Query         gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 135
No_of_seqs    117 out of 1182
Neff          6.9 
Searched_HMMs 13730
Date          Wed Jun  1 03:40:22 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780329.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 d1loua_ d.58.14.1 (A:) Ribosom 100.0 6.3E-31 4.6E-35  199.2  10.2   96    1-96      1-96  (97)
  2 d2j5aa1 d.58.14.1 (A:3-108) Ri 100.0 1.6E-30 1.1E-34  196.9   9.9  100    1-100     5-105 (106)
  3 d2qalf1 d.58.14.1 (F:1-100) Ri 100.0 4.9E-31 3.6E-35  199.8   4.8  100    1-101     1-100 (100)
  4 d1vmba_ d.58.14.1 (A:) Ribosom 100.0 3.6E-30 2.6E-34  194.8   7.1   96    1-96      2-98  (107)
  5 d1sc6a3 d.58.18.1 (A:327-410)   49.1     7.8 0.00057   16.8   7.7   63   19-91     21-83  (84)
  6 d2nzca1 d.58.18.14 (A:2-81) Hy  30.2      16  0.0012   15.1   6.1   58   20-85     15-72  (80)
  7 d1vq3a_ d.284.1.1 (A:) PurS su  27.2      18  0.0013   14.7   8.2   72    1-90      5-83  (86)
  8 d1jjcb4 d.58.13.1 (B:682-785)   23.7      20  0.0015   14.4   2.1   23    5-27     15-37  (104)
  9 d2raqa1 d.58.61.1 (A:3-95) Unc  13.5      36  0.0026   12.9   3.1   18   25-42     62-79  (93)
 10 d3bpda1 d.58.61.1 (A:1-91) Unc  12.8      38  0.0028   12.8   3.0   18   25-42     62-79  (91)

No 1  
>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]}
Probab=99.97  E-value=6.3e-31  Score=199.18  Aligned_cols=96  Identities=26%  Similarity=0.505  Sum_probs=94.6

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||+++|++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         1 M~~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~   80 (97)
T d1loua_           1 MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR   80 (97)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECGGGHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             98613999989999989999999999999986898899985007782420246466369999999968999999999866


Q ss_pred             CCCHHEEEEEEEECCC
Q ss_conf             9802100112441134
Q gi|254780329|r   81 IDENVLRSLTLLVDSH   96 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~~   96 (135)
                      +|++|||||+||++++
T Consensus        81 l~~~VlR~l~vk~~e~   96 (97)
T d1loua_          81 IRDNVRRVMVVKSQEP   96 (97)
T ss_dssp             TSTTEEEEEEEECSSC
T ss_pred             CCCCEEEEEEEEECCC
T ss_conf             7747278999971689


No 2  
>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]}
Probab=99.96  E-value=1.6e-30  Score=196.86  Aligned_cols=100  Identities=29%  Similarity=0.582  Sum_probs=95.8

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECC-HHHHHHHHHHH
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089-77999999980
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASP-PAAIHEMKRKM   79 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~-~~~i~el~~~l   79 (135)
                      ||+||++||++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++ |+.+++|++.|
T Consensus         5 Mr~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~Ikk~~~G~Y~~~~f~~~~~~~i~el~~~l   84 (106)
T d2j5aa1           5 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYFLVQFKTENPQLPNELDFQL   84 (106)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEECSSCSSSCSEEEEEEEEEEESCTTHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCEEECHHHHHHHCCCEEEEEEEEEECCHHHHHHHHHHH
T ss_conf             25021999988999989999999999999997898089984203250154653325308999999978688999999985


Q ss_pred             CCCCHHEEEEEEEECCCCCCC
Q ss_conf             898021001124411345564
Q gi|254780329|r   80 RIDENVLRSLTLLVDSHEQSP  100 (135)
Q Consensus        80 k~~~~VLR~l~vk~~~~~~~~  100 (135)
                      +++++|||||+||+++.....
T Consensus        85 ~l~~~VlR~l~vkl~~~~~~~  105 (106)
T d2j5aa1          85 KIDEDVIRWLNIQIKESEVKK  105 (106)
T ss_dssp             HHCTTEEEEEEEEECGGGCCC
T ss_pred             CCCCCEEEEEEEEECCHHCCC
T ss_conf             777682579999964221004


No 3  
>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]}
Probab=99.96  E-value=4.9e-31  Score=199.81  Aligned_cols=100  Identities=31%  Similarity=0.571  Sum_probs=96.7

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||++||++|++++ +++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         1 M~~YE~~~Il~p~~~e-~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~   79 (100)
T d2qalf1           1 MRHYEIVFMVHPDQSE-QVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFR   79 (100)
T ss_dssp             CCEECEEEEECGGGTT-HHHHHHHHHHHHHHHTTCCCCCCCCCBSCBCSSCTTSCSBCBBCCCCEECCHHHHHHHHHHTT
T ss_pred             CCCCEEEEEECCCCHH-HHHHHHHHHHHHHHHCCCEEEEEEEEEEEECCCCCCCCCEEEEEEEEEECCHHHHHHHHHHHC
T ss_conf             9852499997888078-999999999999986898899986200030244246677359999999528888999999863


Q ss_pred             CCCHHEEEEEEEECCCCCCCC
Q ss_conf             980210011244113455643
Q gi|254780329|r   81 IDENVLRSLTLLVDSHEQSPT  101 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~~~~~~~  101 (135)
                      +|++|||||+||+++..+++|
T Consensus        80 ~~~~VlR~l~vk~~~~~~e~S  100 (100)
T d2qalf1          80 FNDAVIRSMVMRTKHAVTEAS  100 (100)
T ss_dssp             SCTTEEEEEECCCSSCCCSCC
T ss_pred             CCCCEEEEEEEEECCCCCCCC
T ss_conf             765725899998356767898


No 4  
>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]}
Probab=99.96  E-value=3.6e-30  Score=194.75  Aligned_cols=96  Identities=20%  Similarity=0.436  Sum_probs=93.1

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHC-CCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHH
Q ss_conf             987059999878999999999999999999856-9789997036865353032224189999999808977999999980
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQEN-GGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKM   79 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~-gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l   79 (135)
                      ||+||++||++|+++++++..+++++.++|+++ ||+|.++++||+|+|||||+|+++|+|++|+|+++|+.+++|++.|
T Consensus         2 ~R~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l   81 (107)
T d1vmba_           2 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYTVIYFRCDGQNLQELENFY   81 (107)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSTHHHHHHH
T ss_pred             CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEECCCCCEEEEEEEEEEECHHHHHHHHHHH
T ss_conf             73657999988999989999999999999985699889998720223050475888379999999998988899999986


Q ss_pred             CCCCHHEEEEEEEECCC
Q ss_conf             89802100112441134
Q gi|254780329|r   80 RIDENVLRSLTLLVDSH   96 (135)
Q Consensus        80 k~~~~VLR~l~vk~~~~   96 (135)
                      ++|++|||||+||+++.
T Consensus        82 ~l~~~VlR~livk~~~~   98 (107)
T d1vmba_          82 RVTPEIIRWQTFRRFDL   98 (107)
T ss_dssp             HTCTTEEEEEEEECHHH
T ss_pred             CCCCCEEEEEEEECCCC
T ss_conf             57768378999972100


No 5  
>d1sc6a3 d.58.18.1 (A:327-410) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Escherichia coli [TaxId: 562]}
Probab=49.14  E-value=7.8  Score=16.85  Aligned_cols=63  Identities=13%  Similarity=0.192  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHHEEEEEE
Q ss_conf             9999999999998569789997036865353032224189999999808977999999980898021001124
Q gi|254780329|r   19 IKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTL   91 (135)
Q Consensus        19 ~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~VLR~l~v   91 (135)
                      ...++.++.+++.+.|..|.....          +....+-|.++.++.+.....++-..++--+.|+|.-++
T Consensus        21 ~PGvla~I~~~l~~~~iNI~~~~~----------~~~~~~~~a~~~i~~D~~~~~~v~~~i~~l~~Vi~vR~l   83 (84)
T d1sc6a3          21 RPGVLTALNKIFAEQGVNIAAQYL----------QTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLL   83 (84)
T ss_dssp             CTTHHHHHHHHHHHTTCEEEEEEE----------EECSSEEEEEEEEECCHHHHHHHHHHHHTSTTEEEEEEC
T ss_pred             CCCHHHHHHHHHHHCCCCHHHHCC----------CCCCCCCEEEEEEECCCCCHHHHHHHHHCCCCEEEEEEE
T ss_conf             699899999999973999899624----------457877489999978887779999999779987999973


No 6  
>d2nzca1 d.58.18.14 (A:2-81) Hypothetical protein TM1266 {Thermotoga maritima [TaxId: 2336]}
Probab=30.17  E-value=16  Score=15.05  Aligned_cols=58  Identities=14%  Similarity=0.196  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHCCCCHH
Q ss_conf             999999999998569789997036865353032224189999999808977999999980898021
Q gi|254780329|r   20 KDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENV   85 (135)
Q Consensus        20 ~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk~~~~V   85 (135)
                      .+...+++++++++|+-|..     +.-++|+  ...- .-..+.+.++.+.+..|..+|..-+.|
T Consensus        15 ~~~a~kVn~iL~~yg~~I~g-----RmGip~~--~~~v-~iIsl~v~g~~d~I~~L~gkLg~i~gV   72 (80)
T d2nzca1          15 EKAYRQVNELLHNFSEDILL-----RVGYPVR--EENM-AIIFLVLKTDNDTIGALSGKLGQISGV   72 (80)
T ss_dssp             HHHHHHHHHHHHHTGGGEEE-----EEEEEEG--GGTE-EEEEEEEEECHHHHHHHHHHHHTSTTE
T ss_pred             HHHHHHHHHHHHHCCCEEEE-----ECCCCCC--CCCC-EEEEEEEECCHHHHHHHHHHHCCCCCE
T ss_conf             77689999999877887898-----5468705--4692-599999988887999988763699988


No 7  
>d1vq3a_ d.284.1.1 (A:) PurS subunit of FGAM synthetase {Thermotoga maritima [TaxId: 2336]}
Probab=27.24  E-value=18  Score=14.75  Aligned_cols=72  Identities=10%  Similarity=0.191  Sum_probs=48.9

Q ss_pred             CCCC--EEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHH-----HHH
Q ss_conf             9870--599998789999999999999999998569789997036865353032224189999999808977-----999
Q gi|254780329|r    1 MKLY--EHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPA-----AIH   73 (135)
Q Consensus         1 M~~Y--E~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~-----~i~   73 (135)
                      |+.|  ++.+.++|.+.+.+...+.    ..+...|.              ..+++-+.|-|+.+.++++..     .+.
T Consensus         5 m~~~k~~V~V~~K~gVlDPqG~av~----~aL~~lG~--------------~~v~~vr~gK~~~~~i~~~d~e~a~~~v~   66 (86)
T d1vq3a_           5 LPLFKFAIDVQYRSNVRDPRGETIE----RVLREEKG--------------LPVKKLRLGKSIHLEVEAENKEKAYEIVK   66 (86)
T ss_dssp             CCEEEEEEEEEECTTSCCHHHHHHH----HHHHHTTC--------------CCEEEEEEEEEEEEEEECSSHHHHHHHHH
T ss_pred             CCEEEEEEEEEECCCCCCCHHHHHH----HHHHHCCC--------------CCCCEEEEEEEEEEEECCCCHHHHHHHHH
T ss_conf             7338999999989987271799999----99987278--------------77660688889999980699899999999


Q ss_pred             HHHHHHCCCCHHEEEEE
Q ss_conf             99998089802100112
Q gi|254780329|r   74 EMKRKMRIDENVLRSLT   90 (135)
Q Consensus        74 el~~~lk~~~~VLR~l~   90 (135)
                      ++-+.|-.|+-|=+|-+
T Consensus        67 ~~c~~lLaNpvIE~y~i   83 (86)
T d1vq3a_          67 KACEELLVNPVVEEYEV   83 (86)
T ss_dssp             HHHHHTTSCTTTEEEEE
T ss_pred             HHHHHHCCCCCEEEEEE
T ss_conf             99998717765038999


No 8  
>d1jjcb4 d.58.13.1 (B:682-785) Phenylalanyl-tRNA synthetase {Thermus thermophilus [TaxId: 274]}
Probab=23.68  E-value=20  Score=14.44  Aligned_cols=23  Identities=0%  Similarity=0.082  Sum_probs=15.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             59999878999999999999999
Q gi|254780329|r    5 EHVFLLRQDISSQQIKDTIGQYQ   27 (135)
Q Consensus         5 E~~~i~~p~~~~~~~~~~~~~~~   27 (135)
                      .+-|+++.+++-.++.+.+....
T Consensus        15 DiS~~v~~~~~~~~i~~~i~~~~   37 (104)
T d1jjcb4          15 DLAVVVPAPTPYGEVEALVREAA   37 (104)
T ss_dssp             EECCEEESSSCHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHHHC
T ss_conf             08999789888899999999845


No 9  
>d2raqa1 d.58.61.1 (A:3-95) Uncharacterized protein MTH889 {Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=13.52  E-value=36  Score=12.94  Aligned_cols=18  Identities=28%  Similarity=0.525  Sum_probs=11.2

Q ss_pred             HHHHHHHHCCCEEEEEEC
Q ss_conf             999999856978999703
Q gi|254780329|r   25 QYQSLIQENGGEVRLVNE   42 (135)
Q Consensus        25 ~~~~~i~~~gg~i~~~e~   42 (135)
                      .+.+.|++.||.|++.+.
T Consensus        62 ~i~~~IE~~Gg~IHSIDe   79 (93)
T d2raqa1          62 EITRAIESYGGSIHSVDE   79 (93)
T ss_dssp             HHHHHHHHTTCEEEEEEE
T ss_pred             HHHHHHHHCCCEEEEEEE
T ss_conf             999999975985787700


No 10 
>d3bpda1 d.58.61.1 (A:1-91) Uncharacterized protein AF1549 {Archaeoglobus fulgidus [TaxId: 2234]}
Probab=12.78  E-value=38  Score=12.81  Aligned_cols=18  Identities=33%  Similarity=0.630  Sum_probs=10.1

Q ss_pred             HHHHHHHHCCCEEEEEEC
Q ss_conf             999999856978999703
Q gi|254780329|r   25 QYQSLIQENGGEVRLVNE   42 (135)
Q Consensus        25 ~~~~~i~~~gg~i~~~e~   42 (135)
                      .+.+.|++.||.|++.+.
T Consensus        62 ~i~~~IE~~Gg~IHSIDe   79 (91)
T d3bpda1          62 QIKGVIEDMGGVIHSVDE   79 (91)
T ss_dssp             HHHHHHHTTTCEEEEEEE
T ss_pred             HHHHHHHHCCCEEEEEHH
T ss_conf             999999975985787701


Done!