Query         gi|254780607|ref|YP_003065020.1| hypothetical protein CLIBASIA_02470 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs    104 out of 574
Neff          7.8 
Searched_HMMs 39220
Date          Sun May 29 21:20:46 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780607.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG3755 Uncharacterized protei  99.9 5.2E-24 1.3E-28  162.2  10.9  105   15-119    20-126 (127)
  2 pfam07007 DUF1311 Protein of u  99.8 5.5E-20 1.4E-24  138.3  12.3   92   22-113     1-92  (92)
  3 COG4461 LprI Uncharacterized p  99.2 6.6E-11 1.7E-15   84.5   9.0   97    1-115     1-100 (185)
  4 PHA02067 hypothetical protein   97.9 2.5E-05 6.3E-10   51.4   5.8  105    1-128     1-106 (221)
  5 PRK10780 periplasmic chaperone  77.3     5.6 0.00014   19.6   6.6   22    1-22      1-22  (161)
  6 PRK02998 prsA peptidylprolyl i  65.5      10 0.00027   18.0   5.8   18    1-18      1-18  (283)
  7 PRK10626 hypothetical protein;  55.6     9.7 0.00025   18.2   2.4   77    1-77      1-103 (239)
  8 PRK13861 type IV secretion sys  55.1       8  0.0002   18.7   1.9   21    1-21      1-22  (293)
  9 pfam11853 DUF3373 Protein of u  50.3      19 0.00049   16.4   4.5   21    1-21      1-23  (485)
 10 PRK10641 btuB vitamin B12/coba  44.9      15 0.00038   17.1   2.0   22    1-22      1-22  (615)
 11 PRK10877 thiol:disulfide inter  43.8      16 0.00041   16.9   2.0   21    1-21      1-22  (232)
 12 PRK03641 hypothetical protein;  40.9      19 0.00048   16.5   2.0   20    1-20      1-20  (220)
 13 pfam09403 FadA Adhesion protei  38.1      30 0.00076   15.3   4.2   19    1-19      1-19  (126)
 14 PRK03095 prsA peptidylprolyl i  36.4      32 0.00081   15.1   5.5   19    1-19      1-19  (287)
 15 PRK04792 tolB translocation pr  34.9      29 0.00074   15.4   2.2   17    1-17      1-17  (450)
 16 PRK01326 prsA foldase protein   33.0      36 0.00092   14.8   6.7   27   34-60     64-92  (310)
 17 PRK03002 prsA peptidylprolyl i  32.6      37 0.00093   14.8   6.1   14    1-14      1-14  (285)
 18 TIGR02051 MerR Hg(II)-responsi  32.5      30 0.00077   15.3   1.9   17  114-130   105-124 (126)
 19 pfam11777 DUF3316 Protein of u  31.9      38 0.00096   14.7   2.7   52    1-53      1-56  (114)
 20 pfam05079 DUF680 Protein of un  31.0      33 0.00084   15.0   1.9   20    1-20      1-20  (73)
 21 pfam06649 DUF1161 Protein of u  30.9      24  0.0006   15.9   1.2   24    1-24      1-25  (75)
 22 PRK10954 periplasmic protein d  30.2      38 0.00098   14.6   2.2   26   95-120   141-166 (207)
 23 KOG4721 consensus               30.2      40   0.001   14.5   5.1   45   68-119   382-426 (904)
 24 KOG3262 consensus               29.9      20 0.00051   16.3   0.7   23  107-130    50-73  (215)
 25 PRK10290 superoxide dismutase;  27.9      44  0.0011   14.3   2.1   19    1-19      1-19  (173)
 26 TIGR03431 PhnD phosphonate ABC  27.6      43  0.0011   14.3   2.0   22    1-22      1-24  (288)
 27 PRK10894 hypothetical protein;  25.2      48  0.0012   14.1   1.9   22    1-22      8-29  (184)
 28 pfam04076 BOF Bacterial OB fol  24.9      47  0.0012   14.1   1.8   19    1-20      1-19  (126)
 29 PRK10554 outer membrane porin   23.3      54  0.0014   13.8   1.9   22    1-22      1-23  (373)
 30 PRK12789 flgI flagellar basal   23.0      54  0.0014   13.7   2.0   17    1-17      1-17  (367)
 31 PRK10598 hypothetical protein;  22.9      55  0.0014   13.7   4.3   41    1-41      1-41  (186)
 32 TIGR03519 Bac_Flav_fam_1 Bacte  22.4      56  0.0014   13.7   1.9   19    1-19      1-19  (292)
 33 PRK09733 putative fimbrial pro  21.9      57  0.0015   13.6   1.9   20    1-20      2-21  (181)

No 1  
>COG3755 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.91  E-value=5.2e-24  Score=162.24  Aligned_cols=105  Identities=29%  Similarity=0.502  Sum_probs=96.5

Q ss_pred             HHHHCCCCCCCCCCHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             31012202378899899999-9999999999999999999997329356899-999999999999997887551246883
Q gi|254780607|r   15 AFQSMALNCNETLMQADMNQ-CTGNSFALVKEKLEATYKKVLEKVEKHQREL-FEKSQMAWEIYRGSECAFAASGAEEGT   92 (131)
Q Consensus        15 s~~a~a~dC~~a~t~~e~~~-C~~~~~~~ad~~Ln~~y~~l~~~l~~~~~~~-L~~sQr~W~~~R~~~C~~~~~~~~~Gs   92 (131)
                      ..+..+.||..+.++.+++. |+.++++.+|++||+.|+.++++++..++.. |+++||+||+|||++|....+...|||
T Consensus        20 ~~~~~a~~C~~~~~~~d~~~~C~~~e~~~aDa~LN~AY~~ll~~l~~~~~~~aL~kaQRAWi~fRDadC~~~~~~~~ggs   99 (127)
T COG3755          20 TSQSAADDCCRASPQFDSNYDCAGQEYQAADAELNKAYKALLKRLQDSPRTKALQKAQRAWIAFRDADCALIKSQLDGGS   99 (127)
T ss_pred             CCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             00140688657887553144888778999999999999999987205768899999999999972576888751015898


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             567999999999999999999997137
Q gi|254780607|r   93 AQSMIYANCLQGHAIERNEKLESYLTC  119 (131)
Q Consensus        93 ~~~~~~~~C~~~~t~~R~~eL~~~l~~  119 (131)
                      +.++.+.+|++++|++|+.||+.++++
T Consensus       100 ~~~~~~~~C~~d~T~~R~~eL~~~~~~  126 (127)
T COG3755         100 IAPMEVLSCLLDLTNQRTAELEELLQP  126 (127)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             206899999899999999999998646


No 2  
>pfam07007 DUF1311 Protein of unknown function (DUF1311). This family consists of several bacterial proteins of around 120 residues in length. Members of this family contain four highly conserved cysteine residues. The function of this family is unknown.
Probab=99.84  E-value=5.5e-20  Score=138.34  Aligned_cols=92  Identities=30%  Similarity=0.551  Sum_probs=88.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf             23788998999999999999999999999999997329356899999999999999997887551246883567999999
Q gi|254780607|r   22 NCNETLMQADMNQCTGNSFALVKEKLEATYKKVLEKVEKHQRELFEKSQMAWEIYRGSECAFAASGAEEGTAQSMIYANC  101 (131)
Q Consensus        22 dC~~a~t~~e~~~C~~~~~~~ad~~Ln~~y~~l~~~l~~~~~~~L~~sQr~W~~~R~~~C~~~~~~~~~Gs~~~~~~~~C  101 (131)
                      +|..+.++.+|++|+..++..+|++||.+|+.+++.++++.++.|+.+|++|++||+++|.+.+..+++||+.++.+.+|
T Consensus         1 ~C~~~~~~~~~~~C~~~~~~~~d~~L~~~y~~~~~~l~~~~~~~L~~sQ~~W~~~Rd~~C~~~~~~~~~Gs~~~~~~~~C   80 (92)
T pfam07007         1 DCAKASTTAEMAICADAELAAADAELNAAYQALLAALPADARAALRAAQRAWLKYRDAECDFEASLYGGGSIAPLAYAAC   80 (92)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             99987899999999899999999999999999998778767899999999999999978778772238995898999999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780607|r  102 LQGHAIERNEKL  113 (131)
Q Consensus       102 ~~~~t~~R~~eL  113 (131)
                      ++++|++|+.+|
T Consensus        81 ~~~~t~~R~~eL   92 (92)
T pfam07007        81 LARLTRERIAEL   92 (92)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999639


No 3  
>COG4461 LprI Uncharacterized protein conserved in bacteria, putative lipoprotein [Function unknown]
Probab=99.23  E-value=6.6e-11  Score=84.46  Aligned_cols=97  Identities=15%  Similarity=0.369  Sum_probs=81.7

Q ss_pred             CCHHHHHHHHHHHHH---HHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             925999999999963---10122023788998999999999999999999999999997329356899999999999999
Q gi|254780607|r    1 MCRKIIFALTIIAIA---FQSMALNCNETLMQADMNQCTGNSFALVKEKLEATYKKVLEKVEKHQRELFEKSQMAWEIYR   77 (131)
Q Consensus         1 m~k~il~~~~~~~~s---~~a~a~dC~~a~t~~e~~~C~~~~~~~ad~~Ln~~y~~l~~~l~~~~~~~L~~sQr~W~~~R   77 (131)
                      |.++++.+.+++.+.   +.+++|||.++.+..|..+|++..+...|.+|+.+|+.+.   -...+..+++.|+.|++-|
T Consensus         1 ~la~~L~gg~ll~p~~l~a~aaSfDC~KA~~~vEkaICan~~L~~lD~~~~t~Y~ql~---a~~~~~~lr~~qq~Wlk~r   77 (185)
T COG4461           1 VLALLLLGGALLTPLSLTASAASFDCTKASTPVEKAICANRQLNDLDVTLSTAYQQLF---AMGRRGALRDAQQSWLKLR   77 (185)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHH
T ss_conf             9379975346650577630445536666564257775177423067899999999987---1443377999999999988


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99788755124688356799999999999999999999
Q gi|254780607|r   78 GSECAFAASGAEEGTAQSMIYANCLQGHAIERNEKLES  115 (131)
Q Consensus        78 ~~~C~~~~~~~~~Gs~~~~~~~~C~~~~t~~R~~eL~~  115 (131)
                      ++ |....              .|+.+-+.+|+.+|..
T Consensus        78 ~~-C~sDt--------------dcl~~AY~~ri~qL~~  100 (185)
T COG4461          78 NA-CASDT--------------DCLQRAYEQRLAQLSK  100 (185)
T ss_pred             HH-HCCCH--------------HHHHHHHHHHHHHHHC
T ss_conf             75-32213--------------8999999999999702


No 4  
>PHA02067 hypothetical protein
Probab=97.92  E-value=2.5e-05  Score=51.38  Aligned_cols=105  Identities=19%  Similarity=0.228  Sum_probs=78.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             925999999999963101220237889-9899999999999999999999999999732935689999999999999999
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALNCNETL-MQADMNQCTGNSFALVKEKLEATYKKVLEKVEKHQRELFEKSQMAWEIYRGS   79 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~dC~~a~-t~~e~~~C~~~~~~~ad~~Ln~~y~~l~~~l~~~~~~~L~~sQr~W~~~R~~   79 (131)
                      |+-.-++++.+.+.+..++++||..+. +..|..+|+..+....|..|...|..+.. .+     ..+..|+.+++-|++
T Consensus         1 mk~lsviAL~l~as~A~aASfDC~~~gln~iEkaiCaVPels~lDdQlaeAyk~v~h-ip-----~vk~dq~~~ik~rn~   74 (221)
T PHA02067          1 MKFLSVIALGLLSSSAMAASFDCNTTGLNSIEKAICKVPELSMMDQQLADAYKVVRH-IP-----EVKADQKTFIKDRNS   74 (221)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH-CC-----CCCCCHHHHHHCCCC
T ss_conf             917999999997200655216332248878988884274121367999999999860-87-----645015667423677


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             7887551246883567999999999999999999997137236758899
Q gi|254780607|r   80 ECAFAASGAEEGTAQSMIYANCLQGHAIERNEKLESYLTCPEGDLLCPF  128 (131)
Q Consensus        80 ~C~~~~~~~~~Gs~~~~~~~~C~~~~t~~R~~eL~~~l~~~eg~~~~~~  128 (131)
                      .-.                .+-+-+..+.||.||+-..+.+ |-.-.|.
T Consensus        75 ~~s----------------l~~lkd~m~driiel~iiaele-gv~~kp~  106 (221)
T PHA02067         75 APS----------------LGDLKDLMRDRIIELEIIAELE-GVEAKPY  106 (221)
T ss_pred             CCC----------------HHHHHHHHHHHHHHHHHHHHHH-CCCCCCC
T ss_conf             876----------------6888888664302332336543-3335885


No 5  
>PRK10780 periplasmic chaperone; Provisional
Probab=77.28  E-value=5.6  Score=19.61  Aligned_cols=22  Identities=23%  Similarity=0.125  Sum_probs=15.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9259999999999631012202
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALN   22 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~d   22 (131)
                      |+|.++.+++.++++++|.|..
T Consensus         1 mKk~l~~~~l~l~l~~~a~Aa~   22 (161)
T PRK10780          1 MKKWLLAAGLGLALATSAQAAD   22 (161)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9589999999998588887753


No 6  
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=65.51  E-value=10  Score=17.99  Aligned_cols=18  Identities=33%  Similarity=0.373  Sum_probs=11.0

Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             925999999999963101
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQS   18 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a   18 (131)
                      |+|+-++++++++.++.+
T Consensus         1 Mkkkk~~~~~~~~~~~l~   18 (283)
T PRK02998          1 MKKKKLFIGTIISCVVLA   18 (283)
T ss_pred             CCHHHHHHHHHHHHHHHH
T ss_conf             935899999999999999


No 7  
>PRK10626 hypothetical protein; Provisional
Probab=55.62  E-value=9.7  Score=18.19  Aligned_cols=77  Identities=12%  Similarity=0.141  Sum_probs=41.2

Q ss_pred             CCHHHHHHHHHHHHHHHHCC-CCCCC-CCC-------HHHHHH----------------HHHHHHHHHHHHHHHHHH-HH
Q ss_conf             92599999999996310122-02378-899-------899999----------------999999999999999999-99
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMA-LNCNE-TLM-------QADMNQ----------------CTGNSFALVKEKLEATYK-KV   54 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a-~dC~~-a~t-------~~e~~~----------------C~~~~~~~ad~~Ln~~y~-~l   54 (131)
                      |.|++++++++++.+++|.+ .+|.- +..       +.++..                =-.-.+....++.-..|+ .+
T Consensus         1 m~r~~~~~~~l~~~a~~a~a~~qC~V~pqdDIiItpq~VqV~gang~l~I~pdG~l~~nGk~v~Ls~~Qrq~a~~YQ~~l   80 (239)
T PRK10626          1 MMRKTLLAAVLSVTAMTAHADYQCSVTPRDDVIISPQTVQVKGENGNLVITPDGNVMRNGKQYTLNAAQREQAKDYQAEL   80 (239)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEECCCEEEEECCCCCEEECCCCCEEECCEEEECCHHHHHHHHHHHHHH
T ss_conf             90899999999999999860678888878776675763799717786788789876887876301899999999999999


Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             97329356899999999999999
Q gi|254780607|r   55 LEKVEKHQRELFEKSQMAWEIYR   77 (131)
Q Consensus        55 ~~~l~~~~~~~L~~sQr~W~~~R   77 (131)
                      +..+|--.+....+-+++|..--
T Consensus        81 R~dLPwi~~~a~~~l~~ar~aLD  103 (239)
T PRK10626         81 RSDLPWIDEGAKSRLEKARVALD  103 (239)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             87181655778989999999999


No 8  
>PRK13861 type IV secretion system protein VirB9; Provisional
Probab=55.14  E-value=8  Score=18.69  Aligned_cols=21  Identities=24%  Similarity=0.409  Sum_probs=13.5

Q ss_pred             CCHHHHHHHHHHH-HHHHHCCC
Q ss_conf             9259999999999-63101220
Q gi|254780607|r    1 MCRKIIFALTIIA-IAFQSMAL   21 (131)
Q Consensus         1 m~k~il~~~~~~~-~s~~a~a~   21 (131)
                      |+|++++++++++ .+..|.|.
T Consensus         1 mmk~l~~~~~~~l~~~~~a~A~   22 (293)
T PRK13861          1 MIKKLFLTLACLLFAAIGALAE   22 (293)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9089999999999861266787


No 9  
>pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=50.31  E-value=19  Score=16.44  Aligned_cols=21  Identities=19%  Similarity=0.297  Sum_probs=11.5

Q ss_pred             CCHHHHHHHHHH--HHHHHHCCC
Q ss_conf             925999999999--963101220
Q gi|254780607|r    1 MCRKIIFALTII--AIAFQSMAL   21 (131)
Q Consensus         1 m~k~il~~~~~~--~~s~~a~a~   21 (131)
                      |+|.+.++++..  +.|..+.+.
T Consensus         1 Mkk~~~l~~~aall~~s~~~~a~   23 (485)
T pfam11853         1 MKKLVSLSLVAALLALSLPAAAA   23 (485)
T ss_pred             CCHHHHHHHHHHHHHHCCCHHCC
T ss_conf             91147899999999750410013


No 10 
>PRK10641 btuB vitamin B12/cobalamin outer membrane transporter; Provisional
Probab=44.88  E-value=15  Score=17.07  Aligned_cols=22  Identities=23%  Similarity=0.302  Sum_probs=17.7

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9259999999999631012202
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALN   22 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~d   22 (131)
                      |+||+.+..++.+.+..+.|+|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~a~~   22 (615)
T PRK10641          1 MIKKASLLTALSVTAFSAWAQD   22 (615)
T ss_pred             CCHHHHHHHHHHHHCCHHHHCC
T ss_conf             9448999999987513354335


No 11 
>PRK10877 thiol:disulfide interchange protein DsbC; Provisional
Probab=43.82  E-value=16  Score=16.87  Aligned_cols=21  Identities=14%  Similarity=0.012  Sum_probs=11.5

Q ss_pred             CCHHHHHHHHH-HHHHHHHCCC
Q ss_conf             92599999999-9963101220
Q gi|254780607|r    1 MCRKIIFALTI-IAIAFQSMAL   21 (131)
Q Consensus         1 m~k~il~~~~~-~~~s~~a~a~   21 (131)
                      |+|.+++..++ +.++.+|.|+
T Consensus         1 mkk~l~~~~~l~~~~s~~a~aD   22 (232)
T PRK10877          1 MKKGFMLFTLLAAAFSGFAHAD   22 (232)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCC
T ss_conf             9266999999999986252437


No 12 
>PRK03641 hypothetical protein; Provisional
Probab=40.93  E-value=19  Score=16.46  Aligned_cols=20  Identities=20%  Similarity=0.290  Sum_probs=11.2

Q ss_pred             CCHHHHHHHHHHHHHHHHCC
Q ss_conf             92599999999996310122
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMA   20 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a   20 (131)
                      |++.|+.+++.+++|..+.|
T Consensus         1 m~~~~i~~llal~~S~~~~A   20 (220)
T PRK03641          1 MKTGIVTTLLALCLPVSVFA   20 (220)
T ss_pred             CCHHHHHHHHHHHHHHHHHE
T ss_conf             91169999999986236450


No 13 
>pfam09403 FadA Adhesion protein FadA. FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices.
Probab=38.09  E-value=30  Score=15.29  Aligned_cols=19  Identities=11%  Similarity=0.183  Sum_probs=11.0

Q ss_pred             CCHHHHHHHHHHHHHHHHC
Q ss_conf             9259999999999631012
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSM   19 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~   19 (131)
                      |+|.+++++++++.++.++
T Consensus         1 MkK~ll~~~llls~~s~aa   19 (126)
T pfam09403         1 MKKILLCSMLILSSLSYAA   19 (126)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             9169999999999999874


No 14 
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=36.37  E-value=32  Score=15.13  Aligned_cols=19  Identities=16%  Similarity=0.203  Sum_probs=10.2

Q ss_pred             CCHHHHHHHHHHHHHHHHC
Q ss_conf             9259999999999631012
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSM   19 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~   19 (131)
                      |+|.++.++++..++..|.
T Consensus         1 MKK~~la~~~~svl~LaaC   19 (287)
T PRK03095          1 MKKAMLALAATSVIALSAC   19 (287)
T ss_pred             CCHHHHHHHHHHHHHHHHC
T ss_conf             9078999999999999851


No 15 
>PRK04792 tolB translocation protein TolB; Provisional
Probab=34.95  E-value=29  Score=15.37  Aligned_cols=17  Identities=24%  Similarity=0.688  Sum_probs=10.7

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             92599999999996310
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQ   17 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~   17 (131)
                      |+|++++.++++++.+.
T Consensus         1 M~k~~~~~l~lll~~~s   17 (450)
T PRK04792          1 MLKRLILGLFVLLLSFS   17 (450)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             93899999999999865


No 16 
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=33.01  E-value=36  Score=14.80  Aligned_cols=27  Identities=11%  Similarity=0.302  Sum_probs=13.8

Q ss_pred             HHHHHHH--HHHHHHHHHHHHHHHHHCCH
Q ss_conf             9999999--99999999999999973293
Q gi|254780607|r   34 QCTGNSF--ALVKEKLEATYKKVLEKVEK   60 (131)
Q Consensus        34 ~C~~~~~--~~ad~~Ln~~y~~l~~~l~~   60 (131)
                      .-....|  ...|++.++.|....++...
T Consensus        64 kvLe~~Yg~kVsdkeV~~~~~~~k~qyG~   92 (310)
T PRK01326         64 RVFEKQYGDKVSDKEVEKAYHKTAKQYGA   92 (310)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999862617899999999999999868


No 17 
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=32.58  E-value=37  Score=14.76  Aligned_cols=14  Identities=36%  Similarity=0.406  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             92599999999996
Q gi|254780607|r    1 MCRKIIFALTIIAI   14 (131)
Q Consensus         1 m~k~il~~~~~~~~   14 (131)
                      |+|+++++++.++.
T Consensus         1 mkkK~i~~~~~~~s   14 (285)
T PRK03002          1 MRGKHIFIITALIS   14 (285)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             96018999999999


No 18 
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794    This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=32.53  E-value=30  Score=15.26  Aligned_cols=17  Identities=41%  Similarity=1.017  Sum_probs=12.4

Q ss_pred             HHHCC-CC--CCCCCCCCCC
Q ss_conf             99713-72--3675889989
Q gi|254780607|r  114 ESYLT-CP--EGDLLCPFIN  130 (131)
Q Consensus       114 ~~~l~-~~--eg~~~~~~~~  130 (131)
                      +.++. |+  .|+.+||.|.
T Consensus       105 ~el~~~C~~~~~~~~CPIIe  124 (126)
T TIGR02051       105 EELLEQCPANKDNTSCPIIE  124 (126)
T ss_pred             HHHHHHCCCCCCCEECCCCC
T ss_conf             99986151458882167201


No 19 
>pfam11777 DUF3316 Protein of unknown function (DUF3316). This family of bacterial proteins has no known function. Several members are, however, annotated as being putative acyl-CoA synthetase, but this could not be confirmed.
Probab=31.91  E-value=38  Score=14.69  Aligned_cols=52  Identities=19%  Similarity=0.264  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCC-CCC---CCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             92599999999996310122023-788---998999999999999999999999999
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALNC-NET---LMQADMNQCTGNSFALVKEKLEATYKK   53 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~dC-~~a---~t~~e~~~C~~~~~~~ad~~Ln~~y~~   53 (131)
                      |||.++++ +++.++..|.|..- ...   ..+.+...--...|+..-..++..|..
T Consensus         1 mKk~~ll~-~~ll~s~~AfA~~~~~~~~~~~~~~~~~~tk~~AY~~G~~~~~~l~~~   56 (114)
T pfam11777         1 MKKLILLA-LLLLLSATAFAGNYVSTTQTDSLQTDVYATKQAAYGAGFTNLNDLYLS   56 (114)
T ss_pred             CHHHHHHH-HHHHHHHHHHHCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             91089999-999998888755553655625897155305999999999999988606


No 20 
>pfam05079 DUF680 Protein of unknown function (DUF680). This family contains several uncharacterized proteins which seem to be found exclusively in Rhizobium loti.
Probab=31.05  E-value=33  Score=15.03  Aligned_cols=20  Identities=25%  Similarity=0.223  Sum_probs=15.4

Q ss_pred             CCHHHHHHHHHHHHHHHHCC
Q ss_conf             92599999999996310122
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMA   20 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a   20 (131)
                      |+|.+|.+..+|..++.|++
T Consensus         1 M~KiaLtaAAiL~asgsAFA   20 (73)
T pfam05079         1 MKKIALTAAAILAASGSAFA   20 (73)
T ss_pred             CCHHHHHHHHHHHHCCCCCC
T ss_conf             92248999999997065221


No 21 
>pfam06649 DUF1161 Protein of unknown function (DUF1161). This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=30.89  E-value=24  Score=15.88  Aligned_cols=24  Identities=13%  Similarity=0.247  Sum_probs=12.9

Q ss_pred             CCHHHHHHHHHHHH-HHHHCCCCCC
Q ss_conf             92599999999996-3101220237
Q gi|254780607|r    1 MCRKIIFALTIIAI-AFQSMALNCN   24 (131)
Q Consensus         1 m~k~il~~~~~~~~-s~~a~a~dC~   24 (131)
                      |+|.++++.++++. +..|+...|.
T Consensus         1 Mkk~~l~~~l~lla~~alAA~~sCE   25 (75)
T pfam06649         1 MKRLLLAVALLLLAASALAAPKSCE   25 (75)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             9246999999997134531558889


No 22 
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=30.22  E-value=38  Score=14.63  Aligned_cols=26  Identities=12%  Similarity=0.149  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             79999999999999999999971372
Q gi|254780607|r   95 SMIYANCLQGHAIERNEKLESYLTCP  120 (131)
Q Consensus        95 ~~~~~~C~~~~t~~R~~eL~~~l~~~  120 (131)
                      --.+.+-.++.-..|...+..-....
T Consensus       141 ~~~~~Sf~V~~~v~~a~~~~~~~~I~  166 (207)
T PRK10954        141 DAAWNSFVVKSLVAQQEKAAADLQLR  166 (207)
T ss_pred             HHHHHCHHHHHHHHHHHHHHHHCCCC
T ss_conf             99985889999999999999972888


No 23 
>KOG4721 consensus
Probab=30.21  E-value=40  Score=14.52  Aligned_cols=45  Identities=22%  Similarity=0.192  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999997887551246883567999999999999999999997137
Q gi|254780607|r   68 KSQMAWEIYRGSECAFAASGAEEGTAQSMIYANCLQGHAIERNEKLESYLTC  119 (131)
Q Consensus        68 ~sQr~W~~~R~~~C~~~~~~~~~Gs~~~~~~~~C~~~~t~~R~~eL~~~l~~  119 (131)
                      ++|..|..+..  |.+.....+|..++     .-..++.+.|..||.-.++.
T Consensus       382 ~sq~swrEevk--~h~~~it~~gt~ih-----~~eeelirrR~eelrHa~DI  426 (904)
T KOG4721         382 KSQASWREEVK--LHFEKITSEGTCIH-----RLEEELIRRRREELRHALDI  426 (904)
T ss_pred             HHHHHHHHHHH--HHHHHHCCCCCHHH-----HHHHHHHHHHHHHHHHHHHH
T ss_conf             87999999998--76422235861287-----88999999999998888889


No 24 
>KOG3262 consensus
Probab=29.89  E-value=20  Score=16.32  Aligned_cols=23  Identities=43%  Similarity=0.853  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHCC-CCCCCCCCCCCC
Q ss_conf             999999999713-723675889989
Q gi|254780607|r  107 IERNEKLESYLT-CPEGDLLCPFIN  130 (131)
Q Consensus       107 ~~R~~eL~~~l~-~~eg~~~~~~~~  130 (131)
                      -+++.||-.++| | |||+-|-+.|
T Consensus        50 p~evvelg~flh~C-egd~Vck~~~   73 (215)
T KOG3262          50 PEEVVELGKFLHMC-EGDLVCKLTN   73 (215)
T ss_pred             CHHHHHHHHHHHHC-CCCEEEEECC
T ss_conf             35411243455433-7755875035


No 25 
>PRK10290 superoxide dismutase; Provisional
Probab=27.89  E-value=44  Score=14.30  Aligned_cols=19  Identities=16%  Similarity=0.090  Sum_probs=13.5

Q ss_pred             CCHHHHHHHHHHHHHHHHC
Q ss_conf             9259999999999631012
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSM   19 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~   19 (131)
                      |+|.+++++++++.+...+
T Consensus         1 mk~~~~~~~~l~~~~~~~a   19 (173)
T PRK10290          1 MKRFSLAILALVVCTGAQA   19 (173)
T ss_pred             CCHHHHHHHHHHHHHHHHH
T ss_conf             9107999999999766651


No 26 
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=27.60  E-value=43  Score=14.34  Aligned_cols=22  Identities=27%  Similarity=0.381  Sum_probs=12.7

Q ss_pred             CCHHHHHHHHHHH--HHHHHCCCC
Q ss_conf             9259999999999--631012202
Q gi|254780607|r    1 MCRKIIFALTIIA--IAFQSMALN   22 (131)
Q Consensus         1 m~k~il~~~~~~~--~s~~a~a~d   22 (131)
                      |+|++++++++++  .+.++.+.+
T Consensus         1 m~~r~l~~~~~~~~~~~~~a~a~~   24 (288)
T TIGR03431         1 MLRRLILSLVAAFMLISSNAQAED   24 (288)
T ss_pred             CCHHHHHHHHHHHHHHCCHHHHCC
T ss_conf             908899999999999743224304


No 27 
>PRK10894 hypothetical protein; Provisional
Probab=25.21  E-value=48  Score=14.06  Aligned_cols=22  Identities=14%  Similarity=0.416  Sum_probs=15.6

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9259999999999631012202
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALN   22 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~d   22 (131)
                      |...|++++.++++|.+|.|..
T Consensus         8 ~~~~l~l~~~ll~~S~~a~Al~   29 (184)
T PRK10894          8 LSLNLLLASSLLAASIPAFAVT   29 (184)
T ss_pred             CHHHHHHHHHHHHHCCHHHHCC
T ss_conf             2066999999987161243155


No 28 
>pfam04076 BOF Bacterial OB fold (BOF) protein. Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.
Probab=24.94  E-value=47  Score=14.11  Aligned_cols=19  Identities=21%  Similarity=0.211  Sum_probs=9.4

Q ss_pred             CCHHHHHHHHHHHHHHHHCC
Q ss_conf             92599999999996310122
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMA   20 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a   20 (131)
                      |||.+|..++++. +..+.|
T Consensus         1 MKK~~i~~~~~l~-s~~~~A   19 (126)
T pfam04076         1 MKKLAIALASALA-STSALA   19 (126)
T ss_pred             CCHHHHHHHHHHH-HCHHHH
T ss_conf             9568999999998-467879


No 29 
>PRK10554 outer membrane porin protein C; Provisional
Probab=23.27  E-value=54  Score=13.76  Aligned_cols=22  Identities=23%  Similarity=0.080  Sum_probs=12.6

Q ss_pred             CCHHHHHHHHHHH-HHHHHCCCC
Q ss_conf             9259999999999-631012202
Q gi|254780607|r    1 MCRKIIFALTIIA-IAFQSMALN   22 (131)
Q Consensus         1 m~k~il~~~~~~~-~s~~a~a~d   22 (131)
                      |||++|.++...+ ++.++.|.+
T Consensus         1 MKk~~LA~~i~all~ag~a~AAe   23 (373)
T PRK10554          1 MKVKVLSLLVPALLVAGAANAAE   23 (373)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEE
T ss_conf             95408999999998607531799


No 30 
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=23.03  E-value=54  Score=13.73  Aligned_cols=17  Identities=24%  Similarity=0.426  Sum_probs=10.5

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             92599999999996310
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQ   17 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~   17 (131)
                      |+|++++.+++.++...
T Consensus         1 m~~~~~~~~~~~l~~~~   17 (367)
T PRK12789          1 MIRRLLLAVLLALLAGP   17 (367)
T ss_pred             CHHHHHHHHHHHHHHCC
T ss_conf             90899999999998553


No 31 
>PRK10598 hypothetical protein; Provisional
Probab=22.90  E-value=55  Score=13.72  Aligned_cols=41  Identities=12%  Similarity=0.092  Sum_probs=19.9

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             92599999999996310122023788998999999999999
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMALNCNETLMQADMNQCTGNSFA   41 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a~dC~~a~t~~e~~~C~~~~~~   41 (131)
                      |+|.++.++++++......+.=-.-..|..||+.-..+...
T Consensus         1 mkk~~l~~~l~l~~llsGC~~l~qYsISEqEin~YL~~~~~   41 (186)
T PRK10598          1 MKKFLLAAALLVSGLLVGCNQLTQYTISEQEINQYLAKHNN   41 (186)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHCC
T ss_conf             91269999999999971435336440079999999987433


No 32 
>TIGR03519 Bac_Flav_fam_1 Bacteroidetes-specific putative membrane protein. This model describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this motility.
Probab=22.38  E-value=56  Score=13.65  Aligned_cols=19  Identities=16%  Similarity=0.431  Sum_probs=13.1

Q ss_pred             CCHHHHHHHHHHHHHHHHC
Q ss_conf             9259999999999631012
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSM   19 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~   19 (131)
                      |||.+++++++++....+.
T Consensus         1 Mkki~l~~~~~~~~~~~~~   19 (292)
T TIGR03519         1 MKKILLLLLLLLLLTVQAF   19 (292)
T ss_pred             CCCHHHHHHHHHHHHHHHH
T ss_conf             9605788999999987787


No 33 
>PRK09733 putative fimbrial protein; Provisional
Probab=21.88  E-value=57  Score=13.59  Aligned_cols=20  Identities=10%  Similarity=0.180  Sum_probs=11.8

Q ss_pred             CCHHHHHHHHHHHHHHHHCC
Q ss_conf             92599999999996310122
Q gi|254780607|r    1 MCRKIIFALTIIAIAFQSMA   20 (131)
Q Consensus         1 m~k~il~~~~~~~~s~~a~a   20 (131)
                      |||-|+.++..++.+..+.+
T Consensus         2 mKk~ll~~~~~~~~s~~~~A   21 (181)
T PRK09733          2 FKKSLLVAGVAMILSNNVFA   21 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             06889999999998666576


Done!