Query         gi|254780572|ref|YP_003064985.1| hypothetical protein CLIBASIA_02295 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 192
No_of_seqs    106 out of 485
Neff          8.8 
Searched_HMMs 39220
Date          Sun May 29 21:56:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780572.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-21 3.1E-26  126.5  13.6  152    2-168     5-157 (185)
  2 pfam07811 TadE TadE-like prote  99.3 9.4E-12 2.4E-16   77.1   6.1   43   18-60      1-43  (43)
  3 COG3847 Flp Flp pilus assembly  97.8 3.3E-05 8.4E-10   44.3   4.3   34    7-40      3-36  (58)
  4 pfam04964 Flp_Fap Flp/Fap pili  96.6   0.002 5.1E-08   35.4   3.6   28   12-39      1-28  (47)
  5 COG4655 Predicted membrane pro  95.4   0.017 4.4E-07   30.8   3.4   71   10-85      2-72  (565)
  6 pfam04917 Shufflon_N Bacterial  94.2     0.3 7.6E-06   24.6   9.2   48   13-60      2-49  (356)
  7 pfam05307 Bundlin Bundlin. Thi  93.5    0.24 6.1E-06   25.0   5.8   55    1-60      1-55  (97)
  8 COG4966 PilW Tfp pilus assembl  83.1     2.2 5.7E-05   20.2   4.4   38   10-47      6-43  (318)
  9 COG4537 ComGC Competence prote  81.8     1.6   4E-05   21.0   3.2   29    8-36      3-31  (107)
 10 PRK10506 hypothetical protein;  81.4     3.3 8.3E-05   19.4   6.9   49   14-62      2-50  (155)
 11 COG1681 FlaB Archaeal flagelli  69.6       4  0.0001   18.9   2.5   49   15-63      1-51  (209)
 12 COG4970 FimT Tfp pilus assembl  69.5     7.2 0.00018   17.7   6.3   49   13-61      4-52  (181)
 13 pfam04021 Class_IIIsignal Clas  69.0     3.5   9E-05   19.2   2.2   21   16-36      1-21  (28)
 14 TIGR01708 typeII_sec_gspH gene  51.6      16  0.0004   15.9   3.2   50   14-64      1-51  (175)
 15 COG1991 Uncharacterized conser  48.7     6.7 0.00017   17.8   0.7   27   11-37      7-33  (131)
 16 pfam12273 RCR Chitin synthesis  37.1      28 0.00071   14.7   2.7   17   23-39      4-20  (124)
 17 COG2165 PulG Type II secretory  35.8      29 0.00074   14.6   7.3   50   13-62      4-53  (149)
 18 PRK11089 glucose-specific PTS   32.6      33 0.00085   14.3   3.9   14    1-14      1-14  (477)
 19 TIGR01247 drrB daunorubicin re  28.3      30 0.00075   14.6   1.3   28    8-38      2-29  (240)
 20 COG4726 PilX Tfp pilus assembl  22.3      53  0.0013   13.3   4.9   30    8-42      4-33  (196)
 21 COG5605 Predicted small integr  20.7      57  0.0015   13.2   4.1   22   20-41     76-97  (115)
 22 PRK08541 flagellin; Validated   20.7      57  0.0015   13.2   4.0   49   15-63      1-51  (212)
 23 pfam09185 DUF1948 Domain of un  20.3      55  0.0014   13.2   1.4   30   13-42      2-31  (140)

No 1  
>COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion]
Probab=99.88  E-value=1.2e-21  Score=126.48  Aligned_cols=152  Identities=24%  Similarity=0.282  Sum_probs=94.4

Q ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCHHHHHH
Q ss_conf             03578988875202366459999999999999999999999999999999999999988874134457787-78899999
Q gi|254780572|r    2 RKKLLQGIRRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKIRTGEISSKNT-HSLTEFRR   80 (192)
Q Consensus         2 ~~~l~~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~~tg~~~~~~~-~~~~~~~~   80 (192)
                      ++.+....|||+|||+|++||||||++|+||+++||++|+|++++.++.+++|++.++|.+++++...... ....++..
T Consensus         5 ~~~~~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve~~~~~~~~~~l~~a~d~aara~~~~~~~~~~~~~~~~~~~~   84 (185)
T COG4961           5 RRGLRGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVEFGIAFLAKQSLQNAADAAARAAARGLTTDAADLDTIQAAAT   84 (185)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf             26579999988764876899999999999999999999999999999999999999999998507644202567789999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEECCCH
Q ss_conf             99864211003344432233315898651268432553465555667766556676534689997189999999801000
Q gi|254780572|r   81 VFCNDLRVLFNCSENEIGRPYDLYLDVKQIKSLQEITETVPRKDKSDSSSEIDDRNFSFHPGGPSTYNVLRAYYHWPLFT  160 (192)
Q Consensus        81 ~i~~~~~~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~iv~v~v~y~~~~~~  160 (192)
                      ..|+.......+............++......  .....             +.......+..+..+...+..+.++.+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~--~~~~~-------------~~~~~~v~~~~~~~~~~~~~~~~~~~v~  149 (185)
T COG4961          85 AFLNAIAPANAFLTVQSNTPSRGTVTVTANVA--DATLF-------------DTSQFTVTSAVTVSINLARGLVLVAVVP  149 (185)
T ss_pred             HHHHHHCCCCEEECCCCCCCCCEEEEEECCCC--CCCCC-------------CCCCEEEEECCCCEEECCCCCCEEEEEE
T ss_conf             88875164220121322455640589601312--34336-------------7763589614542020123553057873


Q ss_pred             HHHHHHHH
Q ss_conf             01355554
Q gi|254780572|r  161 DLMRQYIS  168 (192)
Q Consensus       161 p~~~~~l~  168 (192)
                      ++.++...
T Consensus       150 ~~t~~~~~  157 (185)
T COG4961         150 DLTGPGTS  157 (185)
T ss_pred             CCCCCCCC
T ss_conf             23476445


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=99.26  E-value=9.4e-12  Score=77.07  Aligned_cols=43  Identities=40%  Similarity=0.657  Sum_probs=42.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6459999999999999999999999999999999999999988
Q gi|254780572|r   18 GAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR   60 (192)
Q Consensus        18 G~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR   60 (192)
                      |+++|||++++|+|++++++++|+|+++++++.+++|+++++|
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=3.3e-05  Score=44.35  Aligned_cols=34  Identities=24%  Similarity=0.314  Sum_probs=28.3

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9888752023664599999999999999999999
Q gi|254780572|r    7 QGIRRSILIREGAVAIEFAILVMPYFMLVFAILE   40 (192)
Q Consensus         7 ~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E   40 (192)
                      +.++||+|||+|+++||.+|++-+.-+.+.+.+.
T Consensus         3 ~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~   36 (58)
T COG3847           3 KLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGS   36 (58)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7899997745651899999999999999999999


No 4  
>pfam04964 Flp_Fap Flp/Fap pilin component.
Probab=96.63  E-value=0.002  Score=35.42  Aligned_cols=28  Identities=21%  Similarity=0.358  Sum_probs=22.7

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5202366459999999999999999999
Q gi|254780572|r   12 SILIREGAVAIEFAILVMPYFMLVFAIL   39 (192)
Q Consensus        12 ~~~d~rG~aaVEFAlv~p~ll~l~~g~~   39 (192)
                      |+|||+|++|||.+|++-+.-+.+.+..
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=95.35  E-value=0.017  Score=30.76  Aligned_cols=71  Identities=10%  Similarity=0.020  Sum_probs=53.8

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             8752023664599999999999999999999999999999999999999888741344577877889999999864
Q gi|254780572|r   10 RRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKIRTGEISSKNTHSLTEFRRVFCND   85 (192)
Q Consensus        10 rr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~~tg~~~~~~~~~~~~~~~~i~~~   85 (192)
                      ..|.|.+|+.+-|--|+.+|+.+..+.-.+|.|+++..++.||+.++.+|-...     +.-...+....+.+.++
T Consensus         2 ~g~~r~~rs~~gvltal~~~lal~~l~l~VD~G~l~leqR~LQ~~ADlAAiaAA-----s~~~~~~~Av~~sf~~n   72 (565)
T COG4655           2 NGWPRRQRSMVGVLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAA-----SNLDDAEQAVQTSFTQN   72 (565)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEHHHHHHHHHHHHHHHH-----HHCCCHHHHHHHHHHHC
T ss_conf             842376766778999999999999886502201244117878887769988877-----62798889999999866


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=94.17  E-value=0.3  Score=24.55  Aligned_cols=48  Identities=13%  Similarity=0.153  Sum_probs=37.5

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             202366459999999999999999999999999999999999999988
Q gi|254780572|r   13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR   60 (192)
Q Consensus        13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR   60 (192)
                      +|+.||.+.+|..+++.++.+++++.+++-.-......-+.+++...+
T Consensus         2 r~~~kGf~LlE~~~~L~I~~~~~~~~~~~~~~~~~~~~~q~aA~q~~~   49 (356)
T pfam04917         2 KKTDKGVSLLEVGAVLLIVVMVIPKVAENIEDYLNNVRWQNAAEHANT   49 (356)
T ss_pred             CEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             120344308999999999999999999999989999999999999999


No 7  
>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=93.50  E-value=0.24  Score=25.03  Aligned_cols=55  Identities=16%  Similarity=0.124  Sum_probs=45.0

Q ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             903578988875202366459999999999999999999999999999999999999988
Q gi|254780572|r    1 MRKKLLQGIRRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR   60 (192)
Q Consensus         1 m~~~l~~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR   60 (192)
                      |..++.+     .+-|+|.+.+|-++|+-+--.++.|++-+=......++.|+|..+.+-
T Consensus         1 ~~~~~~n-----kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~saq~snK~q~Ai~ei~s   55 (97)
T pfam05307         1 MVSKIMN-----KKYEKGLSLIESAMVLALAATVTAGVMFYYQSASDSNKAQNAISEVMS   55 (97)
T ss_pred             CCHHHHH-----HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHHHHHHH
T ss_conf             9337530-----667525219999999999999997751030745663799999999999


No 8  
>COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=83.13  E-value=2.2  Score=20.19  Aligned_cols=38  Identities=21%  Similarity=0.227  Sum_probs=29.6

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             87520236645999999999999999999999999999
Q gi|254780572|r   10 RRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTA   47 (192)
Q Consensus        10 rr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~   47 (192)
                      ++..|++||.+.|||-+.+.+=++++.+++.+-+....
T Consensus         6 ~~~~rrqrG~SLIELMIallIglivL~av~s~y~~sr~   43 (318)
T COG4966           6 RARPRRQRGFSLIELMIALLIGLIVLLAVGSLYLSSRQ   43 (318)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHEEEEHHH
T ss_conf             35545557743999999999999999977630343567


No 9  
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=81.85  E-value=1.6  Score=20.97  Aligned_cols=29  Identities=14%  Similarity=0.360  Sum_probs=21.9

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             88875202366459999999999999999
Q gi|254780572|r    8 GIRRSILIREGAVAIEFAILVMPYFMLVF   36 (192)
Q Consensus         8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~   36 (192)
                      .+..++++++|-+.||+-+|+.+.-.|++
T Consensus         3 ~~~k~~~~~kgFTLvEMLiVLlIISiLlL   31 (107)
T COG4537           3 KMKKFLKHKKGFTLVEMLIVLLIISILLL   31 (107)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             67777776326259999999999999999


No 10 
>PRK10506 hypothetical protein; Provisional
Probab=81.41  E-value=3.3  Score=19.37  Aligned_cols=49  Identities=14%  Similarity=-0.044  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0236645999999999999999999999999999999999999998887
Q gi|254780572|r   14 LIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKI   62 (192)
Q Consensus        14 ~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~   62 (192)
                      ++|+|-+.||.-+++-++-+|....+--=.....++.|..++++....+
T Consensus         2 ~~q~GFTLiEllvvi~ii~il~~~a~p~~~~~~q~~~L~~~a~~l~~fL   50 (155)
T PRK10506          2 KKQRGYTLIETLVAMTLVVILSAWGLYGWQYWQQQQRLWQTAQQLRDFL   50 (155)
T ss_pred             CCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8556627999999999999999887777999999999999999999999


No 11 
>COG1681 FlaB Archaeal flagellins [Cell motility and secretion]
Probab=69.55  E-value=4  Score=18.94  Aligned_cols=49  Identities=18%  Similarity=0.171  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23664599999999999999--99999999999999999999999988874
Q gi|254780572|r   15 IREGAVAIEFAILVMPYFML--VFAILEISLSFTAGQLFESAAYDVARKIR   63 (192)
Q Consensus        15 d~rG~aaVEFAlv~p~ll~l--~~g~~E~g~~~~~~~~l~~A~~~aaR~~~   63 (192)
                      ||||..=+|=++|+..|.++  +++-+=++...|.+++-+...+++.+.+.
T Consensus         1 ~rrG~~GIgtlIVfIAmVlVAAVaA~VlInt~g~lqQKa~~tg~e~t~qvs   51 (209)
T COG1681           1 DRRGATGIGTLIVFIAMVLVAAVAAYVLINTGGFLQQKAKATGEEGTQQVS   51 (209)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHEEE
T ss_conf             984110432899999999999999999865342022456777565451300


No 12 
>COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=69.52  E-value=7.2  Score=17.66  Aligned_cols=49  Identities=18%  Similarity=0.120  Sum_probs=37.6

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2023664599999999999999999999999999999999999999888
Q gi|254780572|r   13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARK   61 (192)
Q Consensus        13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~   61 (192)
                      +++.+|.+.+|.-+++-++-+|..-.+--....+..+.+++++.+-+-.
T Consensus         4 r~~~rGfTL~ELliviAIlAIla~~A~P~fs~~i~~~rl~s~a~eL~a~   52 (181)
T COG4970           4 RSRTRGFTLLELLIVLAILAILAVIAAPNFSQWIRSQRLRSAADELAAA   52 (181)
T ss_pred             CCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4146750499999999999999998510088887787898899999999


No 13 
>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=68.99  E-value=3.5  Score=19.20  Aligned_cols=21  Identities=19%  Similarity=0.716  Sum_probs=16.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHH
Q ss_conf             366459999999999999999
Q gi|254780572|r   16 REGAVAIEFAILVMPYFMLVF   36 (192)
Q Consensus        16 ~rG~aaVEFAlv~p~ll~l~~   36 (192)
                      +||+.++||.++.-.+++...
T Consensus         1 ~kGQ~SlE~~lLi~~vlv~~~   21 (28)
T pfam04021         1 KKGQISLEFLLLILAVLVVAI   21 (28)
T ss_pred             CCCEEEHHHHHHHHHHHHHHH
T ss_conf             986543999999999999997


No 14 
>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=51.58  E-value=16  Score=15.94  Aligned_cols=50  Identities=24%  Similarity=0.287  Sum_probs=39.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             02366459999999999999999999999999-9999999999999888741
Q gi|254780572|r   14 LIREGAVAIEFAILVMPYFMLVFAILEISLSF-TAGQLFESAAYDVARKIRT   64 (192)
Q Consensus        14 ~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~-~~~~~l~~A~~~aaR~~~t   64 (192)
                      +.+.|-+.||.-+|+. ++.|+-+++-.++.- +....|+..+++-++.+++
T Consensus         1 ~r~~GFtLiElLvVl~-i~gL~aa~~~~~l~~~~~~~~l~~~a~rl~~~l~~   51 (175)
T TIGR01708         1 HRQSGFTLIELLVVLA-IMGLVAAAAALSLDSASGTKELDQAAQRLAAELRL   51 (175)
T ss_pred             CCCCCCCHHHHHHHHH-HHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9877510889999999-99999999961167788862178999999999999


No 15 
>COG1991 Uncharacterized conserved protein [Function unknown]
Probab=48.69  E-value=6.7  Score=17.80  Aligned_cols=27  Identities=22%  Similarity=0.530  Sum_probs=21.6

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             752023664599999999999999999
Q gi|254780572|r   11 RSILIREGAVAIEFAILVMPYFMLVFA   37 (192)
Q Consensus        11 r~~~d~rG~aaVEFAlv~p~ll~l~~g   37 (192)
                      .+..+.||+...||.|++|..++....
T Consensus         7 ~~~~~nkgQiSLEf~Ll~l~ivla~~i   33 (131)
T COG1991           7 KIILSNKGQISLEFSLLLLAIVLAASI   33 (131)
T ss_pred             EEEECCCCCEEEEHHHHHHHHHHHHHH
T ss_conf             542246662564138999999997312


No 16 
>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=37.10  E-value=28  Score=14.72  Aligned_cols=17  Identities=29%  Similarity=0.610  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780572|r   23 EFAILVMPYFMLVFAIL   39 (192)
Q Consensus        23 EFAlv~p~ll~l~~g~~   39 (192)
                      =||+++..+|+++|+++
T Consensus         4 ~fav~i~~~~i~~f~~~   20 (124)
T pfam12273         4 LFAIFIIALLILFFLTA   20 (124)
T ss_pred             EHHHHHHHHHHHHHHHH
T ss_conf             08999999999999999


No 17 
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=35.83  E-value=29  Score=14.62  Aligned_cols=50  Identities=18%  Similarity=0.048  Sum_probs=33.6

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20236645999999999999999999999999999999999999998887
Q gi|254780572|r   13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKI   62 (192)
Q Consensus        13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~   62 (192)
                      .+.|||-+.+|.-+++.++-++...++---.....+...+.+.....+.+
T Consensus         4 ~~~qrGFTLiElLVvl~Iigil~~~~~p~~~~~~~~~~~~~~~~~~~~~~   53 (149)
T COG2165           4 MKKQRGFTLIELLVVLAIIGILAALALPSLQGSIDKAKRLEAAQQALRVI   53 (149)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             41456738999999999999999999999999889999999999999999


No 18 
>PRK11089 glucose-specific PTS system IIBC components; Provisional
Probab=32.59  E-value=33  Score=14.33  Aligned_cols=14  Identities=14%  Similarity=0.133  Sum_probs=5.3

Q ss_pred             CCHHHHHHHHHHHC
Q ss_conf             90357898887520
Q gi|254780572|r    1 MRKKLLQGIRRSIL   14 (192)
Q Consensus         1 m~~~l~~~lrr~~~   14 (192)
                      |++++++.+.||.|
T Consensus         1 m~~~~~~~lQk~gk   14 (477)
T PRK11089          1 MFKNAFANLQKVGK   14 (477)
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             92669999999677


No 19 
>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=28.27  E-value=30  Score=14.59  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=16.9

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8887520236645999999999999999999
Q gi|254780572|r    8 GIRRSILIREGAVAIEFAILVMPYFMLVFAI   38 (192)
Q Consensus         8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~   38 (192)
                      .+|||.|.|+=++.   .++-|++.+++||.
T Consensus         2 elKRF~R~rsRi~g---si~nPL~WLifFG~   29 (240)
T TIGR01247         2 ELKRFIRSRSRIVG---SILNPLLWLIFFGK   29 (240)
T ss_pred             CCCHHHCCHHHHHH---HHHHHHHHHHHHHH
T ss_conf             64223023578999---89768999999700


No 20 
>COG4726 PilX Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.26  E-value=53  Score=13.33  Aligned_cols=30  Identities=20%  Similarity=0.310  Sum_probs=16.1

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             88875202366459999999999999999999999
Q gi|254780572|r    8 GIRRSILIREGAVAIEFAILVMPYFMLVFAILEIS   42 (192)
Q Consensus         8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g   42 (192)
                      +.+|..|.|||.+.|     ..++++++++++-++
T Consensus         4 m~~r~~r~qRG~~Li-----vvL~~LvvltLl~l~   33 (196)
T COG4726           4 MLIRGSRRQRGFALI-----VVLMVLVVLTLLGLA   33 (196)
T ss_pred             CCCCCCCCCCCEEEH-----HHHHHHHHHHHHHHH
T ss_conf             667876456764738-----999999999999999


No 21 
>COG5605 Predicted small integral membrane protein [Function unknown]
Probab=20.66  E-value=57  Score=13.15  Aligned_cols=22  Identities=36%  Similarity=0.798  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5999999999999999999999
Q gi|254780572|r   20 VAIEFAILVMPYFMLVFAILEI   41 (192)
Q Consensus        20 aaVEFAlv~p~ll~l~~g~~E~   41 (192)
                      -|.-.|+++||+++++|-..-.
T Consensus        76 lal~yaiilppllvlvfv~lmv   97 (115)
T COG5605          76 LALVYAIILPPLLVLVFVVLMV   97 (115)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999850799999999999


No 22 
>PRK08541 flagellin; Validated
Probab=20.66  E-value=57  Score=13.15  Aligned_cols=49  Identities=20%  Similarity=0.255  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23664599999999999999--99999999999999999999999988874
Q gi|254780572|r   15 IREGAVAIEFAILVMPYFML--VFAILEISLSFTAGQLFESAAYDVARKIR   63 (192)
Q Consensus        15 d~rG~aaVEFAlv~p~ll~l--~~g~~E~g~~~~~~~~l~~A~~~aaR~~~   63 (192)
                      +|||+.=+|=++|+..|+++  +++-+=++-..+-+++-+...+++...+.
T Consensus         1 ~kkG~~GigtlIVfIAmVlVAAvaa~Vli~t~g~lqqka~~tg~~s~~qva   51 (212)
T PRK08541          1 MKKGAVGIGTLIVFIAMVLVAAVAASVLINTSGYLQQKASATGRETTQQVA   51 (212)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHH
T ss_conf             975302420899999999999987752322114555777776565788651


No 23 
>pfam09185 DUF1948 Domain of unknown function (DUF1948). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined.
Probab=20.27  E-value=55  Score=13.23  Aligned_cols=30  Identities=7%  Similarity=0.119  Sum_probs=18.7

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             202366459999999999999999999999
Q gi|254780572|r   13 ILIREGAVAIEFAILVMPYFMLVFAILEIS   42 (192)
Q Consensus        13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g   42 (192)
                      .|.||-.|.|||.+.+..|+---.-.++..
T Consensus         2 trtqrriaivefifa~lfflpk~ad~iqa~   31 (140)
T pfam09185         2 TRTQRRIAIVEFIFALLFFLPKEADQIQAA   31 (140)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             522455779999999999774518899999


Done!