Query         gi|254780786|ref|YP_003065199.1| ribosome-binding factor A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 128
No_of_seqs    102 out of 1288
Neff          6.6 
Searched_HMMs 13730
Date          Wed Jun  1 06:13:12 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780786.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 d1kkga_ d.52.7.1 (A:) Ribosome 100.0 4.8E-30 3.5E-34  187.4   7.1  105    5-112     1-108 (108)
  2 d2e7ga1 d.52.7.1 (A:86-201) Ri 100.0 3.3E-30 2.4E-34  188.3   1.3  113    6-120     2-115 (116)
  3 d1josa_ d.52.7.1 (A:) Ribosome  99.9 1.8E-27 1.3E-31  172.9  11.5   96   11-110     1-99  (100)
  4 d1pa4a_ d.52.7.1 (A:) Ribosome  99.9 1.1E-27 8.3E-32  174.0   1.5   95   12-110     1-95  (96)
  5 d2dyja1 d.52.7.1 (A:4-94) Ribo  99.9 1.4E-23 9.9E-28  151.0  11.6   89   12-107     2-90  (91)
  6 d2uubb1 c.23.15.1 (B:7-240) Ri  19.5      26  0.0019   13.9   2.3   33   77-110   134-166 (234)
  7 d1aoya_ a.4.5.3 (A:) Arginine   17.4     6.6 0.00048   17.3  -1.5   46    1-56      1-53  (78)
  8 d2dita1 d.58.7.1 (A:8-106) HIV  13.9      30  0.0022   13.5   1.1   34   43-76     45-78  (99)
  9 d1fxla2 d.58.7.1 (A:119-203) H  11.6      43  0.0031   12.7   2.7   33   44-76     33-69  (85)
 10 d1b4aa1 a.4.5.3 (A:4-78) Argin  10.8      45  0.0033   12.5   1.4   58   10-77      2-75  (75)

No 1  
>d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]}
Probab=99.96  E-value=4.8e-30  Score=187.42  Aligned_cols=105  Identities=33%  Similarity=0.473  Sum_probs=94.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH
Q ss_conf             8777738999999999999999951413420126516898888985875655999982798647---7899999985689
Q gi|254780786|r    5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF   81 (128)
Q Consensus         5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~   81 (128)
                      |++++.|+.||+++|+++||++|.+ ++.||++++ +||||+|++|+||++|+||||++++.++   ++++++||+++|+
T Consensus         1 M~~~~~R~~rv~~~i~r~is~il~~-~~~dp~l~~-~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~~~L~~~~~~   78 (108)
T d1kkga_           1 MAKEFGRPQRVAQEMQKEIALILQR-EIKDPRLGM-MTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGF   78 (108)
T ss_dssp             CCCCSSSHHHHHHHHHHHHHHHTTS-SSSSGGGTS-CCBCSCEEEETTTTEEEEEEBCSGGGCHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCCC-EEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9986727899999999999999997-563865577-06994899768813189999954772067799999999997899


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCHHHHHH
Q ss_conf             9999999875214578589997386888999
Q gi|254780786|r   82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWK  112 (128)
Q Consensus        82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~  112 (128)
                      ||++||++| ++||||+|+|++|+++|++.+
T Consensus        79 ir~~l~~~l-~lr~~P~L~F~~D~s~e~a~R  108 (108)
T d1kkga_          79 IRSLLGKAM-RLRIVPELTFFYDNSLVEGMR  108 (108)
T ss_dssp             HHHHHHHHT-TCSCCCEEEEEECCTTSSSCC
T ss_pred             HHHHHHHHC-CCEECCEEEEEECCCHHHHCC
T ss_conf             999998447-980898889996595530057


No 2  
>d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.95  E-value=3.3e-30  Score=188.29  Aligned_cols=113  Identities=17%  Similarity=0.232  Sum_probs=101.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCC-HHHHHHHHHHHHHHHHH
Q ss_conf             77773899999999999999995141342012651689888898587565599998279864-77899999985689999
Q gi|254780786|r    6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS-PDRVISALNCNIKFIRG   84 (128)
Q Consensus         6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~-~~~~~~~L~~~~~~ir~   84 (128)
                      +++|.|+.|++++|+++|+++|.++.+.++ +.+..||||+|+||+||++|+||||++|+.+ .+.+.++|++++|+||+
T Consensus         2 k~~s~R~~kv~~li~k~is~il~~~~~~~~-l~~~~ItIt~V~vS~Dl~~AkVy~s~~~~~~~~~~~~~~L~~~~~~ir~   80 (116)
T d2e7ga1           2 KEDHARLRALNGLLYKALTDLLCTPEVSQE-LYDLNVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAVLQRSAAHMRH   80 (116)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHTTCTTTCHH-HHHHTCCEEEEEECTTSCCEEEEECCCSCHHHHHHHHHHHHHTHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCEEEEEEEEECCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             841478999999999999999985475766-5685699999997588767899998479656677779999999999999


Q ss_pred             HHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCH
Q ss_conf             999987521457858999738688899999985576
Q gi|254780786|r   85 RIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLP  120 (128)
Q Consensus        85 ~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~  120 (128)
                      .|++++ .+||+|+|+|++|++++++.+|++||+..
T Consensus        81 ~l~~~l-~lr~~P~L~F~~D~s~~~~~~i~~ll~~~  115 (116)
T d2e7ga1          81 LLMSQQ-TLRNVPPIVFVQDKGNAALAELDQLLAVA  115 (116)
T ss_dssp             HHHTCT-TCSCCCCEEEEETTCCCCCCCCCCCSCCC
T ss_pred             HHHHHH-CCCCCCEEEEEECCCHHHHHHHHHHHHHC
T ss_conf             999771-86233607999579888999999998723


No 3  
>d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]}
Probab=99.95  E-value=1.8e-27  Score=172.89  Aligned_cols=96  Identities=30%  Similarity=0.549  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCC---HHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999995141342012651689888898587565599998279864---77899999985689999999
Q gi|254780786|r   11 RALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS---PDRVISALNCNIKFIRGRIG   87 (128)
Q Consensus        11 R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~---~~~~~~~L~~~~~~ir~~l~   87 (128)
                      |+.||+++|+++||++|.+ ++.||+++  +||||+|++|+|+++|+||||++++.+   .++++++||+++|+||+++|
T Consensus         1 R~~rv~~~i~~~is~il~~-~i~d~~l~--~vtIt~V~~S~Dl~~A~Vy~s~~~~~~~~~~~~~~~~L~~~~~~ir~~la   77 (100)
T d1josa_           1 RSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPYIRSLLG   77 (100)
T ss_dssp             CHHHHHHHHHHHHHHHHHH-HCCCTTTC--CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9189999999999999997-56586668--05898999769834279999965761245599999999998999999999


Q ss_pred             HHHHHCCCCCEEEEEECCCHHHH
Q ss_conf             98752145785899973868889
Q gi|254780786|r   88 RSLRNLRYVPELRFRYDTSLQSY  110 (128)
Q Consensus        88 ~~l~~lr~~P~L~F~~D~s~e~~  110 (128)
                      +++ ++||+|+|+|++|+++|++
T Consensus        78 ~~l-~~r~~P~L~F~~D~s~e~g   99 (100)
T d1josa_          78 KAM-RLRIVPEIRFIYDQSLVEG   99 (100)
T ss_dssp             HHH-CCSSCCEEEEEECCCCCCC
T ss_pred             HHC-CCCCCCEEEEEECCCHHCC
T ss_conf             766-8816986899956862135


No 4  
>d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]}
Probab=99.93  E-value=1.1e-27  Score=173.99  Aligned_cols=95  Identities=19%  Similarity=0.250  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999995141342012651689888898587565599998279864778999999856899999999875
Q gi|254780786|r   12 ALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLR   91 (128)
Q Consensus        12 ~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~~l~   91 (128)
                      ++|++++|+++||++|.+ +++||+++  +||||+|++|+||++|+||||++++.+.++++++||+++|+||++||+++.
T Consensus         1 ~eR~~~~i~r~is~~l~~-ei~d~~l~--~vtIt~V~vS~Dl~~AkVy~s~~~~~~~~~~~~~L~~~~g~ir~~l~~~l~   77 (96)
T d1pa4a_           1 KERLENDIIRLINRTVIH-EIYNETVK--TGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVLAHNLY   77 (96)
T ss_dssp             CCHHHHHHHHHHHHHHTT-CSSSSCHH--HHCCSCCEEETTTTEEEECCCCSSSSSHHHHHHHHHHTHHHHHHHHHTTCC
T ss_pred             CHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             957999999999999998-67796668--158979997799767999998278410689999999989999999997668


Q ss_pred             HCCCCCEEEEEECCCHHHH
Q ss_conf             2145785899973868889
Q gi|254780786|r   92 NLRYVPELRFRYDTSLQSY  110 (128)
Q Consensus        92 ~lr~~P~L~F~~D~s~e~~  110 (128)
                       ||++|+|+|++|+++|++
T Consensus        78 -lr~~P~L~F~~D~s~e~~   95 (96)
T d1pa4a_          78 -LAKAVQIHFVKDKAIDNA   95 (96)
T ss_dssp             -CGGGCCCEECSSSTTSSC
T ss_pred             -CCCCCEEEEEECCCHHCC
T ss_conf             -703886899967864405


No 5  
>d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]}
Probab=99.90  E-value=1.4e-23  Score=150.98  Aligned_cols=89  Identities=19%  Similarity=0.272  Sum_probs=80.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999995141342012651689888898587565599998279864778999999856899999999875
Q gi|254780786|r   12 ALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLR   91 (128)
Q Consensus        12 ~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~~l~   91 (128)
                      ..|++++|+++||++|.  ++.||+++  +||||+|++|+|+++|+||||++++  .++++++||+++|+||+++++.+ 
T Consensus         2 k~rle~~i~r~is~il~--~~~d~~~~--~vtIt~V~~S~Dl~~akVyvs~~~~--~~~~~~~L~~~~~~ir~~l~~~l-   74 (91)
T d2dyja1           2 KAHLEAQLKRALAEEIQ--ALEDPRLF--LLTVEAVRLSKDGSVLSVYVEAFRE--EEGALRALSRAERRLVAALARRV-   74 (91)
T ss_dssp             HHHHHHHHHHHHHHHHH--TCCCGGGT--TCEEEEEEECTTSSEEEEEEECSSC--HHHHHHHHHHTHHHHHHHHHTTS-
T ss_pred             HHHHHHHHHHHHHHHHH--HCCCCCCC--CEEEEEEEECCCCCCEEEEEEECCC--HHHHHHHHHHHHHHHHHHHHHHC-
T ss_conf             37899999999999999--80686659--4599799988980037999996243--47899999998999999998567-


Q ss_pred             HCCCCCEEEEEECCCH
Q ss_conf             2145785899973868
Q gi|254780786|r   92 NLRYVPELRFRYDTSL  107 (128)
Q Consensus        92 ~lr~~P~L~F~~D~s~  107 (128)
                      ++|++|+|+|++|++.
T Consensus        75 ~~r~~P~L~F~~D~s~   90 (91)
T d2dyja1          75 RMRRLPRLEFLPWRAS   90 (91)
T ss_dssp             CCSSCCEEEEEEGGGC
T ss_pred             CCCCCCEEEEEECCCC
T ss_conf             9816987999968999


No 6  
>d2uubb1 c.23.15.1 (B:7-240) Ribosomal protein S2 {Thermus thermophilus [TaxId: 274]}
Probab=19.52  E-value=26  Score=13.90  Aligned_cols=33  Identities=15%  Similarity=0.318  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHH
Q ss_conf             8568999999998752145785899973868889
Q gi|254780786|r   77 CNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSY  110 (128)
Q Consensus        77 ~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~  110 (128)
                      +....+.+.++. ++.|+..|++.|..|...+..
T Consensus       134 ~~~~kl~k~~~G-i~~m~~~Pd~viv~d~~~~~~  166 (234)
T d2uubb1         134 HELERLQKYLSG-FRLLKRLPDAIFVVDPTKEAI  166 (234)
T ss_dssp             HHHHHHHHHSTT-GGGCSSCCSEEEESCTTTTHH
T ss_pred             HHHHHHHHHHCC-CHHHHHCCEEEEEECCCCCHH
T ss_conf             999999986222-000110331688705774288


No 7  
>d1aoya_ a.4.5.3 (A:) Arginine repressor (ArgR), N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}
Probab=17.41  E-value=6.6  Score=17.27  Aligned_cols=46  Identities=9%  Similarity=0.056  Sum_probs=25.2

Q ss_pred             CCCCCCCCCHHHHHHHHHH-------HHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEE
Q ss_conf             9988877773899999999-------9999999951413420126516898888985875655
Q gi|254780786|r    1 MKNKNPKNSRRALRVGEEV-------RSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVA   56 (128)
Q Consensus         1 mk~~~~~~s~R~~rv~~~i-------~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~A   56 (128)
                      |++..++. .|..-+..+|       |++|.+.|...         ++.+||..-+|+||+--
T Consensus         1 M~k~~kq~-~~l~~I~~li~~~~i~tQ~eL~~~L~~~---------G~~~vTQaTiSRDL~eL   53 (78)
T d1aoya_           1 MRSSAKQE-ELVKAFKALLKEEKFSSQGEIVAALQEQ---------GFDNINQSKVSRMLTKF   53 (78)
T ss_dssp             CCCCCCST-THHHHHHHHHHTCCCCSHHHHHHHHHHH---------TCSSCCHHHHHHHHHHH
T ss_pred             CCCHHHHH-HHHHHHHHHHHHCCCCCHHHHHHHHHHC---------CCCCHHHHHHHHHHHHH
T ss_conf             97157899-9999999999848867899999999983---------98501098899999992


No 8  
>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=13.87  E-value=30  Score=13.53  Aligned_cols=34  Identities=15%  Similarity=0.095  Sum_probs=21.4

Q ss_pred             EEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             9888898587565599998279864778999999
Q gi|254780786|r   43 SISEVCMSVDLRVATVYISLPLDVSPDRVISALN   76 (128)
Q Consensus        43 tIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~   76 (128)
                      .|+.|.+..+-....+||.+....+...++..||
T Consensus        45 ~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1          45 QIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCSEEEEETTCTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHC
T ss_conf             0799963477886479999898999999999868


No 9  
>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}
Probab=11.62  E-value=43  Score=12.69  Aligned_cols=33  Identities=21%  Similarity=0.282  Sum_probs=14.1

Q ss_pred             EEEEEECCCC----CEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             8888985875----65599998279864778999999
Q gi|254780786|r   44 ISEVCMSVDL----RVATVYISLPLDVSPDRVISALN   76 (128)
Q Consensus        44 It~V~vS~Dl----~~AkVyvs~~~~~~~~~~~~~L~   76 (128)
                      |.+|++-.|-    .....|+.+....+.+.+++.||
T Consensus        33 v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~ln   69 (85)
T d1fxla2          33 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN   69 (85)
T ss_dssp             EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHC
T ss_conf             6310301245443578716999858999999999838


No 10 
>d1b4aa1 a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]}
Probab=10.78  E-value=45  Score=12.53  Aligned_cols=58  Identities=12%  Similarity=0.190  Sum_probs=0.0

Q ss_pred             HHHHHHHHHH-------HHHHHHHHHHCCCCCCCCCCCEEEEEEEEECC---CCCEEEE------EEEECCCCCHHHHHH
Q ss_conf             3899999999-------99999999514134201265168988889858---7565599------998279864778999
Q gi|254780786|r   10 RRALRVGEEV-------RSALMWVILNNEFQDRLISRDVISISEVCMSV---DLRVATV------YISLPLDVSPDRVIS   73 (128)
Q Consensus        10 ~R~~rv~~~i-------~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~---Dl~~AkV------yvs~~~~~~~~~~~~   73 (128)
                      +|+..+.++|       |++|.+.|...        |  ++||..-+|+   +|...||      |+..+++.......+
T Consensus         2 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~--------G--i~vTQaTlSRDL~eLg~vKv~~~~g~~~Y~lp~~~~~~~~~   71 (75)
T d1b4aa1           2 QRHIKIREIIMSNDIETQDELVDRLREA--------G--FNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQ   71 (75)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHHT--------T--CCCCHHHHHHHHHHTTCEEEECSSSCEEEECTTCSSSCHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHC--------C--CCEEHHHHHHHHHHHCCEEEECCCCCEEEECCCCCCCCHHH
T ss_conf             2799999999868977899999999985--------9--86308999979999298881479986898628756669887


Q ss_pred             HHHH
Q ss_conf             9998
Q gi|254780786|r   74 ALNC   77 (128)
Q Consensus        74 ~L~~   77 (128)
                      .|.+
T Consensus        72 ~L~r   75 (75)
T d1b4aa1          72 KLKR   75 (75)
T ss_dssp             HHHH
T ss_pred             HHCC
T ss_conf             7349


Done!