Query         gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 83
No_of_seqs    108 out of 995
Neff          5.3 
Searched_HMMs 13730
Date          Wed Jun  1 03:04:17 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780330.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 d2uubr1 a.4.8.1 (R:19-88) Ribo  99.9 1.6E-25 1.2E-29  161.6   6.3   64   19-82      2-65  (70)
  2 d2qalr1 a.4.8.1 (R:19-73) Ribo  99.9 3.2E-24 2.3E-28  154.3   5.3   53   30-82      1-53  (55)
  3 d1twfa_ e.29.1.2 (A:) RBP1 {Ba  14.4      22  0.0016   15.4   0.6   28   30-57   1361-1388(1449)
  4 d2aama1 c.1.8.15 (A:28-312) Hy   8.8      59  0.0043   13.1   1.3   21   62-82    246-266 (285)
  5 d1su3a1 a.20.1.2 (A:32-98) Fib   7.3      51  0.0037   13.5   0.3   45   38-82      2-46  (67)
  6 d1knga_ c.47.1.10 (A:) Thiored   6.7      81  0.0059   12.3   2.8   31   42-72    112-143 (144)
  7 d1slma1 a.20.1.2 (A:16-80) Str   6.6      60  0.0044   13.0   0.5   42   41-82      4-45  (65)
  8 d2pbza2 d.142.1.9 (A:100-312)    6.6      83   0.006   12.3   2.3   24   56-79    186-209 (213)
  9 d1lrza2 d.108.1.4 (A:1-165) Me   5.7      73  0.0053   12.6   0.4   18   28-45     75-92  (165)
 10 d1em9a_ a.73.1.1 (A:) RSV caps   5.2      39  0.0028   14.1  -1.2   23   29-51     12-34  (147)

No 1  
>d2uubr1 a.4.8.1 (R:19-88) Ribosomal protein S18 {Thermus thermophilus [TaxId: 274]}
Probab=99.91  E-value=1.6e-25  Score=161.57  Aligned_cols=64  Identities=42%  Similarity=0.647  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             8854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   19 KSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        19 k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +.|..+..+++.+||||+++|++||||+|+|+||++||+|++|||+|++|||+||+||||||++
T Consensus         2 ~k~k~~~~~~~~iDYKn~~lL~~Fis~~GkIlprr~TGl~~k~Qr~l~~aIkrAR~~gLlPy~~   65 (70)
T d2uubr1           2 AKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFTE   65 (70)
T ss_dssp             CCTTTSSCSCCTTCTTCHHHHGGGBCSSSCBCCHHHHCCCHHHHHHHHHHHHHHHHTTSSCSCC
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             8756562546845866879999866998758167448978999999999999999974353108


No 2  
>d2qalr1 a.4.8.1 (R:19-73) Ribosomal protein S18 {Escherichia coli [TaxId: 562]}
Probab=99.89  E-value=3.2e-24  Score=154.31  Aligned_cols=53  Identities=57%  Similarity=0.940  Sum_probs=51.6

Q ss_pred             CCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             11446889999962899848550331748999999999999999704658676
Q gi|254780330|r   30 RIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        30 ~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      .|||||+++|++|||++|+|+||++||+|+++||+|++|||+||+|||||||+
T Consensus         1 ~iDYKn~~lL~~Fis~~GkI~~rr~Tgl~~k~Qr~l~~aIkrAR~~gLlP~~~   53 (55)
T d2qalr1           1 EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTD   53 (55)
T ss_dssp             CCCSSCHHHHGGGBCTTSSBCCSTTTCCCHHHHHHHHHHHHHHHHTTSSCSSS
T ss_pred             CCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             97833689999876998858387407878999999999999999840677245


No 3  
>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=14.41  E-value=22  Score=15.44  Aligned_cols=28  Identities=14%  Similarity=0.395  Sum_probs=20.1

Q ss_pred             CCCCCCHHHHHHHCCCCCEECCCHHHCC
Q ss_conf             1144688999996289984855033174
Q gi|254780330|r   30 RIDYKDIRLLNRFLSQRGKIVPSRISSV   57 (83)
Q Consensus        30 ~iDYKn~~lL~~Fis~~GkI~prr~TG~   57 (83)
                      .||+|+++++..+++..|.+.|=-..|+
T Consensus      1361 ~Id~rHi~LIad~MT~~G~~~~i~R~gi 1388 (1449)
T d1twfa_        1361 YVNYRHMALLVDVMTTQGGLTSVTRHGF 1388 (1449)
T ss_dssp             CCCHHHHHHHHHHTTTBSSCCCSSSCSS
T ss_pred             EECHHHHHHHHHHHCCCCEEEECCHHHH
T ss_conf             8879999999999775885710118981


No 4  
>d2aama1 c.1.8.15 (A:28-312) Hypothetical protein TM1410 {Thermotoga maritima [TaxId: 2336]}
Probab=8.81  E-value=59  Score=13.07  Aligned_cols=21  Identities=19%  Similarity=0.298  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCC
Q ss_conf             999999999999704658676
Q gi|254780330|r   62 QRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        62 Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      -.++....++++..|+.|||+
T Consensus       246 ~~~~~~~~~~~~~~GF~pyvs  266 (285)
T d2aama1         246 ISRILDYYEKAKRNGCIPYAA  266 (285)
T ss_dssp             HHHHHHHHHHHHHTTEEEEEE
T ss_pred             HHHHHHHHHHHHHCCCEEEEE
T ss_conf             999999999999759966771


No 5  
>d1su3a1 a.20.1.2 (A:32-98) Fibroblast collagenase (MMP-1) {Human (Homo sapiens) [TaxId: 9606]}
Probab=7.30  E-value=51  Score=13.46  Aligned_cols=45  Identities=7%  Similarity=0.112  Sum_probs=25.2

Q ss_pred             HHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             999962899848550331748999999999999999704658676
Q gi|254780330|r   38 LLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        38 lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +.+.|+...|-+-+.............+..||+.=+..+=||-|.
T Consensus         2 l~~~YL~~fgyl~~~~~~~~~~~~~~~~~~Aik~fQ~f~~L~~TG   46 (67)
T d1su3a1           2 LVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGLKVTG   46 (67)
T ss_dssp             HHHHHHHHHSCCC------------CHHHHHHHHHHHHTTCCCCS
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             899999981899988653224456589999999999982998546


No 6  
>d1knga_ c.47.1.10 (A:) Thioredoxin-like protein CcmG (CycY, DsbE) {Bradyrhizobium japonicum [TaxId: 375]}
Probab=6.70  E-value=81  Score=12.30  Aligned_cols=31  Identities=16%  Similarity=0.312  Sum_probs=18.6

Q ss_pred             HCCCCCEECCCHHHCCCHHHH-HHHHHHHHHH
Q ss_conf             628998485503317489999-9999999999
Q gi|254780330|r   42 FLSQRGKIVPSRISSVSHKKQ-RELAKAIKRA   72 (83)
Q Consensus        42 Fis~~GkI~prr~TG~~~k~Q-r~i~~aIKrA   72 (83)
                      +|...|+|.-+.+.-+....- ..|.++|+.|
T Consensus       112 liD~~G~i~~~~~G~~~~~~l~~~i~~~l~ka  143 (144)
T d1knga_         112 VVGREGTIVYKLVGPITPDNLRSVLLPQMEKA  143 (144)
T ss_dssp             EECTTSBEEEEEESCCCHHHHHHTHHHHHHHH
T ss_pred             EECCCCEEEEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             99589949999968899999999999999974


No 7  
>d1slma1 a.20.1.2 (A:16-80) Stromelysin-1 (MMP-3) {Human (Homo sapiens), fibroblast [TaxId: 9606]}
Probab=6.62  E-value=60  Score=13.03  Aligned_cols=42  Identities=12%  Similarity=0.111  Sum_probs=23.1

Q ss_pred             HHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             962899848550331748999999999999999704658676
Q gi|254780330|r   41 RFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        41 ~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +|+...|-+-+.............+..||+.=+..+=||-|.
T Consensus         4 ~YL~~fgyl~~~~~~~~~~~~~~~l~~Ai~~~Q~f~~L~~TG   45 (65)
T d1slma1           4 KYLENYYDLKKDVKQFVRRKDSGPVVKKIREMQKFLGLEVTG   45 (65)
T ss_dssp             HHHHHHSCCCCC---------CHHHHHHHHHHHHHTTCCCCS
T ss_pred             HHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             999980899987430024566799999999999983997425


No 8  
>d2pbza2 d.142.1.9 (A:100-312) 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP {Thermococcus kodakaraensis [TaxId: 311400]}
Probab=6.56  E-value=83  Score=12.26  Aligned_cols=24  Identities=13%  Similarity=0.119  Sum_probs=18.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             748999999999999999704658
Q gi|254780330|r   56 SVSHKKQRELAKAIKRARYLGLIA   79 (83)
Q Consensus        56 G~~~k~Qr~i~~aIKrAR~~gLlP   79 (83)
                      |-....-|+||++||.|-..+-|.
T Consensus       186 ~epmS~GrRIA~EIk~A~e~~~L~  209 (213)
T d2pbza2         186 GERLSMGRRIARELRLAEEEDRLE  209 (213)
T ss_dssp             SSCCCHHHHHHHHHHHHHTTTCCS
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCHH
T ss_conf             798518889999999998729554


No 9  
>d1lrza2 d.108.1.4 (A:1-165) Methicillin resistance protein FemA {Staphylococcus aureus [TaxId: 1280]}
Probab=5.66  E-value=73  Score=12.56  Aligned_cols=18  Identities=33%  Similarity=0.739  Sum_probs=12.9

Q ss_pred             CCCCCCCCHHHHHHHCCC
Q ss_conf             851144688999996289
Q gi|254780330|r   28 APRIDYKDIRLLNRFLSQ   45 (83)
Q Consensus        28 ~~~iDYKn~~lL~~Fis~   45 (83)
                      ...+||.|.++|..|+.+
T Consensus        75 GPv~d~~d~~ll~~~l~~   92 (165)
T d1lrza2          75 GPVIDYENQELVHFFFNE   92 (165)
T ss_dssp             CCEECTTCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHH
T ss_conf             976684688999999999


No 10 
>d1em9a_ a.73.1.1 (A:) RSV capsid protein {Rous sarcoma virus [TaxId: 11886]}
Probab=5.25  E-value=39  Score=14.12  Aligned_cols=23  Identities=22%  Similarity=0.242  Sum_probs=14.7

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECC
Q ss_conf             51144688999996289984855
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVP   51 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~p   51 (83)
                      +++|||.+.-|+.-+.++|--.|
T Consensus        12 ~pl~~k~ikeL~~av~~yG~~sp   34 (147)
T d1em9a_          12 TPLEPKLITRLADTVRTKGLRSP   34 (147)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTCH
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             68898999999999997198982


Done!