  Similarity=0.151  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHCC--C-CEEEEEEEEEE
Q ss_conf             2189999999998418988950889999999999999854235--6-31257643220
Q gi|254780373|r  116 FLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRSQ--G-FVSSVIFRTFI  170 (172)
Q Consensus       116 ~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~~--g-~V~~V~Ft~fV  170 (172)
                      ..+.+++.+-..++..+.+|+-+  ++..+.+++.+++|....  | .|.+|.++++-
T Consensus        91 l~~~~~~~lr~~~~~~~~~~~~~--~r~~i~~~v~~~l~~~l~~~Gi~i~~v~i~~i~  146 (177)
T pfam01145        91 LRPLVRSALREVIARYTLDELLS--NREEIAQEVKEALQEELDKYGIEIEDVQITDID  146 (177)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHH--HHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECC
T ss_conf             99999999999860466999986--189999999999999998669889999997448


No 79 
>pfam09576 COX9 Cytochrome c oxidase subunit COX9. COX9 is subunit VIIa of yeast cytochrome c oxidase. Cells lacking this subunit do not have a functional cytochrome c oxidase holoenzyme.
Probab=24.90  E-value=52  Score=14.11  Aligned_cols=36  Identities=11%  Similarity=-0.154  Sum_probs=21.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             234676320599999999999999999999997067
Q gi|254780373|r    9 QYIRGNQHKLFVTWFVVYTFIGIFCGWLGGIVMLFL   44 (172)
Q Consensus         9 ~~~kG~~~kl~Iii~~vv~ll~~g~g~~~~~~~~~~   44 (172)
                      ++.-|.-++-+|.=+.+-..+|...+.++++.....
T Consensus         4 aPItG~Lrrrii~Disig~glG~~~a~~~Wyg~H~p   39 (57)
T pfam09576         4 APITGMLRRRIITDISIGFGLGTVMASYWWYGYHKP   39 (57)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             764125654456423577765777877777652147


No 80 
>smart00019 SF_P Pulmonary surfactant proteins. Pulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-C, a component of surfactant, is a highly hydrophobic peptide of 35 amino acid residues which is processed from a larger precursor protein. SP-C is post-translationally modified by the covalent attachment of two palmitoyl groups on two adjacent cysteines
Probab=24.16  E-value=15  Score=17.01  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=11.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             63205999999999999999999
Q gi|254780373|r   14 NQHKLFVTWFVVYTFIGIFCGWL   36 (172)
Q Consensus        14 ~~~kl~Iii~~vv~ll~~g~g~~   36 (172)
                      +-|+++|++++|++++.+..|++
T Consensus        32 ~lKrLlivVvVvVlvVvViVGaL   54 (191)
T smart00019       32 HLKRLLIVVVVVVLVVVVIVGAL   54 (191)
T ss_pred             CHHHEEEEEEEEHHHHHHHHHHH
T ss_conf             71007778742025799999999


No 81 
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.03  E-value=54  Score=14.02  Aligned_cols=28  Identities=14%  Similarity=0.062  Sum_probs=14.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6320599999999999999999999997
Q gi|254780373|r   14 NQHKLFVTWFVVYTFIGIFCGWLGGIVM   41 (172)
Q Consensus        14 ~~~kl~Iii~~vv~ll~~g~g~~~~~~~   41 (172)
                      .+++++.+..+.++++.++..++++-++
T Consensus        48 skK~ii~was~a~~lIlii~~~~fgk~f   75 (465)
T COG4640          48 SKKKIIPWASGAFILILIIILFFFGKNF   75 (465)
T ss_pred             CCCEEEHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             6111200478899999999999975403


No 82 
>pfam03597 CcoS Cytochrome oxidase maturation protein cbb3-type.
Probab=23.66  E-value=55  Score=13.98  Aligned_cols=28  Identities=7%  Similarity=-0.198  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf             9999999999999999970678765201
Q gi|254780373|r   24 VVYTFIGIFCGWLGGIVMLFLFAGQKEE   51 (172)
Q Consensus        24 ~vv~ll~~g~g~~~~~~~~~~~~~~~~~   51 (172)
                      +-+++.+++.++|++..-.++.++-+.+
T Consensus         9 isl~l~~~~l~~f~Wavk~gQfDDle~~   36 (45)
T pfam03597         9 ISLLLGAVGLAAFLWAVKSGQFDDLEGP   36 (45)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             9999999999999998505877788775


No 83 
>COG4093 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.51  E-value=49  Score=14.23  Aligned_cols=26  Identities=8%  Similarity=-0.064  Sum_probs=9.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             32059999999999999999999999706
Q gi|254780373|r   15 QHKLFVTWFVVYTFIGIFCGWLGGIVMLF   43 (172)
Q Consensus        15 ~~kl~Iii~~vv~ll~~g~g~~~~~~~~~   43 (172)
                      ++.+++.|.+|++.   |..-+.|||+..
T Consensus        14 kr~~wl~i~ivv~~---g~ySaGWFylA~   39 (338)
T COG4093          14 KRLFWLVIAIVVLI---GAYSAGWFYLAD   39 (338)
T ss_pred             CCHHHHHHHHHHHH---HHHCCHHHHHHH
T ss_conf             22348999999988---775010766776


No 84 
>pfam09680 Tiny_TM_bacill Protein of unknown function (Tiny_TM_bacill). This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=23.01  E-value=57  Score=13.90  Aligned_cols=17  Identities=6%  Similarity=0.100  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780373|r   20 VTWFVVYTFIGIFCGWL   36 (172)
Q Consensus        20 Iii~~vv~ll~~g~g~~   36 (172)
                      +|+++.++|+.+|+.|+
T Consensus         8 LiVVLFILLIIVG~s~~   24 (26)
T pfam09680         8 LIVVLFILLIIVGASYF   24 (26)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             69999999999833540


No 85 
>cd02106 Band_7 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic HflK/C plays a role i
Probab=22.87  E-value=57  Score=13.89  Aligned_cols=54  Identities=7%  Similarity=0.083  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHHHHC---CCCEEEEEEEEEE
Q ss_conf             4218999999999841898895088999999999999985423---5631257643220
Q gi|254780373|r  115 VFLETLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVKLRS---QGFVSSVIFRTFI  170 (172)
Q Consensus       115 ~~~p~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in~~~---~g~V~~V~Ft~fV  170 (172)
                      ...+.+++.+-..++..+.+++  ..+++.|.+++.+.++...   +=.|.+|.+++.-
T Consensus        52 ~i~~~~~~~lr~~i~~~~~~~~--~~~r~~i~~~i~~~l~~~~~~~Gi~v~~v~i~~i~  108 (121)
T cd02106          52 ALRQLAQSALRSVIGKMTLDEL--LEDRDEIAAEVREALQEDLDKYGIEVVDVRIKDID  108 (121)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHH--HHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEECC
T ss_conf             9999999999999711537765--20166689999999988787519589999998638


No 86 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=22.74  E-value=42  Score=14.61  Aligned_cols=18  Identities=11%  Similarity=0.371  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999
Q gi|254780373|r   20 VTWFVVYTFIGIFCGWLG   37 (172)
Q Consensus        20 Iii~~vv~ll~~g~g~~~   37 (172)
                      ||+++|+++++.++++++
T Consensus         2 ii~iivivii~~~~~~~~   19 (559)
T pfam06160         2 IIGIIVIVIVAYLAGYFL   19 (559)
T ss_pred             EEEHHHHHHHHHHHHHHH
T ss_conf             440899999999999999


No 87 
>pfam06097 DUF945 Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=22.43  E-value=58  Score=13.84  Aligned_cols=20  Identities=15%  Similarity=0.129  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254780373|r   19 FVTWFVVYTFIGIFCGWLGG   38 (172)
Q Consensus        19 ~Iii~~vv~ll~~g~g~~~~   38 (172)
                      .+.++++++++.+|+.||.|
T Consensus         6 a~gviv~l~a~~~g~~wytG   25 (460)
T pfam06097         6 AIGVIVALGAVWTGGPWYTG   25 (460)
T ss_pred             EEHHHHHHHHHHHHHHHHHH
T ss_conf             20989999999853465767


No 88 
>pfam11772 EpuA DNA-directed RNA polymerase subunit beta. This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA.
Probab=22.28  E-value=30  Score=15.44  Aligned_cols=23  Identities=9%  Similarity=-0.002  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999999997067876
Q gi|254780373|r   25 VYTFIGIFCGWLGGIVMLFLFAG   47 (172)
Q Consensus        25 vv~ll~~g~g~~~~~~~~~~~~~   47 (172)
                      ++.++....|...+|..++...+
T Consensus         6 ~L~~~~l~~G~miGYgviG~G~p   28 (47)
T pfam11772         6 LLAALALVIGLMIGYGVIGGGNP   28 (47)
T ss_pred             HHHHHHHHHHHHEEEEEECCCCH
T ss_conf             99999999877801323169987


No 89 
>pfam00155 Aminotran_1_2 Aminotransferase class I and II.
Probab=22.21  E-value=59  Score=13.81  Aligned_cols=11  Identities=27%  Similarity=0.573  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999999
Q gi|254780373|r  142 FRYFKEDIEER  152 (172)
Q Consensus       142 k~~Lk~el~~~  152 (172)
                      ..++|+.+.++
T Consensus       262 ~~~~~~~~~~~  272 (351)
T pfam00155       262 LEEMRQRIKER  272 (351)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 90 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.86  E-value=60  Score=13.77  Aligned_cols=16  Identities=25%  Similarity=0.434  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780373|r   19 FVTWFVVYTFIGIFCG   34 (172)
Q Consensus        19 ~Iii~~vv~ll~~g~g   34 (172)
                      ++|+++|+++++.+++
T Consensus         5 iii~iivlvii~~~~~   20 (569)
T PRK04778          5 LIIAIVVIIIIAYLVG   20 (569)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             7899999999999999


No 91 
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=21.54  E-value=61  Score=13.74  Aligned_cols=19  Identities=0%  Similarity=-0.043  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHCCCH
Q ss_conf             4218999999999841898
Q gi|254780373|r  115 VFLETLHQDIMAYIRTVSI  133 (172)
Q Consensus       115 ~~~p~Ird~il~~L~~~~~  133 (172)
                      ....+..+.+...|.+..+
T Consensus        82 ~~k~qyg~~f~~~L~q~gl  100 (285)
T PRK03002         82 KAKSQYGDQFKNVLENNGL  100 (285)
T ss_pred             HHHHHHHHHHHHHHHHCCC
T ss_conf             9999987899999998699


No 92 
>COG2268 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.19  E-value=62  Score=13.69  Aligned_cols=34  Identities=18%  Similarity=0.262  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             999999999841898895088999999999999985
Q gi|254780373|r  119 TLHQDIMAYIRTVSIKQITGAQGFRYFKEDIEERVK  154 (172)
Q Consensus       119 ~Ird~il~~L~~~~~~dl~~~~Gk~~Lk~el~~~in  154 (172)
                      ...+.+=..++++++.+|..  -|.....++.+.+-
T Consensus       143 ~l~~~lR~i~a~~t~~el~e--dR~~F~~~V~~~v~  176 (548)
T COG2268         143 TLEGALRAVLAQMTVEELNE--DRLGFAQVVQEVVG  176 (548)
T ss_pred             HHHHHHHHHHHHCCHHHHHH--HHHHHHHHHHHHHH
T ss_conf             99999999987559998746--67627999999988


No 93 
>pfam03672 UPF0154 Uncharacterized protein family (UPF0154). This family contains a set of short bacterial proteins of unknown function.
Probab=20.86  E-value=63  Score=13.65  Aligned_cols=16  Identities=19%  Similarity=0.374  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780373|r   24 VVYTFIGIFCGWLGGI   39 (172)
Q Consensus        24 ~vv~ll~~g~g~~~~~   39 (172)
                      ++.+++|+.+|+|+..
T Consensus         4 il~ll~G~~~Gff~ar   19 (64)
T pfam03672         4 VLCLLAGFILGYFISR   19 (64)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             8999998999999999


No 94 
>PRK10905 hypothetical protein; Validated
Probab=20.72  E-value=33  Score=15.18  Aligned_cols=18  Identities=17%  Similarity=-0.011  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999
Q gi|254780373|r   19 FVTWFVVYTFIGIFCGWL   36 (172)
Q Consensus        19 ~Iii~~vv~ll~~g~g~~   36 (172)
                      +-|-++|++||.+|+|-.
T Consensus         2 ~gigi~vl~lliigiGSA   19 (323)
T PRK10905          2 MGVGILVLLLLIIGIGSA   19 (323)
T ss_pred             CCEEHHHHHHHHHHHHHH
T ss_conf             410024577888620043


No 95 
>PRK01833 tatA twin arginine translocase protein A; Provisional
Probab=20.55  E-value=64  Score=13.62  Aligned_cols=11  Identities=9%  Similarity=0.286  Sum_probs=3.8

Q ss_pred             HHHHHHHHHHH
Q ss_conf             59999999999
Q gi|254780373|r   18 LFVTWFVVYTF   28 (172)
Q Consensus        18 l~Iii~~vv~l   28 (172)
                      ++||.++|++|
T Consensus         9 llIi~~iv~ll   19 (75)
T PRK01833          9 LLIIVAIIVLL   19 (75)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 96 
>PRK10856 hypothetical protein; Provisional
Probab=20.48  E-value=64  Score=13.61  Aligned_cols=19  Identities=26%  Similarity=0.632  Sum_probs=8.2

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             2059999999999999999
Q gi|254780373|r   16 HKLFVTWFVVYTFIGIFCG   34 (172)
Q Consensus        16 ~kl~Iii~~vv~ll~~g~g   34 (172)
                      ..|++.++++++++++.+.
T Consensus       112 ~l~~~~~lv~~vvl~l~~~  130 (332)
T PRK10856        112 WLMSFTWLVLFVVIGLTGA  130 (332)
T ss_pred             HHHHHHHHHHHHHHHHHHH
T ss_conf             3789999999999998888


No 97 
>TIGR01411 tatAE twin arginine-targeting protein translocase, TatA/E family; InterPro: IPR006312   This family represents TatA and TatE. The Tat (twin-arginine translocation) system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane. Functionally equivalent systems are found in the chloroplast and some in archaeal species. The signal peptide recognized by the Tat system is modeled by IPR006311 from INTERPRO. ; GO: 0015031 protein transport, 0016021 integral to membrane.
Probab=20.30  E-value=62  Score=13.70  Aligned_cols=13  Identities=15%  Similarity=0.153  Sum_probs=6.9

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             5999999999999
Q gi|254780373|r   18 LFVTWFVVYTFIG   30 (172)
Q Consensus        18 l~Iii~~vv~ll~   30 (172)
                      -||+|++|++|+-
T Consensus         7 ~~liiL~v~~LlF   19 (48)
T TIGR01411         7 HLLIILVVILLLF   19 (48)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999988641


No 98 
>PRK04561 tatA twin arginine translocase protein A; Provisional
Probab=20.13  E-value=65  Score=13.57  Aligned_cols=12  Identities=8%  Similarity=0.246  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780373|r   19 FVTWFVVYTFIG   30 (172)
Q Consensus        19 ~Iii~~vv~ll~   30 (172)
                      |+|++++++|+-
T Consensus         9 ~lIv~~ivvllF   20 (75)
T PRK04561          9 WLVVLVIVLLVF   20 (75)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999983


Done!