Query         gi|254780722|ref|YP_003065135.1| pilus assembly protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 187
No_of_seqs    118 out of 2435
Neff          9.5 
Searched_HMMs 13730
Date          Wed Jun  1 08:06:49 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780722.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1gpja1 a.151.1.1 (A:303-404)   26.5      14   0.001   13.5   4.9   93    9-107     6-99  (102)
  2 d1xkpa1 a.243.1.3 (A:73-269) O  22.1      17  0.0013   13.0   9.2   16   64-79     45-60  (197)
  3 d2imha1 d.153.1.7 (A:1-229) Hy  20.0      15  0.0011   13.4   0.8   77   22-98     54-158 (229)
  4 d2ea9a1 d.110.8.1 (A:8-110) Hy  17.7      22  0.0016   12.4   3.2   24    9-32     45-68  (103)
  5 d2inwa1 d.110.8.1 (A:4-120) Hy  16.9      23  0.0016   12.3   3.2   24    8-31     55-78  (117)
  6 d1seda_ a.219.1.1 (A:) Hypothe  14.9      26  0.0019   12.0   4.6   15   64-78     66-80  (112)
  7 d1sqga1 a.79.1.3 (A:5-144) Rib  11.6      32  0.0023   11.4   7.4   57   19-75      7-64  (140)
  8 d1np3a1 a.100.1.2 (A:183-327)   11.3      33  0.0024   11.3   8.9   81   22-102    27-109 (145)
  9 d2ezla_ a.4.1.2 (A:) Ibeta sub  10.0      36  0.0026   11.0   7.9   57   18-76     37-93  (99)
 10 d2iuba2 f.17.3.1 (A:286-349) M   9.1      39  0.0029   10.8   1.2   40  130-170    11-50  (64)

No 1  
>d1gpja1 a.151.1.1 (A:303-404) Glutamyl tRNA-reductase dimerization domain {Archaeon Methanopyrus kandleri [TaxId: 2320]}
Probab=26.46  E-value=14  Score=13.53  Aligned_cols=93  Identities=11%  Similarity=0.095  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999999999999999995699989999999992484289999999998630388889999977534873479999999
Q gi|254780722|r    9 TAKFLDDFPNALDIIVRSVRAGLPVSDAVAVIVGQSSDPVRSEFRRVIETQHLGLSLSESISRMVRYMPLQEVSFFSTVI   88 (187)
Q Consensus         9 ~~~~~~~l~~~l~~l~~~l~aG~sl~~Al~~~a~~~~~~l~~e~~~i~~~~~~G~~~~~al~~~~~~~~~~~~~~~~~~l   88 (187)
                      ..-+++++..|...+-..     .....+...-+....--..|+.+..+++..| +.++++..++.+.-.+-+......+
T Consensus         6 E~II~ee~~~F~~w~~~~-----~~~p~I~~lr~~~e~ir~~Elekal~kl~~~-~~e~vie~l~~~l~nKllH~pt~~l   79 (102)
T d1gpja1           6 EKLIEEELSTVEEELEKL-----KERRLVADVAKSLHEIKDRELERALRRLKTG-DPENVLQDFAEAYTKRLINVLTSAI   79 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHSCSCC------CCTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999866-----3237999999999999999999999764789-9899999999999998887799999


Q ss_pred             HHHHHCCCC-HHHHHHHHHH
Q ss_conf             998742574-6899999999
Q gi|254780722|r   89 SVQSQLGGN-LSEALANLSR  107 (187)
Q Consensus        89 ~~~~~~gg~-~~~~L~~la~  107 (187)
                      ....+.|.+ ....|+++.+
T Consensus        80 r~~~~e~~~~~~~~lr~~~~   99 (102)
T d1gpja1          80 MELPDEYRRAASRALRRASE   99 (102)
T ss_dssp             HSSCTTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHC
T ss_conf             98887544899999999862


No 2  
>d1xkpa1 a.243.1.3 (A:73-269) Outer membrane protein yopN (LcrE) {Yersinia pestis [TaxId: 632]}
Probab=22.05  E-value=17  Score=13.01  Aligned_cols=16  Identities=19%  Similarity=-0.037  Sum_probs=5.4

Q ss_pred             CHHHHHHHHHHHCCCH
Q ss_conf             8889999977534873
Q gi|254780722|r   64 SLSESISRMVRYMPLQ   79 (187)
Q Consensus        64 ~~~~al~~~~~~~~~~   79 (187)
                      ++.+-+..+...++.|
T Consensus        45 t~~ql~~~L~q~f~d~   60 (197)
T d1xkpa1          45 SLSQLKAYLEGKSEEP   60 (197)
T ss_dssp             CHHHHHHHHHHHCSCH
T ss_pred             CHHHHHHHHHHHCCCH
T ss_conf             8999999998769996


No 3  
>d2imha1 d.153.1.7 (A:1-229) Hypothetical protein SPO2555 {Silicibacter pomeroyi [TaxId: 89184]}
Probab=20.05  E-value=15  Score=13.41  Aligned_cols=77  Identities=13%  Similarity=0.095  Sum_probs=43.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHH----------------------------HHHHHHCCCCHHHHHHHHH
Q ss_conf             999999569998999999999248428999999----------------------------9998630388889999977
Q gi|254780722|r   22 IIVRSVRAGLPVSDAVAVIVGQSSDPVRSEFRR----------------------------VIETQHLGLSLSESISRMV   73 (187)
Q Consensus        22 ~l~~~l~aG~sl~~Al~~~a~~~~~~l~~e~~~----------------------------i~~~~~~G~~~~~al~~~~   73 (187)
                      ..-..++.|.+..+++..+.+..+++-.+.+.-                            +.-++-.|..+.++|.+..
T Consensus        54 ~~l~~l~~G~s~~~al~~l~~~D~~~~~RQ~~vvD~~G~~A~~TG~~~~~~~gh~~g~~~~~aGN~L~~~~Vl~aM~~aF  133 (229)
T d2imha1          54 EVLQHLRDGSHPEDAVNHVTSQDSGRAYRQLAAMDLLGNAAAFTGSENQDIKGSVTFASGIASGNMLGDNSVLGAMTEAF  133 (229)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHTCTTGGGCEEEEEETTSCEEEEECTTSCSSCEEEEETTEEEEEESCSCTHHHHHHHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEECCCCCEEEEECCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHH
T ss_conf             99999986999999999997448873200388980889989988866643300401698698705678712999999999


Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf             5348734799999999987425746
Q gi|254780722|r   74 RYMPLQEVSFFSTVISVQSQLGGNL   98 (187)
Q Consensus        74 ~~~~~~~~~~~~~~l~~~~~~gg~~   98 (187)
                      +...-+--.++..+|......||+.
T Consensus       134 ~~~~g~LaeRLl~AL~AG~~aGGD~  158 (229)
T d2imha1         134 VASDLTFERRLLAALIAAEGAGSDF  158 (229)
T ss_dssp             HHCCSCHHHHHHHHHHHHHHTC---
T ss_pred             HHCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             8569999999999999998742798


No 4  
>d2ea9a1 d.110.8.1 (A:8-110) Hypothetical protein YfjZ {Escherichia coli [TaxId: 562]}
Probab=17.69  E-value=22  Score=12.42  Aligned_cols=24  Identities=21%  Similarity=0.200  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999999956999
Q gi|254780722|r    9 TAKFLDDFPNALDIIVRSVRAGLP   32 (187)
Q Consensus         9 ~~~~~~~l~~~l~~l~~~l~aG~s   32 (187)
                      ..+++..||.++.+|..++.+|.-
T Consensus        45 ~~~Ld~aFP~~i~qle~ml~sGeL   68 (103)
T d2ea9a1          45 CPKLDVVFPHFISQIESMLTTGEL   68 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             989999999999999998645998


No 5  
>d2inwa1 d.110.8.1 (A:4-120) Hypothetical protein YeeU {Shigella flexneri [TaxId: 623]}
Probab=16.90  E-value=23  Score=12.31  Aligned_cols=24  Identities=13%  Similarity=0.173  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999999999995699
Q gi|254780722|r    8 RTAKFLDDFPNALDIIVRSVRAGL   31 (187)
Q Consensus         8 R~~~~~~~l~~~l~~l~~~l~aG~   31 (187)
                      -..+++..||.++.+|..++.+|.
T Consensus        55 ~~~~Ld~aFP~~ikqlE~ml~sGe   78 (117)
T d2inwa1          55 DAYHLDQAFPLLMKQLELMLTGGE   78 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             999999999999999999864478


No 6  
>d1seda_ a.219.1.1 (A:) Hypothetical protein YhaI {Bacillus subtilis [TaxId: 1423]}
Probab=14.86  E-value=26  Score=11.99  Aligned_cols=15  Identities=0%  Similarity=0.067  Sum_probs=6.0

Q ss_pred             CHHHHHHHHHHHCCC
Q ss_conf             888999997753487
Q gi|254780722|r   64 SLSESISRMVRYMPL   78 (187)
Q Consensus        64 ~~~~al~~~~~~~~~   78 (187)
                      .++.-|..|+...+.
T Consensus        66 ~F~~Ll~~Fag~L~~   80 (112)
T d1seda_          66 TFDKLLALFAGQLNE   80 (112)
T ss_dssp             CCHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             399999999753565


No 7  
>d1sqga1 a.79.1.3 (A:5-144) Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain {Escherichia coli [TaxId: 562]}
Probab=11.62  E-value=32  Score=11.40  Aligned_cols=57  Identities=14%  Similarity=0.129  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH-HCCCCHHHHHHHHHHH
Q ss_conf             99999999956999899999999924842899999999986-3038888999997753
Q gi|254780722|r   19 ALDIIVRSVRAGLPVSDAVAVIVGQSSDPVRSEFRRVIETQ-HLGLSLSESISRMVRY   75 (187)
Q Consensus        19 ~l~~l~~~l~aG~sl~~Al~~~a~~~~~~l~~e~~~i~~~~-~~G~~~~~al~~~~~~   75 (187)
                      +++.+...+..|.++.+++....+...+.-+.-+..++... +.-..++..+..+.++
T Consensus         7 A~q~L~~v~~~g~~l~~~l~~~~~~l~~~dr~~~~~lv~gvlr~~~~ld~~i~~~l~~   64 (140)
T d1sqga1           7 AAQAVEQVVEQGQSLSNILPPLQQKVSDKDKALLQELCFGVLRTLSQLDWLINKLMAR   64 (140)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999998199899999999985988889999999999998699999999987230


No 8  
>d1np3a1 a.100.1.2 (A:183-327) Class I ketol-acid reductoisomerase {Pseudomonas aeruginosa [TaxId: 287]}
Probab=11.28  E-value=33  Score=11.33  Aligned_cols=81  Identities=12%  Similarity=-0.093  Sum_probs=41.5

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHCCCHHHHHHHHHHHHHHHCCCCHH
Q ss_conf             99999956999899999999924842899999999986303888899999--7753487347999999999874257468
Q gi|254780722|r   22 IIVRSVRAGLPVSDAVAVIVGQSSDPVRSEFRRVIETQHLGLSLSESISR--MVRYMPLQEVSFFSTVISVQSQLGGNLS   99 (187)
Q Consensus        22 ~l~~~l~aG~sl~~Al~~~a~~~~~~l~~e~~~i~~~~~~G~~~~~al~~--~~~~~~~~~~~~~~~~l~~~~~~gg~~~   99 (187)
                      ..-.+..+|.++..|..++.++.+.+..-..+.-...+....|-..-...  .+.+.-....+..........++|.-..
T Consensus        27 ~fe~lve~G~~pe~Ay~e~~he~~lI~~li~~~Gl~~m~~~iSdTAeyG~y~~~~~~~~~~~k~~mk~~l~~IqsG~fak  106 (145)
T d1np3a1          27 GFETLVEAGYAPEMAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAK  106 (145)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHTTHHHH
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCHHHC
T ss_conf             99999983986999999999701136899999739999998530888999998778645977799999999981442411


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780722|r  100 EAL  102 (187)
Q Consensus       100 ~~L  102 (187)
                      +..
T Consensus       107 ~~i  109 (145)
T d1np3a1         107 MFI  109 (145)
T ss_dssp             HHH
T ss_pred             CCC
T ss_conf             022


No 9  
>d2ezla_ a.4.1.2 (A:) Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase {Bacteriophage mu [TaxId: 10677]}
Probab=9.99  E-value=36  Score=11.05  Aligned_cols=57  Identities=12%  Similarity=0.101  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf             99999999995699989999999992484289999999998630388889999977534
Q gi|254780722|r   18 NALDIIVRSVRAGLPVSDAVAVIVGQSSDPVRSEFRRVIETQHLGLSLSESISRMVRYM   76 (187)
Q Consensus        18 ~~l~~l~~~l~aG~sl~~Al~~~a~~~~~~l~~e~~~i~~~~~~G~~~~~al~~~~~~~   76 (187)
                      +++..+..+.++|.+...|+..++.+..-..+....+..  .-.|.+..|-|-.+..+.
T Consensus        37 ~~l~~V~~L~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~--~V~g~~r~DWLpaLl~~~   93 (99)
T d2ezla_          37 PAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYY--QVQKFAKPDWAAALVDGR   93 (99)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHSSSCHHHHHHHHH--HHHTSCSTTHHHHTTSCS
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHH--HHCCCCHHHHHHHHCCCC
T ss_conf             999999999986970899999999995988999999999--978998888899875674


No 10 
>d2iuba2 f.17.3.1 (A:286-349) Magnesium transport protein CorA {Thermotoga maritima [TaxId: 2336]}
Probab=9.07  E-value=39  Score=10.83  Aligned_cols=40  Identities=13%  Similarity=0.010  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             79999999999999999787899999508008999999999
Q gi|254780722|r  130 AWIIGSLPFCVSTLVYFTSPGYMNVLINDPRGHMLLGVAAA  170 (187)
Q Consensus       130 ~~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~l~~~~~  170 (187)
                      ..-+..+|..++.-+..++-... +..+.+.|-........
T Consensus        11 ~it~iflP~t~i~gifGMN~~~~-P~~~~~~~~~~~~~~~~   50 (64)
T d2iuba2          11 IIATIFMPLTFIAGIYGMNFEYM-PELRWKWGYPVVLAVMG   50 (64)
T ss_dssp             HHHHHHHHHHHHTTSCC---------------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCC-CCCCCCHHHHHHHHHHH
T ss_conf             99999999999996631677889-88786279999999999


Done!