Query         gi|254780520|ref|YP_003064933.1| flagellar basal body rod modification protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs    110 out of 613
Neff          5.5 
Searched_HMMs 39220
Date          Sun May 29 22:51:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780520.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK06009 flgD flagellar basal  100.0 2.2E-38 5.7E-43  241.2  16.3  120   11-130    16-135 (135)
  2 PRK09618 flgD flagellar basal  100.0 1.5E-35 3.9E-40  224.8  15.7  118   14-131    19-143 (146)
  3 PRK11911 flgD flagellar basal  100.0 2.8E-35 7.1E-40  223.3  16.0  128    3-130     4-140 (140)
  4 PRK12812 flgD flagellar basal  100.0 3.8E-32 9.7E-37  205.2  13.0   76   17-92     38-116 (259)
  5 PRK12634 flgD flagellar basal  100.0 1.4E-31 3.6E-36  202.0  14.5   82   13-94     17-101 (221)
  6 PRK06792 flgD flagellar basal  100.0 1.3E-31 3.3E-36  202.2  13.8  114   18-131    46-165 (190)
  7 COG1843 FlgD Flagellar hook ca 100.0 1.9E-31 4.8E-36  201.2  13.0   90   16-105    22-114 (222)
  8 PRK12813 flgD flagellar basal  100.0 2.4E-30 6.2E-35  194.8  14.4   75   18-92     25-102 (223)
  9 pfam03963 FlgD Flagellar hook  100.0 2.2E-30 5.6E-35  195.1  14.0   80   18-97     21-103 (140)
 10 PRK12633 flgD flagellar basal  100.0 2.1E-30 5.4E-35  195.2  12.6   82   16-97     19-103 (230)
 11 PRK06655 flgD flagellar basal  100.0 3.9E-30 9.9E-35  193.7  12.6   80   18-97     26-108 (225)
 12 PRK05842 flgD flagellar basal  100.0 3.1E-30 7.9E-35  194.2  11.4   66   11-76     15-80  (269)
 13 PRK09619 flgD flagellar basal  100.0 3.1E-29 7.8E-34  188.5  12.8   78   19-96     26-106 (220)
 14 TIGR02004 PTS-IIBC-malX PTS sy  66.6     4.1  0.0001   20.5   2.1   29   29-57    259-291 (540)
 15 pfam11562 EDC3_LSm Enhancer of  33.1      37 0.00095   15.0   3.8   24   82-105     2-29  (84)
 16 KOG2830 consensus               31.6      16 0.00041   17.1   0.4   39   22-69     29-67  (324)
 17 COG1873 Protein implicated in   29.5      43  0.0011   14.6   6.4   52   80-131     6-72  (87)
 18 pfam10842 DUF2642 Protein of u  24.6      48  0.0012   14.3   1.9   24   82-105    16-41  (66)
 19 cd00213 S-100 S-100: S-100 dom  22.3      59  0.0015   13.8   2.8   25   14-38     18-42  (88)
 20 pfam10748 DUF2531 Protein of u  22.0      46  0.0012   14.4   1.3   20   38-57     18-37  (133)
 21 pfam05239 PRC PRC-barrel domai  21.7      60  0.0015   13.7   4.2   38   81-118     5-44  (77)

No 1  
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=100.00  E-value=2.2e-38  Score=241.20  Aligned_cols=120  Identities=44%  Similarity=0.690  Sum_probs=112.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEE
Q ss_conf             55555667733338899999999983299899988978999999999999999999999999999999764553226146
Q gi|254780520|r   11 QQEFSKSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLKSNNLAQASSYIGKNI   90 (131)
Q Consensus        11 ~~~~~~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~~~~~~~a~sliGk~V   90 (131)
                      ...++....+..||+|+|||||++||+||||++|||++||++|||||++|||+.++|+.|+.++.++++.+|++||||+|
T Consensus        16 ~~~s~s~~~~~~l~~d~Fl~Ll~aQl~nQDP~~P~d~~e~~~QlAqfs~lEq~~~~n~~l~~ll~~~~l~qA~~lIGktV   95 (135)
T PRK06009         16 ASSSTSAANKATVNYDSFLQLLVAQMKNQDPTQPMDSTQYMSQLATFSQVEQSVQTNSKLDTLLASSSLSQAEGLIGRTV   95 (135)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEE
T ss_conf             66665554313269999999999998348989999879999999999999999999999999999888887887628079


Q ss_pred             ECCCCEEEEEEEEEEECCCCEEEEEECCEEEECCCCEEEE
Q ss_conf             6389718999978886279669999789789623105860
Q gi|254780520|r   91 TNADGSISGVVNAIQVSSTGLTAITVDNTEIPITTGIRIS  130 (131)
Q Consensus        91 ~~~~~~~~G~v~~V~~~~~g~~~~~v~~~~v~~~~v~~V~  130 (131)
                      +..||.++|+|++|++.++|.+....+|++|++..+++|+
T Consensus        96 t~~Dg~vtG~V~sV~~~~dg~~a~l~dG~~v~~~~gv~is  135 (135)
T PRK06009         96 TSADGSITGVVKSVTIYSDGIIATLEDGKKVLLGPGVTIS  135 (135)
T ss_pred             ECCCCEEEEEEEEEEEECCCEEEEEECCCEEEECCCCEEC
T ss_conf             7079748999999999389449998389889837871619


No 2  
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=100.00  E-value=1.5e-35  Score=224.85  Aligned_cols=118  Identities=34%  Similarity=0.541  Sum_probs=104.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCCEE
Q ss_conf             55667733338899999999983299899988978999999999999999999999999999---999764553226146
Q gi|254780520|r   14 FSKSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLK---SNNLAQASSYIGKNI   90 (131)
Q Consensus        14 ~~~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~---~~~~~~a~sliGk~V   90 (131)
                      ..+..++++||||+|||||+|||+||||++|||++|||+|||||++|||+.+||++++.++.   +.++.+|++||||+|
T Consensus        19 ~~~~~~~~~L~kd~FLkLL~aQLqnQDP~~PmD~~efiaQmAqfS~lEq~~~mn~~l~~l~~~~~~~~~~~a~slIGk~V   98 (146)
T PRK09618         19 AQRRSNKSNLGKDDFLKLLITQLQNQDPTNPMEDKEFIAQMAQFSSLEQMTNMNKSMQQFVKLQSSFTLLKYLEWIGKEV   98 (146)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEE
T ss_conf             34567633369899999999997248989998778999999999999999999999999999887899999985559878


Q ss_pred             ECCC--C-EEEEEEEEEEECCCCEEEEEE-CCEEEECCCCEEEEC
Q ss_conf             6389--7-189999788862796699997-897896231058609
Q gi|254780520|r   91 TNAD--G-SISGVVNAIQVSSTGLTAITV-DNTEIPITTGIRISN  131 (131)
Q Consensus        91 ~~~~--~-~~~G~v~~V~~~~~g~~~~~v-~~~~v~~~~v~~V~d  131 (131)
                      ++.+  | .++|.|.+|+...+|.+.+.+ +|+.|++..|+.|++
T Consensus        99 ~~~~~dg~~~sG~V~sv~~~~~g~v~~~ldnG~~i~~~~V~~V~~  143 (146)
T PRK09618         99 EWEHGDGEIVKGTVTSVKTGINGQVMVELDDGKWYVASNVTSVGL  143 (146)
T ss_pred             EEECCCCCEEEEEEEEEEECCCCEEEEEECCCCEECHHHCEEECC
T ss_conf             997389988877899999865984999976994985798747334


No 3  
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=100.00  E-value=2.8e-35  Score=223.33  Aligned_cols=128  Identities=34%  Similarity=0.551  Sum_probs=107.8

Q ss_pred             CCCCCCCCCCCC--CCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH
Q ss_conf             455557665555--56677333388999999999832998999889789999999999999999999999999---9999
Q gi|254780520|r    3 INTEVNPTQQEF--SKSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQEL---LKSN   77 (131)
Q Consensus         3 v~t~~~~~~~~~--~~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~---~~~~   77 (131)
                      |++..+|.+...  .....+++||||+|||||++||+||||++|||++|||+|||||++|||+.+||+.++.+   +++.
T Consensus         4 vs~~~~~~~~~~~a~t~~~~~~L~kd~FLkLl~~Ql~nQDP~~Pmd~~e~iaQlAqfs~lEq~~~mn~~l~~l~~~~~s~   83 (140)
T PRK11911          4 ISSLSGASQDTNNAVTSSVSKTLGKDDFMKLFLTSLQYQDPSSPLDTNEMMSQMAQLSLMEQVANMTTAVDKLSEQAQNS   83 (140)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             35454667666777667512103988999999999614898999877999999999999999999999999999999889


Q ss_pred             HHHHHHHHCCCEEECCC--C-EEEEEEEEEEECCCCEEEEEECC-EEEECCCCEEEE
Q ss_conf             97645532261466389--7-18999978886279669999789-789623105860
Q gi|254780520|r   78 NLAQASSYIGKNITNAD--G-SISGVVNAIQVSSTGLTAITVDN-TEIPITTGIRIS  130 (131)
Q Consensus        78 ~~~~a~sliGk~V~~~~--~-~~~G~v~~V~~~~~g~~~~~v~~-~~v~~~~v~~V~  130 (131)
                      ++.+|++||||+|++.+  | .++|+|++|++.++|......|| +.++++.|.+|+
T Consensus        84 ~l~qas~lIGK~V~~~d~dG~~~sG~V~sV~~~~~g~~l~l~dg~~~v~~~~V~~V~  140 (140)
T PRK11911         84 ALQSAVNFIGKDIKGVSLNGEVISGKVESVQQTTNGVMLKLKDNDSLVPMTYVTEIN  140 (140)
T ss_pred             HHHHHHHHCCCEEEEECCCCCEEEEEEEEEEEECCCEEEEEECCCEEEEHHHEEECC
T ss_conf             999887333846788769998877888999982895699995399898857717549


No 4  
>PRK12812 flgD flagellar basal body rod modification protein; Reviewed
Probab=100.00  E-value=3.8e-32  Score=205.24  Aligned_cols=76  Identities=37%  Similarity=0.567  Sum_probs=69.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCCEEEC
Q ss_conf             67733338899999999983299899988978999999999999999999999999999---99976455322614663
Q gi|254780520|r   17 SKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLK---SNNLAQASSYIGKNITN   92 (131)
Q Consensus        17 ~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~---~~~~~~a~sliGk~V~~   92 (131)
                      +..+++|+||+|||||++|||||||++|||++||++|||||++|||+.++|++|+.|..   ..+.++|++||||.|.+
T Consensus        38 ~np~s~LdkDaFLkLL~TQLqNQDPlnPMDn~eftaQLAQfSsvEqi~~lN~tL~sL~~~~~s~q~lqA~slIGK~V~v  116 (259)
T PRK12812         38 SNPNSQLDKDAFLKLLLIELQHQDPTDPMDSDKMLTQTSQLAALEMQENTNTTMQKLVEQMQSSMSTSALSALGKMATV  116 (259)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEE
T ss_conf             8860244288999999999731799998667999999998888999999999999999998778999998740847996


No 5  
>PRK12634 flgD flagellar basal body rod modification protein; Reviewed
Probab=99.98  E-value=1.4e-31  Score=201.99  Aligned_cols=82  Identities=30%  Similarity=0.549  Sum_probs=72.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCE
Q ss_conf             5556677333388999999999832998999889789999999999999999999999999---9999976455322614
Q gi|254780520|r   13 EFSKSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQEL---LKSNNLAQASSYIGKN   89 (131)
Q Consensus        13 ~~~~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~---~~~~~~~~a~sliGk~   89 (131)
                      .+...+.+.+||++|||+||+||||||||++|||++||++||||||+|||+.++|++|+.+   +.+.+..++++||||+
T Consensus        17 ~~~~~~~~~~Lg~~dFL~LL~tQLqNQDPl~PmD~~ef~aQLAQfS~vE~~~~~n~~l~~l~~~~~s~q~l~a~slIGk~   96 (221)
T PRK12634         17 SSKVAKKEEALGQADFLKLMTEQLQHQDPLKPMENSAFLGQLAQFSTVQGIGDLNTKVSNFSDSMNSDQVLKGAALVGHN   96 (221)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
T ss_conf             78888752101889999999999852899998866889999998999999999999999999999888998888631967


Q ss_pred             EECCC
Q ss_conf             66389
Q gi|254780520|r   90 ITNAD   94 (131)
Q Consensus        90 V~~~~   94 (131)
                      |.+.+
T Consensus        97 V~v~~  101 (221)
T PRK12634         97 VLVPS  101 (221)
T ss_pred             EEECC
T ss_conf             99738


No 6  
>PRK06792 flgD flagellar basal body rod modification protein; Validated
Probab=99.98  E-value=1.3e-31  Score=202.18  Aligned_cols=114  Identities=27%  Similarity=0.482  Sum_probs=104.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCEEECC-
Q ss_conf             77333388999999999832998999889789999999999999999999999999---99999764553226146638-
Q gi|254780520|r   18 KSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQEL---LKSNNLAQASSYIGKNITNA-   93 (131)
Q Consensus        18 ~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~---~~~~~~~~a~sliGk~V~~~-   93 (131)
                      +....||||||||||++||+||||++|||+++||+|||||++||||++|+++++.|   +++..+.++..+|||+|... 
T Consensus        46 ktpGvLgKDdFLKLLltQLqnQDPlnPMD~~qmmaQmAQfSsLEQmqNMtkaVdkL~~t~~~taldggmkflgkyv~g~~  125 (190)
T PRK06792         46 KTPGVMGKDDFLKLFLASFQHQDPFNAMDMNQMMNQTAQLSLMEQVQNMTKAVDKLQSTMYSTALDGGMKFLGKYVRGVS  125 (190)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             68873678899999999960179999657899999999998999999999999999999988776405888877750667


Q ss_pred             --CCEEEEEEEEEEECCCCEEEEEECCEEEECCCCEEEEC
Q ss_conf             --97189999788862796699997897896231058609
Q gi|254780520|r   94 --DGSISGVVNAIQVSSTGLTAITVDNTEIPITTGIRISN  131 (131)
Q Consensus        94 --~~~~~G~v~~V~~~~~g~~~~~v~~~~v~~~~v~~V~d  131 (131)
                        +..++|.|++|++.+++.+.++++++.|+++.|.+|||
T Consensus       126 ~~g~~v~g~v~~vrla~nn~vqlvv~~kvv~~r~v~~vsd  165 (190)
T PRK06792        126 NDGKQVTGQVETVRLAENNDVQLVVDNKVVSLRFVERVSD  165 (190)
T ss_pred             CCCCEEEEEEEEEEECCCCCEEEEECCEEEEEEEEHHCCC
T ss_conf             9887776556678731478158997686887630023266


No 7  
>COG1843 FlgD Flagellar hook capping protein [Cell motility and secretion]
Probab=99.97  E-value=1.9e-31  Score=201.25  Aligned_cols=90  Identities=47%  Similarity=0.664  Sum_probs=78.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCEEEC
Q ss_conf             6677333388999999999832998999889789999999999999999999999999999997---6455322614663
Q gi|254780520|r   16 KSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLKSNNL---AQASSYIGKNITN   92 (131)
Q Consensus        16 ~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~~~~~---~~a~sliGk~V~~   92 (131)
                      ....+..|+||+|||||+||||||||++|||++|||+|||||++|||+.+||+.|+++..+...   .+|++||||.|.+
T Consensus        22 ~~~~~~~l~kd~FLkLLiaQLknQDPtnPmd~~q~isQmAQfS~vEq~~nmn~~l~~l~~~~~~~~~l~a~~lIGk~V~v  101 (222)
T COG1843          22 STSSNASLGKDDFLKLLIAQLKNQDPTNPMDNTEFISQLAQFSQVEQMENMNTTLESLSSQMTSSQTLQASNLIGKTVMV  101 (222)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             46665442688899999999742799998760479999998988999999999999999876420456777405857996


Q ss_pred             CCCEEEEEEEEEE
Q ss_conf             8971899997888
Q gi|254780520|r   93 ADGSISGVVNAIQ  105 (131)
Q Consensus        93 ~~~~~~G~v~~V~  105 (131)
                      +++.+++....+.
T Consensus       102 ~~~~~~~~~~~~~  114 (222)
T COG1843         102 ADGKVTLVDGTVK  114 (222)
T ss_pred             ECCCEEEEEEEEE
T ss_conf             0671365200478


No 8  
>PRK12813 flgD flagellar basal body rod modification protein; Reviewed
Probab=99.97  E-value=2.4e-30  Score=194.83  Aligned_cols=75  Identities=40%  Similarity=0.562  Sum_probs=67.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCCEEEC
Q ss_conf             7733338899999999983299899988978999999999999999999999999999---99976455322614663
Q gi|254780520|r   18 KSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLK---SNNLAQASSYIGKNITN   92 (131)
Q Consensus        18 ~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~---~~~~~~a~sliGk~V~~   92 (131)
                      ......++|+|||||+|||||||||+|||++||++|||||++|||+.++|++|+.|..   +.+..++++||||+|.+
T Consensus        25 ~~~~~~d~d~FLkLL~tQLqNQDPl~PmDn~ef~sQLAQfS~vEq~~~~n~~l~~l~~~~~s~~~~qa~~lIGk~V~~  102 (223)
T PRK12813         25 DSALTSDFETFLRMLTTQLQNQDPLNPMDSSDYAAQLATFSGVEQQVKTNDLLTGLGASLGSMGLSQLAGWIGREARA  102 (223)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             432200499999999999851899999887899999998998999999999999999998878999999755977997


No 9  
>pfam03963 FlgD Flagellar hook capping protein. FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum. It appears to act as a hook-capping protein to enable assembly of hook protein subunits.
Probab=99.97  E-value=2.2e-30  Score=195.07  Aligned_cols=80  Identities=44%  Similarity=0.620  Sum_probs=72.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHCCCEEECCC
Q ss_conf             77333388999999999832998999889789999999999999999999999999999---997645532261466389
Q gi|254780520|r   18 KSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLKS---NNLAQASSYIGKNITNAD   94 (131)
Q Consensus        18 ~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~~---~~~~~a~sliGk~V~~~~   94 (131)
                      .+...+|+|+|||||+|||+||||++|||++||++|||||++|||+.++|+.|+.+...   .+..++++||||+|.+.+
T Consensus        21 ~~~~~l~~d~FLkLLvaQLqnQDPl~P~D~~ef~sQlAQfS~vEq~~~~n~~l~~l~~~~~~~~~~~a~~lIGk~V~~~~  100 (140)
T pfam03963        21 TSSSELDKDDFLKLLTAQLQNQDPLNPMDNTEFIAQLAQFSTVEQIQNLNTTLESLAASMQSSQALQASSLIGKTVLVPG  100 (140)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf             66442589999999999984489999976699999999999999999999999999999999999999986499899628


Q ss_pred             CEE
Q ss_conf             718
Q gi|254780520|r   95 GSI   97 (131)
Q Consensus        95 ~~~   97 (131)
                      ..+
T Consensus       101 ~~~  103 (140)
T pfam03963       101 NTV  103 (140)
T ss_pred             CEE
T ss_conf             614


No 10 
>PRK12633 flgD flagellar basal body rod modification protein; Provisional
Probab=99.97  E-value=2.1e-30  Score=195.18  Aligned_cols=82  Identities=33%  Similarity=0.440  Sum_probs=72.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHCCCEEEC
Q ss_conf             66773333889999999998329989998897899999999999999999999999999---999976455322614663
Q gi|254780520|r   16 KSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELL---KSNNLAQASSYIGKNITN   92 (131)
Q Consensus        16 ~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~---~~~~~~~a~sliGk~V~~   92 (131)
                      .+.+.....||+|||||+||||||||++|||++||++|||||++|||+.+||++|+.+.   ...+..++++||||+|.+
T Consensus        19 ~~~~~~~~~qd~FLkLL~tQLqNQDPl~PmDn~ef~aQLAQfStvE~~~~~n~~l~~l~~~~~~~q~l~a~slIGk~V~~   98 (230)
T PRK12633         19 GSNSAAQGIQDQFLTLLVTQLRNQDPLNPMENAELTSQLAQISTVEGINNLKNTMLAISGQIDVSQSMDAVSMIGKGVLM   98 (230)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             78852156799999999999841899998777899999999999999999999999999999999999998743967997


Q ss_pred             CCCEE
Q ss_conf             89718
Q gi|254780520|r   93 ADGSI   97 (131)
Q Consensus        93 ~~~~~   97 (131)
                      +++.+
T Consensus        99 ~g~~~  103 (230)
T PRK12633         99 PGDKV  103 (230)
T ss_pred             CCCEE
T ss_conf             26567


No 11 
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=99.97  E-value=3.9e-30  Score=193.67  Aligned_cols=80  Identities=38%  Similarity=0.517  Sum_probs=70.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHCCCEEECCC
Q ss_conf             773333889999999998329989998897899999999999999999999999999---99997645532261466389
Q gi|254780520|r   18 KSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELL---KSNNLAQASSYIGKNITNAD   94 (131)
Q Consensus        18 ~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~---~~~~~~~a~sliGk~V~~~~   94 (131)
                      .+...+.||+|||||+||||||||++|||++||++|||||++|||+.++|++|+.+.   .+.+..+|++||||+|.+.+
T Consensus        26 ~~~~~~~qd~FL~LL~tQLqNQDPl~PmDn~~f~aQLAQfSsvE~~~~~n~~l~~l~~~~~~~q~l~a~slIGk~V~v~g  105 (225)
T PRK06655         26 GSSAADLQDDFLTLLVAQLKNQDPLNPMDNSQMTSQLAQFSTVSGIEKLNTTLGSLASQMTSSQALQASSLVGRGVLVPG  105 (225)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEC
T ss_conf             88778889999999999985189999887799999999999999999999999999999988899888764163589866


Q ss_pred             CEE
Q ss_conf             718
Q gi|254780520|r   95 GSI   97 (131)
Q Consensus        95 ~~~   97 (131)
                      +.+
T Consensus       106 ~~~  108 (225)
T PRK06655        106 DTV  108 (225)
T ss_pred             CEE
T ss_conf             557


No 12 
>PRK05842 flgD flagellar basal body rod modification protein; Reviewed
Probab=99.97  E-value=3.1e-30  Score=194.22  Aligned_cols=66  Identities=32%  Similarity=0.529  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             555556677333388999999999832998999889789999999999999999999999999999
Q gi|254780520|r   11 QQEFSKSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQELLKS   76 (131)
Q Consensus        11 ~~~~~~~~~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~~~~   76 (131)
                      ....-......+||||+|||||++|||||||++|||++||++||||||+|||+.++|++|+++...
T Consensus        15 ~~~~~~~~~~~~LdkDaFLkLLvtQLqnQDPlnPMDn~e~iaQLAQfStvEq~~~~n~tl~~~s~~   80 (269)
T PRK05842         15 ERKKEQPTIANGLDKDAFMKLFLEQLKNQDPTAPMETDKIITQTAQLTQVEMQEENKKTMQEVASA   80 (269)
T ss_pred             HHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             877543556455588899999999973279999866799999999898899888776789999987


No 13 
>PRK09619 flgD flagellar basal body rod modification protein; Reviewed
Probab=99.96  E-value=3.1e-29  Score=188.49  Aligned_cols=78  Identities=23%  Similarity=0.397  Sum_probs=69.7

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCEEECCCC
Q ss_conf             7333388999999999832998999889789999999999999999999999999---9999976455322614663897
Q gi|254780520|r   19 SKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNSTLQEL---LKSNNLAQASSYIGKNITNADG   95 (131)
Q Consensus        19 ~~~~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~l~~~---~~~~~~~~a~sliGk~V~~~~~   95 (131)
                      ..++..||+|||||+|||+|||||+|||++||++||||||+||++.+||++++.+   +.+.+..++++||||+|.+.+.
T Consensus        26 ~g~~~~qddFL~LL~aQLqNQDPl~PmDn~ef~aQLAQFStvE~i~~ln~~l~~l~~~~~s~q~lqaaslVGk~V~v~g~  105 (220)
T PRK09619         26 PGAEQLNNQFMTLLVAQIQNQDPLNPADGTEFVSQLAQLSQVQSTENMAKLMKSNTVLMDNMQTLATANLVGQQVMVESH  105 (220)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             74146799999999999852899998877899999998988999999999999999998878999999754987996476


Q ss_pred             E
Q ss_conf             1
Q gi|254780520|r   96 S   96 (131)
Q Consensus        96 ~   96 (131)
                      .
T Consensus       106 ~  106 (220)
T PRK09619        106 E  106 (220)
T ss_pred             E
T ss_conf             3


No 14 
>TIGR02004 PTS-IIBC-malX PTS system, maltose and glucose-specific IIBC component; InterPro: IPR011301   This entry represents a family of PTS enzyme II fused B and C components including and most closely related to the MalX maltose and glucose-specific transporter of Escherichia coli ..
Probab=66.62  E-value=4.1  Score=20.49  Aligned_cols=29  Identities=14%  Similarity=0.307  Sum_probs=25.6

Q ss_pred             HHHHHHHHCCCCCCC--CCCHHHHHHH--HHHH
Q ss_conf             999999832998999--8897899999--9999
Q gi|254780520|r   29 LKLLITQIKHQDPTE--PMKASEQVAQ--LAVF   57 (131)
Q Consensus        29 LkLL~aQL~nQDP~~--P~d~~e~isQ--lAqf   57 (131)
                      |+|+=+||++-+|..  -.|-|.|+||  |+.|
T Consensus       259 LNiFYaeL~c~~~~~s~~p~aTaFLSQGKMptf  291 (540)
T TIGR02004       259 LNIFYAELDCAAAISSAVPEATAFLSQGKMPTF  291 (540)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHCCCCHHHH
T ss_conf             777887631367766665330424125504355


No 15 
>pfam11562 EDC3_LSm Enhancer of mRNA-decapping protein 3- N terminal. EDC3 functions in mRNA decapping. This family represents the N-terminal LSm domain of EDC3. This LSm domain mediates DCP1 binding and P-body localisation. The LSm domain adopts a divergent Sm fold that has a disrupted beta4-strand and lacks the usual N-terminal alpha-helix.
Probab=33.13  E-value=37  Score=14.97  Aligned_cols=24  Identities=21%  Similarity=0.533  Sum_probs=17.0

Q ss_pred             HHHHCCCEEEC---CC-CEEEEEEEEEE
Q ss_conf             55322614663---89-71899997888
Q gi|254780520|r   82 ASSYIGKNITN---AD-GSISGVVNAIQ  105 (131)
Q Consensus        82 a~sliGk~V~~---~~-~~~~G~v~~V~  105 (131)
                      +..|||+.|..   .+ |.+-|.+.+|.
T Consensus         2 a~~~iG~~VSi~C~d~lGvyQG~I~~vd   29 (84)
T pfam11562         2 ADDWIGSSVSINCGDTLGVYQGKIKQVD   29 (84)
T ss_pred             CCCCCCCEEEEEECCCCCEEEEEEEEEC
T ss_conf             6232131799985798537888999862


No 16 
>KOG2830 consensus
Probab=31.57  E-value=16  Score=17.09  Aligned_cols=39  Identities=33%  Similarity=0.461  Sum_probs=26.0

Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             338899999999983299899988978999999999999999999999
Q gi|254780520|r   22 TLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQMNST   69 (131)
Q Consensus        22 ~l~~d~FLkLL~aQL~nQDP~~P~d~~e~isQlAqfs~leq~~~~~~~   69 (131)
                      ..+++-|++.. -|+++        -++|+.|||-||+-|.+..+.++
T Consensus        29 ~~~~~~~~~~i-~q~~~--------~t~m~~ql~lFSsNE~iedIsT~   67 (324)
T KOG2830          29 EVATEPVLKRI-KQLKV--------ATEMVNQLALFSSNETIEDISTN   67 (324)
T ss_pred             HHHHHHHHHHH-HHHHH--------HHHHHHHHHHHCCCCHHHHCCCC
T ss_conf             12146466689-98888--------99988777751253224330235


No 17 
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General    function prediction only]
Probab=29.48  E-value=43  Score=14.61  Aligned_cols=52  Identities=23%  Similarity=0.392  Sum_probs=33.2

Q ss_pred             HHHHHHCCCEEECCCCEEEEEEEEEEECCC-C-EEEEEEC-------------CEEEECCCCEEEEC
Q ss_conf             645532261466389718999978886279-6-6999978-------------97896231058609
Q gi|254780520|r   80 AQASSYIGKNITNADGSISGVVNAIQVSST-G-LTAITVD-------------NTEIPITTGIRISN  131 (131)
Q Consensus        80 ~~a~sliGk~V~~~~~~~~G~v~~V~~~~~-g-~~~~~v~-------------~~~v~~~~v~~V~d  131 (131)
                      ...++|.||+|...+|..-|.|.-+.+... | ...+.+.             .-.+|.+.|..|+|
T Consensus         6 ~~~s~l~gk~V~~~~G~~vG~V~dv~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~~~V~aIGd   72 (87)
T COG1873           6 MRLSELLGKEVITNDGKYVGTVSDVVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPYEYVKAIGD   72 (87)
T ss_pred             HEHHHHCCCEEECCCCEEEEEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCEEEEEHHHEEEECC
T ss_conf             1487742968984788499999738998468938999995688520005779689975457578557


No 18 
>pfam10842 DUF2642 Protein of unknown function (DUF2642). This family of proteins with unknown function appear to be restricted to Bacillus spp.
Probab=24.57  E-value=48  Score=14.30  Aligned_cols=24  Identities=25%  Similarity=0.531  Sum_probs=17.9

Q ss_pred             HHHHCCCEEEC--CCCEEEEEEEEEE
Q ss_conf             55322614663--8971899997888
Q gi|254780520|r   82 ASSYIGKNITN--ADGSISGVVNAIQ  105 (131)
Q Consensus        82 a~sliGk~V~~--~~~~~~G~v~~V~  105 (131)
                      ..++|||.|..  .-|+..|.+..|+
T Consensus        16 lqs~iG~~vvVeT~rgsvrG~L~dVk   41 (66)
T pfam10842        16 LQSLIGRRVVVQTVRGSVRGRLRDVK   41 (66)
T ss_pred             HHHHHCCEEEEEEECCCEEEEEEEEC
T ss_conf             99874837999983251687896107


No 19 
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=22.31  E-value=59  Score=13.82  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             5566773333889999999998329
Q gi|254780520|r   14 FSKSKSKKTLGQDAFLKLLITQIKH   38 (131)
Q Consensus        14 ~~~~~~~~~l~~d~FLkLL~aQL~n   38 (131)
                      +.+...+.+|.+.+|-.||-.||.+
T Consensus        18 a~~~g~~~~Lsk~Elk~Ll~~El~~   42 (88)
T cd00213          18 SGKEGDKDTLSKKELKELLETELPN   42 (88)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             5548973527799999999999889


No 20 
>pfam10748 DUF2531 Protein of unknown function (DUF2531). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.95  E-value=46  Score=14.42  Aligned_cols=20  Identities=25%  Similarity=0.506  Sum_probs=14.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHH
Q ss_conf             99899988978999999999
Q gi|254780520|r   38 HQDPTEPMKASEQVAQLAVF   57 (131)
Q Consensus        38 nQDP~~P~d~~e~isQlAqf   57 (131)
                      .-|||.|..+.=-++|+.|.
T Consensus        18 mRDPF~Pped~C~~~~l~qW   37 (133)
T pfam10748        18 MRDPFKPPEDRCRIAELSQW   37 (133)
T ss_pred             CCCCCCCCHHHHHHHHHHHH
T ss_conf             57889995234323024354


No 21 
>pfam05239 PRC PRC-barrel domain. The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain.
Probab=21.70  E-value=60  Score=13.75  Aligned_cols=38  Identities=26%  Similarity=0.359  Sum_probs=26.8

Q ss_pred             HHHHHCCCEEECCCCEEEEEEEEEEECC-CCEE-EEEECC
Q ss_conf             4553226146638971899997888627-9669-999789
Q gi|254780520|r   81 QASSYIGKNITNADGSISGVVNAIQVSS-TGLT-AITVDN  118 (131)
Q Consensus        81 ~a~sliGk~V~~~~~~~~G~v~~V~~~~-~g~~-~~~v~~  118 (131)
                      .++.|+|++|...+|..-|.|..+-+.. .|.+ .+.++.
T Consensus         5 ~~~~l~G~~V~~~~G~~lG~V~Dv~id~~~g~i~~i~~~~   44 (77)
T pfam05239         5 YASDLIGLEVYTEDGEKLGKVKDVVIDEGEGDVLYLVVSV   44 (77)
T ss_pred             EEEEEECCEEECCCCCEEEEEEEEEEECCCCCEEEEEECC
T ss_conf             9789748887999999998999999978999599999876


Done!