Query         gi|254780571|ref|YP_003064984.1| hypothetical protein CLIBASIA_02290 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 182
No_of_seqs    111 out of 492
Neff          8.9 
Searched_HMMs 39220
Date          Mon May 30 00:49:25 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780571.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4961 TadG Flp pilus assembl  99.9 1.2E-20   3E-25  143.1  15.2  178    1-182     5-185 (185)
  2 pfam07811 TadE TadE-like prote  98.9 5.1E-09 1.3E-13   73.0   5.9   43   17-59      1-43  (43)
  3 COG3847 Flp Flp pilus assembly  97.8 0.00012   3E-09   46.8   7.1   36    4-39      1-36  (58)
  4 pfam04964 Flp_Fap Flp/Fap pili  95.9  0.0095 2.4E-07   35.2   3.6   28   11-38      1-28  (47)
  5 COG4655 Predicted membrane pro  95.6    0.11 2.7E-06   28.9   8.0   55   10-64      3-57  (565)
  6 pfam04917 Shufflon_N Bacterial  94.6     0.2 5.1E-06   27.3   7.1   49   12-60      2-50  (356)
  7 PRK10506 hypothetical protein;  93.4    0.39 9.9E-06   25.5   6.7   52   13-64      2-53  (155)
  8 COG4970 FimT Tfp pilus assembl  90.8       1 2.6E-05   23.0   6.3   52   11-62      3-54  (181)
  9 pfam05307 Bundlin Bundlin. Thi  89.5    0.79   2E-05   23.7   4.9   49   12-60      8-56  (97)
 10 COG4966 PilW Tfp pilus assembl  85.3    0.56 1.4E-05   24.6   2.0   39    7-45      4-42  (318)
 11 COG4537 ComGC Competence prote  77.2     2.7 6.8E-05   20.5   3.1   28    8-35      4-31  (107)
 12 KOG3970 consensus               74.8       2 5.2E-05   21.2   2.0   12  128-139   184-195 (299)
 13 COG1681 FlaB Archaeal flagelli  66.4       5 0.00013   18.9   2.5   53   14-66      1-55  (209)
 14 pfam04021 Class_IIIsignal Clas  64.4     5.1 0.00013   18.8   2.2   22   15-36      1-22  (28)
 15 PRK10913 dipeptide transporter  61.9      10 0.00027   16.9   4.3   32    3-36     18-49  (300)
 16 TIGR01708 typeII_sec_gspH gene  59.4     7.1 0.00018   17.9   2.2   50   13-63      1-51  (175)
 17 COG1991 Uncharacterized conser  56.8    0.75 1.9E-05   23.8  -3.1   30    7-36      4-33  (131)
 18 COG2165 PulG Type II secretory  49.4      17 0.00043   15.7   7.4   49   13-61      5-53  (149)
 19 PRK10332 hypothetical protein;  47.6      18 0.00046   15.5   5.6   54   12-65      5-58  (107)
 20 pfam11688 DUF3285 Protein of u  38.5      25 0.00064   14.6   3.8   34    3-41     11-44  (45)
 21 pfam12273 RCR Chitin synthesis  35.2      28 0.00072   14.3   2.2   16   22-37      4-19  (124)
 22 TIGR01247 drrB daunorubicin re  35.1      25 0.00064   14.6   1.9   27    8-37      3-29  (240)
 23 PRK08541 flagellin; Validated   34.0      30 0.00075   14.2   4.1   51   14-64      1-53  (212)
 24 COG4726 PilX Tfp pilus assembl  32.6      31 0.00079   14.1   5.5   35    7-41      4-38  (196)
 25 PRK10574 putative major pilin   28.4      37 0.00094   13.6   6.5   46   13-58      2-47  (146)
 26 COG5605 Predicted small integr  27.6      38 0.00097   13.5   4.1   24   20-43     77-100 (115)
 27 PRK09881 ATP-dependent peptide  24.3      44  0.0011   13.2   3.3   31    5-37     21-51  (296)
 28 TIGR03061 pip_yhgE_Nterm YhgE/  23.6      45  0.0012   13.1   3.4   27    8-34      3-29  (164)
 29 KOG2856 consensus               22.2      48  0.0012   12.9   2.5   19  129-147   408-426 (472)

No 1  
>COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion]
Probab=99.87  E-value=1.2e-20  Score=143.06  Aligned_cols=178  Identities=13%  Similarity=0.087  Sum_probs=114.7

Q ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             92479999975124455489999999999999999999999999999999999999999985288879788877999999
Q gi|254780571|r    1 MKCIKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETSINKQYLQGFENFLR   80 (182)
Q Consensus         1 ~~~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~~~~~~~~~~~~~~~~   80 (182)
                      +|..+.+.+||+||++|++||||||++|+||+++++++|++.+++.++.+++|+++++|.++++...+..+.   ..+..
T Consensus         5 ~~~~~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve~~~~~~~~~~l~~a~d~aara~~~~~~~~~~~~---~~~~~   81 (185)
T COG4961           5 RRGLRGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVEFGIAFLAKQSLQNAADAAARAAARGLTTDAADL---DTIQA   81 (185)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHH
T ss_conf             265799999887648768999999999999999999999999999999999999999999985076442025---67789


Q ss_pred             HHHHCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCC-CCCCEEEEEEEEEEEE--ECCCCCCCCCCC
Q ss_conf             8752347887389999999537885278960467877763565666677-9996799999999623--112233445367
Q gi|254780571|r   81 ATMYPYRTPNHSIIVTGYWLDNKQIVRKMWNWSSSNVKVEREDIPASIK-DASTFIVRAEVSINYR--TLVFSKILPDSL  157 (182)
Q Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~~v~~s~~~~~~~~~~~~~p~~~~-~~~~~~v~v~v~y~y~--p~~~~~~~~~~~  157 (182)
                      ....++............+.+......++|+....+..... ..+.... .....+..++..+.+.  +.+..+......
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~v~~~~~~~~~~~~~~~~~~~v~~~t~~~~~~~~  160 (185)
T COG4961          82 AATAFLNAIAPANAFLTVQSNTPSRGTVTVTANVADATLFD-TSQFTVTSAVTVSINLARGLVLVAVVPDLTGPGTSGSR  160 (185)
T ss_pred             HHHHHHHHHCCCCEEECCCCCCCCCEEEEEECCCCCCCCCC-CCCEEEEECCCCEEECCCCCCEEEEEECCCCCCCCCCC
T ss_conf             99988875164220121322455640589601312343367-76358961454202012355305787323476445551


Q ss_pred             CCCEEEEEEEEECCCCCCCEECCCC
Q ss_conf             7847899899974753473425899
Q gi|254780571|r  158 KGDIVLRKVYYYRQRLGDQIVCRDC  182 (182)
Q Consensus       158 ~~~~~l~~t~~~rpR~~~~i~c~~c  182 (182)
                      ..++.+.++.++++|....++|.+|
T Consensus       161 ~~~i~~~~~~~~~~~~~~~~~~~~~  185 (185)
T COG4961         161 SATIPVGATTLVRVRIDETITPGID  185 (185)
T ss_pred             EEEEECCCEEEEEECCCCCCCCCCC
T ss_conf             2453114104675312311367899


No 2  
>pfam07811 TadE TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues.
Probab=98.86  E-value=5.1e-09  Score=72.96  Aligned_cols=43  Identities=33%  Similarity=0.564  Sum_probs=41.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5489999999999999999999999999999999999999999
Q gi|254780571|r   17 GVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGD   59 (182)
Q Consensus        17 G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar   59 (182)
                      |+++|||+|++|+|++++++++|++++++.++.+++|+++++|
T Consensus         1 G~a~VEfalv~p~~l~l~~~~~~~~~~~~~~~~~~~Aa~~aaR   43 (43)
T pfam07811         1 GAAAVEFALVLPVLLLLLFGIVELGRLFYARQVLQNAAREAAR   43 (43)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9169999999999999999999999999999999999986749


No 3  
>COG3847 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]
Probab=97.76  E-value=0.00012  Score=46.75  Aligned_cols=36  Identities=28%  Similarity=0.524  Sum_probs=30.1

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             799999751244554899999999999999999999
Q gi|254780571|r    4 IKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYE   39 (182)
Q Consensus         4 ~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e   39 (182)
                      |+..+|||+|||+|+++||.+|++-+.=+.+.+.+.
T Consensus         1 m~~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~   36 (58)
T COG3847           1 MKKLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGS   36 (58)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             917899997745651899999999999999999999


No 4  
>pfam04964 Flp_Fap Flp/Fap pilin component.
Probab=95.87  E-value=0.0095  Score=35.24  Aligned_cols=28  Identities=29%  Similarity=0.579  Sum_probs=22.5

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5124455489999999999999999999
Q gi|254780571|r   11 FLSRENGVVAVEMAIILPILLLIYMAVY   38 (182)
Q Consensus        11 f~rd~~G~aaVEFAli~P~ll~ll~~~~   38 (182)
                      |+|||+|++|||.+|++-+.=+.+.+.+
T Consensus         1 F~kde~GaTAIEYgLIaalIav~iI~~~   28 (47)
T pfam04964         1 FLKDESGATAIEYGLIAALIAVVIIAYV   28 (47)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9656564159999999999999999999


No 5  
>COG4655 Predicted membrane protein [Function unknown]
Probab=95.56  E-value=0.11  Score=28.90  Aligned_cols=55  Identities=22%  Similarity=0.303  Sum_probs=46.6

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             7512445548999999999999999999999999999999999999999998528
Q gi|254780571|r   10 RFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE   64 (182)
Q Consensus        10 rf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~   64 (182)
                      -|+|.+|+.+-|--|+.+|+.+..+.-.+|+|+.+..++.+++.++-+|--.+..
T Consensus         3 g~~r~~rs~~gvltal~~~lal~~l~l~VD~G~l~leqR~LQ~~ADlAAiaAAs~   57 (565)
T COG4655           3 GWPRRQRSMVGVLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAASN   57 (565)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEHHHHHHHHHHHHHHHHHH
T ss_conf             4237676677899999999999988650220124411787888776998887762


No 6  
>pfam04917 Shufflon_N Bacterial shufflon protein, N-terminal constant region. This family represents the high-similarity N-terminal 'constant region' shared by shufflon proteins.
Probab=94.58  E-value=0.2  Score=27.27  Aligned_cols=49  Identities=22%  Similarity=0.266  Sum_probs=40.2

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1244554899999999999999999999999999999999999999999
Q gi|254780571|r   12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDM   60 (182)
Q Consensus        12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~   60 (182)
                      ||..||.+++|..+.+-++.+++++.+++-.-.......+.+++.+.++
T Consensus         2 r~~~kGf~LlE~~~~L~I~~~~~~~~~~~~~~~~~~~~~q~aA~q~~~v   50 (356)
T pfam04917         2 KKTDKGVSLLEVGAVLLIVVMVIPKVAENIEDYLNNVRWQNAAEHANTY   50 (356)
T ss_pred             CEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1203443089999999999999999999999899999999999999999


No 7  
>PRK10506 hypothetical protein; Provisional
Probab=93.40  E-value=0.39  Score=25.54  Aligned_cols=52  Identities=12%  Similarity=0.173  Sum_probs=45.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             2445548999999999999999999999999999999999999999998528
Q gi|254780571|r   13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE   64 (182)
Q Consensus        13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~   64 (182)
                      +.|+|.+.||+-+++-++-++....+--..-...+++|..++++...++.+.
T Consensus         2 ~~q~GFTLiEllvvi~ii~il~~~a~p~~~~~~q~~~L~~~a~~l~~fL~~~   53 (155)
T PRK10506          2 KKQRGYTLIETLVAMTLVVILSAWGLYGWQYWQQQQRLWQTAQQLRDFLLYL   53 (155)
T ss_pred             CCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8556627999999999999999887777999999999999999999999999


No 8  
>COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=90.82  E-value=1  Score=23.04  Aligned_cols=52  Identities=25%  Similarity=0.350  Sum_probs=44.2

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5124455489999999999999999999999999999999999999999985
Q gi|254780571|r   11 FLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVA   62 (182)
Q Consensus        11 f~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~   62 (182)
                      +|+..+|...+|+-+++-++=+|..-.+-.+.-....+++.+++++.+-.+.
T Consensus         3 ~r~~~rGfTL~ELliviAIlAIla~~A~P~fs~~i~~~rl~s~a~eL~a~l~   54 (181)
T COG4970           3 FRSRTRGFTLLELLIVLAILAILAVIAAPNFSQWIRSQRLRSAADELAAALQ   54 (181)
T ss_pred             CCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5414675049999999999999999851008888778789889999999999


No 9  
>pfam05307 Bundlin Bundlin. This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells.
Probab=89.53  E-value=0.79  Score=23.68  Aligned_cols=49  Identities=16%  Similarity=0.108  Sum_probs=41.5

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1244554899999999999999999999999999999999999999999
Q gi|254780571|r   12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDM   60 (182)
Q Consensus        12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~   60 (182)
                      ++-|+|.+.||-++++-+--.++.|++-+-.-....++.++|..+.+-.
T Consensus         8 kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~saq~snK~q~Ai~ei~s~   56 (97)
T pfam05307         8 KKYEKGLSLIESAMVLALAATVTAGVMFYYQSASDSNKAQNAISEVMSA   56 (97)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHHHHHHHH
T ss_conf             6675252199999999999999977510307456637999999999999


No 10 
>COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=85.27  E-value=0.56  Score=24.59  Aligned_cols=39  Identities=23%  Similarity=0.220  Sum_probs=29.0

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999751244554899999999999999999999999999
Q gi|254780571|r    7 YILRFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYT   45 (182)
Q Consensus         7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~   45 (182)
                      +.+...|.++|.+.||+-+-+.+=++++.+++.+.+...
T Consensus         4 ~~~~~~rrqrG~SLIELMIallIglivL~av~s~y~~sr   42 (318)
T COG4966           4 HRRARPRRQRGFSLIELMIALLIGLIVLLAVGSLYLSSR   42 (318)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHEEEEHH
T ss_conf             443554555774399999999999999997763034356


No 11 
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=77.18  E-value=2.7  Score=20.49  Aligned_cols=28  Identities=32%  Similarity=0.647  Sum_probs=19.7

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9975124455489999999999999999
Q gi|254780571|r    8 ILRFLSRENGVVAVEMAIILPILLLIYM   35 (182)
Q Consensus         8 lrrf~rd~~G~aaVEFAli~P~ll~ll~   35 (182)
                      +..|+++++|-..||+-|++.+.=.+++
T Consensus         4 ~~k~~~~~kgFTLvEMLiVLlIISiLlL   31 (107)
T COG4537           4 MKKFLKHKKGFTLVEMLIVLLIISILLL   31 (107)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             7777776326259999999999999999


No 12 
>KOG3970 consensus
Probab=74.78  E-value=2  Score=21.20  Aligned_cols=12  Identities=0%  Similarity=-0.111  Sum_probs=4.4

Q ss_pred             CCCCCCEEEEEE
Q ss_conf             779996799999
Q gi|254780571|r  128 IKDASTFIVRAE  139 (182)
Q Consensus       128 ~~~~~~~~v~v~  139 (182)
                      ...++..++..+
T Consensus       184 ~~sp~h~V~~m~  195 (299)
T KOG3970         184 YSSPNHDVTFMR  195 (299)
T ss_pred             CCCCCCCEEEEC
T ss_conf             878997047633


No 13 
>COG1681 FlaB Archaeal flagellins [Cell motility and secretion]
Probab=66.37  E-value=5  Score=18.86  Aligned_cols=53  Identities=13%  Similarity=0.095  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             445548999999999--99999999999999999999999999999999852888
Q gi|254780571|r   14 RENGVVAVEMAIILP--ILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETS   66 (182)
Q Consensus        14 d~~G~aaVEFAli~P--~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~~   66 (182)
                      ||||..-||-+|++-  +|..-.++.+-++..+|.+|+-+..-+++.+.++.+-.
T Consensus         1 ~rrG~~GIgtlIVfIAmVlVAAVaA~VlInt~g~lqQKa~~tg~e~t~qvsSgi~   55 (209)
T COG1681           1 DRRGATGIGTLIVFIAMVLVAAVAAYVLINTGGFLQQKAKATGEEGTQQVSSGIE   55 (209)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHEEECCEE
T ss_conf             9841104328999999999999999998653420224567775654513003359


No 14 
>pfam04021 Class_IIIsignal Class III signal peptide. This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase.
Probab=64.37  E-value=5.1  Score=18.80  Aligned_cols=22  Identities=14%  Similarity=0.495  Sum_probs=17.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             4554899999999999999999
Q gi|254780571|r   15 ENGVVAVEMAIILPILLLIYMA   36 (182)
Q Consensus        15 ~~G~aaVEFAli~P~ll~ll~~   36 (182)
                      +||+.++||.++.-.+++....
T Consensus         1 ~kGQ~SlE~~lLi~~vlv~~~i   22 (28)
T pfam04021         1 KKGQISLEFLLLILAVLVVAII   22 (28)
T ss_pred             CCCEEEHHHHHHHHHHHHHHHH
T ss_conf             9865439999999999999977


No 15 
>PRK10913 dipeptide transporter; Provisional
Probab=61.89  E-value=10  Score=16.91  Aligned_cols=32  Identities=13%  Similarity=0.318  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             4799999751244554899999999999999999
Q gi|254780571|r    3 CIKNYILRFLSRENGVVAVEMAIILPILLLIYMA   36 (182)
Q Consensus         3 ~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~   36 (182)
                      -++..+|||+||+.+  .+-+++++-++++-+|+
T Consensus        18 p~~~~w~r~~r~~~a--~~g~~il~~~~l~alfa   49 (300)
T PRK10913         18 PLQEFWHYFKRNKGA--VVGLVYVVIVLFIAIFA   49 (300)
T ss_pred             HHHHHHHHHHHCHHH--HHHHHHHHHHHHHHHHH
T ss_conf             899999998538799--99999999999999999


No 16 
>TIGR01708 typeII_sec_gspH general secretion pathway protein H; InterPro: IPR010053   This entry represents GspH, protein H of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=59.39  E-value=7.1  Score=17.94  Aligned_cols=50  Identities=16%  Similarity=0.290  Sum_probs=38.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHC
Q ss_conf             24455489999999999999999999999999-9999999999999999852
Q gi|254780571|r   13 SRENGVVAVEMAIILPILLLIYMAVYEITMLY-TLSKRLTRFASHMGDMVAQ   63 (182)
Q Consensus        13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~-~~~~~l~~A~~~~ar~~~~   63 (182)
                      +.+.|-+.||+-+++ +++.|+.+++-.++-- +....|++.++..++....
T Consensus         1 ~r~~GFtLiElLvVl-~i~gL~aa~~~~~l~~~~~~~~l~~~a~rl~~~l~~   51 (175)
T TIGR01708         1 HRQSGFTLIELLVVL-AIMGLVAAAAALSLDSASGTKELDQAAQRLAAELRL   51 (175)
T ss_pred             CCCCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             987751088999999-999999999961167788862178999999999999


No 17 
>COG1991 Uncharacterized conserved protein [Function unknown]
Probab=56.75  E-value=0.75  Score=23.79  Aligned_cols=30  Identities=20%  Similarity=0.486  Sum_probs=23.3

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999751244554899999999999999999
Q gi|254780571|r    7 YILRFLSRENGVVAVEMAIILPILLLIYMA   36 (182)
Q Consensus         7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~   36 (182)
                      ++..+..+.+|+...||.|++|+.++....
T Consensus         4 ~i~~~~~~nkgQiSLEf~Ll~l~ivla~~i   33 (131)
T COG1991           4 YITKIILSNKGQISLEFSLLLLAIVLAASI   33 (131)
T ss_pred             EEEEEEECCCCCEEEEHHHHHHHHHHHHHH
T ss_conf             662542246662564138999999997312


No 18 
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=49.37  E-value=17  Score=15.66  Aligned_cols=49  Identities=10%  Similarity=0.122  Sum_probs=31.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2445548999999999999999999999999999999999999999998
Q gi|254780571|r   13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMV   61 (182)
Q Consensus        13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~   61 (182)
                      +.|+|-+.||.-+++-++=++...++--.......+....+.....+.+
T Consensus         5 ~~qrGFTLiElLVvl~Iigil~~~~~p~~~~~~~~~~~~~~~~~~~~~~   53 (149)
T COG2165           5 KKQRGFTLIELLVVLAIIGILAALALPSLQGSIDKAKRLEAAQQALRVI   53 (149)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1456738999999999999999999999999889999999999999999


No 19 
>PRK10332 hypothetical protein; Provisional
Probab=47.57  E-value=18  Score=15.49  Aligned_cols=54  Identities=15%  Similarity=0.103  Sum_probs=35.1

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             124455489999999999999999999999999999999999999999985288
Q gi|254780571|r   12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQET   65 (182)
Q Consensus        12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~   65 (182)
                      .++++|-+..|.-+.+.+|.+.+.|...+-.+....=....=-+++=|++-+..
T Consensus         5 l~~Q~GFSLpEvlvA~lLf~isl~aL~~Yqq~L~~sf~~~~Q~rQ~Wr~a~qq~   58 (107)
T PRK10332          5 LKNQRGFSLPEVLLAMVLMVMIVTALSGYQRTLMNSFASRNQYQQLWRHAWQQT   58 (107)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             213678872999999999999999999999999999999999999999999861


No 20 
>pfam11688 DUF3285 Protein of unknown function (DUF3285). This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=38.47  E-value=25  Score=14.63  Aligned_cols=34  Identities=12%  Similarity=0.192  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             479999975124455489999999999999999999999
Q gi|254780571|r    3 CIKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYEIT   41 (182)
Q Consensus         3 ~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~   41 (182)
                      +|||+.|+     .|.+...|.|.+.-|+.++.++.-++
T Consensus        11 AMRNMVRK-----g~~SL~HF~LT~~gll~~lv~la~l~   44 (45)
T pfam11688        11 AMRNMVRK-----GGKSLLHFGLTALGLLGFLVLIAYLG   44 (45)
T ss_pred             HHHHHHHH-----CCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999980-----68400568999999999999999952


No 21 
>pfam12273 RCR Chitin synthesis regulation, resistance to Congo red. RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5.
Probab=35.21  E-value=28  Score=14.32  Aligned_cols=16  Identities=25%  Similarity=0.515  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780571|r   22 EMAIILPILLLIYMAV   37 (182)
Q Consensus        22 EFAli~P~ll~ll~~~   37 (182)
                      -|||++..+|+++|+.
T Consensus         4 ~fav~i~~~~i~~f~~   19 (124)
T pfam12273         4 LFAIFIIALLILFFLT   19 (124)
T ss_pred             EHHHHHHHHHHHHHHH
T ss_conf             0899999999999999


No 22 
>TIGR01247 drrB daunorubicin resistance ABC transporter membrane protein; InterPro: IPR005942   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents the Daunorubicin resistance ABC transporter membrane protein, which is associated with the effux of the drug daunorubicin and found in bacteria and archaea. It functions as an ATP dependent antiporter. In eukaryotes proteins of similar function include p-glyco-proteins and a multidrug resistance protein..
Probab=35.11  E-value=25  Score=14.61  Aligned_cols=27  Identities=26%  Similarity=0.555  Sum_probs=17.4

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             997512445548999999999999999999
Q gi|254780571|r    8 ILRFLSRENGVVAVEMAIILPILLLIYMAV   37 (182)
Q Consensus         8 lrrf~rd~~G~aaVEFAli~P~ll~ll~~~   37 (182)
                      +|||.|.+.=+   ==.++-|++.+++||.
T Consensus         3 lKRF~R~rsRi---~gsi~nPL~WLifFG~   29 (240)
T TIGR01247         3 LKRFIRSRSRI---VGSILNPLLWLIFFGK   29 (240)
T ss_pred             CCHHHCCHHHH---HHHHHHHHHHHHHHHH
T ss_conf             42230235789---9989768999999700


No 23 
>PRK08541 flagellin; Validated
Probab=34.04  E-value=30  Score=14.20  Aligned_cols=51  Identities=18%  Similarity=0.176  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             44554899999999--9999999999999999999999999999999998528
Q gi|254780571|r   14 RENGVVAVEMAIIL--PILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE   64 (182)
Q Consensus        14 d~~G~aaVEFAli~--P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~   64 (182)
                      ++||+.-||-+|++  .+|..-+++.+=+.-.++.+++.+...++..+.++.+
T Consensus         1 ~kkG~~GigtlIVfIAmVlVAAvaa~Vli~t~g~lqqka~~tg~~s~~qvasg   53 (212)
T PRK08541          1 MKKGAVGIGTLIVFIAMVLVAAVAASVLINTSGYLQQKASATGRETTQQVASG   53 (212)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             97530242089999999999998775232211455577777656578865155


No 24 
>COG4726 PilX Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=32.62  E-value=31  Score=14.06  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=19.9

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99975124455489999999999999999999999
Q gi|254780571|r    7 YILRFLSRENGVVAVEMAIILPILLLIYMAVYEIT   41 (182)
Q Consensus         7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~   41 (182)
                      +.+|-.|.|||.+.|---+++.++-++-++.+-..
T Consensus         4 m~~r~~r~qRG~~LivvL~~LvvltLl~l~~~r~~   38 (196)
T COG4726           4 MLIRGSRRQRGFALIVVLMVLVVLTLLGLAAARSV   38 (196)
T ss_pred             CCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66787645676473899999999999999999999


No 25 
>PRK10574 putative major pilin subunit; Provisional
Probab=28.39  E-value=37  Score=13.62  Aligned_cols=46  Identities=13%  Similarity=0.239  Sum_probs=25.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2445548999999999999999999999999999999999999999
Q gi|254780571|r   13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMG   58 (182)
Q Consensus        13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~a   58 (182)
                      .+|+|...||.-++.-++=.|..-.+-.-.-+..+.++..+...++
T Consensus         2 ~~q~gftLiElmivvaii~il~~ia~p~y~~y~~~a~~~~~l~~~~   47 (146)
T PRK10574          2 TKQRGFTLIELMVVIGIIAILSAIGIPAYQNYLRKAALTDMLQTFV   47 (146)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7556816589999999999999999999999999999999999878


No 26 
>COG5605 Predicted small integral membrane protein [Function unknown]
Probab=27.60  E-value=38  Score=13.54  Aligned_cols=24  Identities=38%  Similarity=0.509  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999
Q gi|254780571|r   20 AVEMAIILPILLLIYMAVYEITML   43 (182)
Q Consensus        20 aVEFAli~P~ll~ll~~~~e~~~~   43 (182)
                      |.-.|++.|+++++.|...-.+.+
T Consensus        77 al~yaiilppllvlvfv~lmv~ea  100 (115)
T COG5605          77 ALVYAIILPPLLVLVFVVLMVAEA  100 (115)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999850799999999999985


No 27 
>PRK09881 ATP-dependent peptide transporter membrane subunit; Provisional
Probab=24.32  E-value=44  Score=13.17  Aligned_cols=31  Identities=16%  Similarity=0.239  Sum_probs=16.9

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999997512445548999999999999999999
Q gi|254780571|r    5 KNYILRFLSRENGVVAVEMAIILPILLLIYMAV   37 (182)
Q Consensus         5 ~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~   37 (182)
                      .++++|||||..+.  +-+.+++.++++.+|+-
T Consensus        21 ~~~~~~~~r~~~a~--~g~~il~~~~l~ai~~p   51 (296)
T PRK09881         21 AKLVWMLKGSPLTV--TGAVIIVLMLLMMIFSP   51 (296)
T ss_pred             HHHHHHHHHCHHHH--HHHHHHHHHHHHHHHHH
T ss_conf             19999983188999--99999999999999999


No 28 
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=23.56  E-value=45  Score=13.08  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=14.7

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             997512445548999999999999999
Q gi|254780571|r    8 ILRFLSRENGVVAVEMAIILPILLLIY   34 (182)
Q Consensus         8 lrrf~rd~~G~aaVEFAli~P~ll~ll   34 (182)
                      |||++|..--..++=..+++|+|+..+
T Consensus         3 ~k~~~~~~~~~~~~~~~~liP~ly~~~   29 (164)
T TIGR03061         3 LKRLRKNKLLRIALIAIMLIPLLYGGL   29 (164)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             788763828999999999999999999


No 29 
>KOG2856 consensus
Probab=22.17  E-value=48  Score=12.91  Aligned_cols=19  Identities=16%  Similarity=0.146  Sum_probs=13.1

Q ss_pred             CCCCCEEEEEEEEEEEEEC
Q ss_conf             7999679999999962311
Q gi|254780571|r  129 KDASTFIVRAEVSINYRTL  147 (182)
Q Consensus       129 ~~~~~~~v~v~v~y~y~p~  147 (182)
                      ...+...|.|++-|+|.+-
T Consensus       408 ~a~~g~~v~vraLYDY~gq  426 (472)
T KOG2856         408 DAKGGDFVRVRALYDYAGQ  426 (472)
T ss_pred             CCCCCCEEEEEEEECCCCC
T ss_conf             2347751567764125764


Done!