Query         gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 124
No_of_seqs    127 out of 756
Neff          3.8 
Searched_HMMs 13730
Date          Tue May 24 09:07:31 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780266.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 d2uubl1 b.40.4.5 (L:5-122) Rib 100.0       0       0  395.9  11.6  118    2-120     1-118 (118)
  2 d1ah9a_ b.40.4.5 (A:) Translat  78.0     1.1 7.8E-05   22.6   3.7   45   30-84      7-55  (71)
  3 d1hr0w_ b.40.4.5 (W:) Translat  54.9     1.1   8E-05   22.5  -0.2   37   45-85     17-57  (71)
  4 d1jt8a_ b.40.4.5 (A:) Archaeal  38.2     7.7 0.00056   17.6   2.0   46   29-84     20-68  (102)
  5 d1d7qa_ b.40.4.5 (A:) Translat  36.3      14   0.001   16.1   4.2   46   29-84     31-79  (143)
  6 d1pb1a_ c.77.1.1 (A:) Isocitra  33.5     8.5 0.00062   17.3   1.6   17   68-84    134-153 (416)
  7 d3bula2 c.23.6.1 (A:741-896) M  25.5      17  0.0012   15.6   2.0   17   59-75      5-21  (156)
  8 d1q2la4 d.185.1.1 (A:24-263) P  24.4      22  0.0016   14.8   5.1   51   40-93      8-59  (240)
  9 d1ju2a1 c.3.1.2 (A:1-293,A:464  22.4     9.4 0.00068   17.0   0.2   15   64-78    284-298 (351)
 10 d1yrra1 b.92.1.5 (A:1-53,A:351  17.1      19  0.0014   15.3   0.8   26   58-89      4-29  (85)

No 1  
>d2uubl1 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]}
Probab=100.00  E-value=0  Score=395.87  Aligned_cols=118  Identities=69%  Similarity=1.083  Sum_probs=114.6

Q ss_pred             CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEE
Q ss_conf             55023542687378646666770006862124787567518456744243288999669969999807888754646789
Q gi|254780266|r    2 PTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVV   81 (124)
Q Consensus         2 pTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~V   81 (124)
                      ||||||+|++|+++. .+.++++|++|||++|||++++|++|||||||+||||+|+||||++||||||||||||||||+|
T Consensus         1 PTinQL~rk~R~kk~-~k~k~~aL~~~PqkkGvc~kv~~~~PKKPNSA~RKvarVrLsng~~v~AyIPG~GhnlqEHs~V   79 (118)
T d2uubl1           1 PTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV   79 (118)
T ss_dssp             CCHHHHHHHCCCCCC-CCCSCCCTTTCSCEEEEEEEEEEECCCTTCCSCEEEEEEEETTSCEEEEECCSSCCCCCTTCEE
T ss_pred             CCHHHHCCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCEEEEEECCCCCCCCCCCCEE
T ss_conf             987671036888776-6788852236976043888988822688861021389999629909999818997674557889


Q ss_pred             EEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             995378388887547898040014433420012112561
Q gi|254780266|r   82 MLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA  120 (124)
Q Consensus        82 LvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~  120 (124)
                      ||||||++|||||+||+|||+|||++|.+|+++||||||
T Consensus        80 LvrGGrv~DlPGVry~vvrG~~D~~~v~~Rk~~RSkYGt  118 (118)
T d2uubl1          80 LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT  118 (118)
T ss_dssp             EECCCCCTTSTTCCEEBCTTSTTCCCCTTCCSSTTTTTC
T ss_pred             EEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf             994886666777478997231014333665326676789


No 2  
>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]}
Probab=78.04  E-value=1.1  Score=22.56  Aligned_cols=45  Identities=22%  Similarity=0.382  Sum_probs=31.3

Q ss_pred             CCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC--C--CCCCCCEEEEE
Q ss_conf             2124787567518456744243288999669969999807888--7--54646789995
Q gi|254780266|r   30 QKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG--H--NLQEHSVVMLC   84 (124)
Q Consensus        30 qkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG--h--nlqehs~VLvr   84 (124)
                      +..|++++..      ||.    --+|+|.||.++.|||||-=  +  .+.+.+.|+|.
T Consensus         7 e~~G~V~e~l------g~~----~f~V~l~ng~~~~a~i~Gkmrk~ri~i~~GD~V~Ve   55 (71)
T d1ah9a_           7 EMQGTVLETL------PNT----MFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVE   55 (71)
T ss_dssp             ECCEEEEEEC------SSS----EEEEEETTSCEEEEEECSSGGGTTCCCCTTCEECCE
T ss_pred             EEEEEEEEEC------CCC----EEEEEECCCCEEEEECCCHHHEEEEEECCCCEEEEE
T ss_conf             9999999986------998----899996799799998464343027996499999999


No 3  
>d1hr0w_ b.40.4.5 (W:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]}
Probab=54.91  E-value=1.1  Score=22.50  Aligned_cols=37  Identities=30%  Similarity=0.536  Sum_probs=27.9

Q ss_pred             CCCCCCCEEEEEEECCCCEEEEEECCCC--C--CCCCCCEEEEEC
Q ss_conf             6744243288999669969999807888--7--546467899953
Q gi|254780266|r   45 KPNSALRKVIKARLTSGVEVIAYVPGEG--H--NLQEHSVVMLCG   85 (124)
Q Consensus        45 KPNSA~RKvarV~Lsng~~v~ayIPGeG--h--nlqehs~VLvrG   85 (124)
                      -||.-    -+|+|.||.++.|||||-=  +  .+.+.|.|+|.=
T Consensus        17 l~~~~----f~V~l~ng~~~~a~i~GkmRk~ri~i~~GD~V~Vel   57 (71)
T d1hr0w_          17 LPNAT----FRVKLDSGPEILAYISGKMRMHYIRILPGDRVVVEI   57 (71)
T ss_dssp             CTTTB----CCCEESSSCBCCCEECHHHHHTCCCCCTTCEEEEEC
T ss_pred             CCCCE----EEEEECCCCEEEEEECCHHHEEEEEECCCCEEEEEE
T ss_conf             89989----999987999999980544321269735999999997


No 4  
>d1jt8a_ b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Archaeon Methanococcus jannaschii [TaxId: 2190]}
Probab=38.21  E-value=7.7  Score=17.56  Aligned_cols=46  Identities=17%  Similarity=0.266  Sum_probs=34.6

Q ss_pred             CCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCC---CCCCCCCEEEEE
Q ss_conf             62124787567518456744243288999669969999807888---754646789995
Q gi|254780266|r   29 PQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEG---HNLQEHSVVMLC   84 (124)
Q Consensus        29 PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeG---hnlqehs~VLvr   84 (124)
                      -|.=|+|++.+.      |    --+.|.+.+|.+..|.|||--   -.+...+.|||.
T Consensus        20 ~e~y~~V~k~lG------~----~~~~V~c~dg~~rl~~irGK~Rk~~~I~~Gd~VlV~   68 (102)
T d1jt8a_          20 NEILGIIEQMLG------A----SRVRVRCLDGKTRLGRIPGRLKNRIWVREGDVVIVK   68 (102)
T ss_dssp             CCEEEEEECSSC------S----SEEEEEEETTEEEEEECCHHHHHHHCCCSCEEEEEC
T ss_pred             CEEEEEEEEECC------C----CEEEEEECCCCEEEEEECCCCCEEEEECCCCEEEEE
T ss_conf             889999999829------9----889999799999999984775104696499999999


No 5  
>d1d7qa_ b.40.4.5 (A:) Translation initiation factor-1a, eIF1a {Human (Homo sapiens) [TaxId: 9606]}
Probab=36.34  E-value=14  Score=16.07  Aligned_cols=46  Identities=11%  Similarity=0.198  Sum_probs=33.9

Q ss_pred             CCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCC---CCCCCCEEEEE
Q ss_conf             621247875675184567442432889996699699998078887---54646789995
Q gi|254780266|r   29 PQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGH---NLQEHSVVMLC   84 (124)
Q Consensus        29 PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGh---nlqehs~VLvr   84 (124)
                      -|.=|+|++.+.-          --+.|.+.+|.+.+|.|||--.   -+...+.|||-
T Consensus        31 ~e~ya~V~k~lG~----------~~~~V~~~dg~~rl~~irgk~r~r~~i~~Gd~VlV~   79 (143)
T d1d7qa_          31 GQEYAQVIKMLGN----------GRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVG   79 (143)
T ss_dssp             TEEEEEEEEECSS----------SEEEEEETTTEEEEEECCSGGGGSCCCCTTCEEEEE
T ss_pred             CEEEEEEEEECCC----------CEEEEEECCCCEEEEEECCCCEEEEEEECCCEEEEE
T ss_conf             8089999997399----------779999789999999953765147898189999994


No 6  
>d1pb1a_ c.77.1.1 (A:) Isocitrate dehydrogenase, ICDH {Escherichia coli [TaxId: 562]}
Probab=33.45  E-value=8.5  Score=17.29  Aligned_cols=17  Identities=12%  Similarity=0.208  Sum_probs=7.2

Q ss_pred             ECCCCCCCC---CCCEEEEE
Q ss_conf             078887546---46789995
Q gi|254780266|r   68 VPGEGHNLQ---EHSVVMLC   84 (124)
Q Consensus        68 IPGeGhnlq---ehs~VLvr   84 (124)
                      +||.-+.+.   .-+.|.||
T Consensus       134 ~pg~~spl~~~~~iD~vIvR  153 (416)
T d1pb1a_         134 YQGTPSPVKHPELTDMVIFR  153 (416)
T ss_dssp             CTTCCCSSSCGGGCEEEEEE
T ss_pred             CCCCCCCCCCCCCCCEEEEE
T ss_conf             67888643455644659986


No 7  
>d3bula2 c.23.6.1 (A:741-896) Methionine synthase, C-terminal domain {Escherichia coli [TaxId: 562]}
Probab=25.47  E-value=17  Score=15.56  Aligned_cols=17  Identities=47%  Similarity=0.667  Sum_probs=14.8

Q ss_pred             CCCCEEEEEECCCCCCC
Q ss_conf             69969999807888754
Q gi|254780266|r   59 TSGVEVIAYVPGEGHNL   75 (124)
Q Consensus        59 sng~~v~ayIPGeGhnl   75 (124)
                      ++|+.|++-++||.|.|
T Consensus         5 ~~gkivi~tv~gD~Hdi   21 (156)
T d3bula2           5 TNGKMVIATVKGDVHDI   21 (156)
T ss_dssp             CSCEEEEEEBTTCCCCH
T ss_pred             CCCEEEEEEECCCHHHH
T ss_conf             69979999618870068


No 8  
>d1q2la4 d.185.1.1 (A:24-263) Protease III {Escherichia coli [TaxId: 562]}
Probab=24.38  E-value=22  Score=14.85  Aligned_cols=51  Identities=20%  Similarity=0.227  Sum_probs=33.2

Q ss_pred             ECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEE-EEECCCCCCCCC
Q ss_conf             518456744243288999669969999807888754646789-995378388887
Q gi|254780266|r   40 TVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVV-MLCGGRVKDLPG   93 (124)
Q Consensus        40 ~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~V-LvrGGrv~DlPG   93 (124)
                      --|.+||.+-.|..-.++|+||.+|.. +|-.  ...--++. .+.+|-..|-|+
T Consensus         8 ~~~~~k~~~d~~~~~~~~L~NGl~V~~-~~~~--~~~~v~~~l~~~~Gs~~e~~~   59 (240)
T d1q2la4           8 QETIRKSDKDNRQYQAIRLDNGMVVLL-VSDP--QAVKSLSALVVPVGSLEDPEA   59 (240)
T ss_dssp             CSCCCCCTTCCCEEEEEEETTSCEEEE-EECT--TCSSEEEEEEESCCGGGCCGG
T ss_pred             CCCCCCCCCCCCCEEEEECCCCCEEEE-EECC--CCCEEEEEEEEECCCCCCCCC
T ss_conf             014779988874428999289999999-9979--998799999996774210234


No 9  
>d1ju2a1 c.3.1.2 (A:1-293,A:464-521) Hydroxynitrile lyase {Almond (Prunus dulcis) [TaxId: 3755]}
Probab=22.42  E-value=9.4  Score=17.04  Aligned_cols=15  Identities=27%  Similarity=0.255  Sum_probs=7.2

Q ss_pred             EEEEECCCCCCCCCC
Q ss_conf             999807888754646
Q gi|254780266|r   64 VIAYVPGEGHNLQEH   78 (124)
Q Consensus        64 v~ayIPGeGhnlqeh   78 (124)
                      +.+-.||.|.|||+|
T Consensus       284 ~~~dlPgVG~NL~DH  298 (351)
T d1ju2a1         284 VVLSHPYVGQCLVGK  298 (351)
T ss_dssp             CSEECTTTTESCBTT
T ss_pred             EECCCCCCCCCCCCC
T ss_conf             460398756341047


No 10 
>d1yrra1 b.92.1.5 (A:1-53,A:351-382) N-acetylglucosamine-6-phosphate deacetylase, NagA {Escherichia coli [TaxId: 562]}
Probab=17.11  E-value=19  Score=15.30  Aligned_cols=26  Identities=31%  Similarity=0.566  Sum_probs=16.0

Q ss_pred             ECCCCEEEEEECCCCCCCCCCCEEEEECCCCC
Q ss_conf             66996999980788875464678999537838
Q gi|254780266|r   58 LTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVK   89 (124)
Q Consensus        58 Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~   89 (124)
                      |+|++.++      |..+.+...|+|++|+..
T Consensus         4 l~n~rI~d------g~~~~~~~~i~i~~g~I~   29 (85)
T d1yrra1           4 LTQGRIFT------GHEFLDDHAVVIADGLIK   29 (85)
T ss_dssp             EESSEEEC------SSCEESSEEEEEETTEEE
T ss_pred             EEEEEEEC------CCCCEECCEEEEECCEEE
T ss_conf             98369988------998574128999322999


Done!