Query         gi|254780122|ref|YP_003064535.1| hypothetical protein CLIBASIA_00005 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 123
No_of_seqs    2 out of 4
Neff          1.5 
Searched_HMMs 13730
Date          Wed May 18 18:29:04 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780122.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 d2au5a1 a.244.1.1 (A:1-132) Hy  22.9      22  0.0016   14.4   4.1   58   25-84     41-98  (132)
  2 d1oi0a_ c.97.3.1 (A:) Hypothet  14.2      17  0.0012   15.1  -0.1   13   17-29     68-80  (121)
  3 d1s7za_ a.159.3.1 (A:) B-form   11.3      15  0.0011   15.4  -1.1   32   67-100    65-96  (106)
  4 d1yuaa2 g.41.3.3 (A:66-122) Pr   9.7      50  0.0036   12.3   1.3   16   16-31      4-19  (57)
  5 d1j7qa_ a.39.1.5 (A:) Calcium    7.8      59  0.0043   11.8   1.6   49   43-94     11-60  (86)
  6 d1tbua1 d.38.1.3 (A:13-116) Pe   6.5      69   0.005   11.4   1.1   24   15-38     55-78  (104)
  7 d2f1fa1 d.58.18.6 (A:2-77) Ace   6.3      62  0.0045   11.7   0.4   36   21-56     35-71  (76)
  8 d2oqma1 a.213.1.3 (A:1-171) Hy   5.7      76  0.0056   11.1   1.6   13   25-37     34-46  (171)
  9 d1ayia_ a.28.2.1 (A:) ImmE7 pr   5.4      80  0.0058   11.0   2.6   10  104-113    42-51  (86)
 10 d1jnra3 d.168.1.1 (A:257-401)    5.2      82   0.006   10.9   1.9   23   78-100    87-109 (145)

No 1  
>d2au5a1 a.244.1.1 (A:1-132) Hypothetical protein EF2947 {Enterococcus faecalis [TaxId: 1351]}
Probab=22.93  E-value=22  Score=14.38  Aligned_cols=58  Identities=22%  Similarity=0.248  Sum_probs=39.8

Q ss_pred             CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             876605766500036899999975889999875577888799999999999999998788
Q gi|254780122|r   25 DPDISIEMQISENQRYLDEEISQCNAVVDVFKRSDSTILDKLDAMDDLKTYISLLQATAK   84 (123)
Q Consensus        25 ~P~~~~E~~i~E~~~~L~~~i~~~~~~v~~~~Rs~~T~l~~~D~~~~~~~~I~L~~A~~k   84 (123)
                      +|+.--+|+  +...+|+++..-|..||-----.+..--+...+|+++++.|-|--|-++
T Consensus        41 ~P~VL~~ME--~~P~WL~Es~~~~Q~~iV~SL~~~~N~~~~~~L~~E~~~Li~LY~~~~~   98 (132)
T d2au5a1          41 SPIVLAEME--KDPNWLEEAAGGMQGVIVQSLLEDENFSSVEQLKGELARLIRLYFALAK   98 (132)
T ss_dssp             CHHHHHHHH--HCTTHHHHHHHHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHH--HCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999885--1830899998776788998875257857499999999999999999987


No 2  
>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
Probab=14.22  E-value=17  Score=15.10  Aligned_cols=13  Identities=38%  Similarity=0.460  Sum_probs=7.8

Q ss_pred             HHHHCCCCCCCCE
Q ss_conf             6563799987660
Q gi|254780122|r   17 YFHSHPNADPDIS   29 (123)
Q Consensus        17 ~F~S~~N~~P~~~   29 (123)
                      -|||||+..|.-|
T Consensus        68 i~HSHP~~~a~PS   80 (121)
T d1oi0a_          68 TVHSHPSPSCRPS   80 (121)
T ss_dssp             EEEEESSSCCSCC
T ss_pred             EEEECCCCCCCCC
T ss_conf             9972689999769


No 3  
>d1s7za_ a.159.3.1 (A:) B-form DNA mimic Ocr {Bacteriophage T7 [TaxId: 10760]}
Probab=11.30  E-value=15  Score=15.44  Aligned_cols=32  Identities=34%  Similarity=0.495  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999987888999999997543138
Q gi|254780122|r   67 DAMDDLKTYISLLQATAKNLKSLLKEYWEESLDG  100 (123)
Q Consensus        67 D~~~~~~~~I~L~~A~~k~L~~~l~E~WE~~~D~  100 (123)
                      .+|.++|-.+-.+||  |--+-+++.+|..++||
T Consensus        65 GLmpdtkDV~~ILqa--RIyE~L~ndl~~d~ed~   96 (106)
T d1s7za_          65 GLMPDTKDVIRILQA--RIYEQLTIDLWEDAEDL   96 (106)
T ss_dssp             GGSCCCSCHHHHHHH--HHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCHHHHHHHHH--HHHHHHHHHCCCCHHHH
T ss_conf             778881899999999--99999987431448999


No 4  
>d1yuaa2 g.41.3.3 (A:66-122) Prokaryotic DNA topoisomerase I, a C-terminal fragment {Escherichia coli [TaxId: 562]}
Probab=9.69  E-value=50  Score=12.26  Aligned_cols=16  Identities=25%  Similarity=0.476  Sum_probs=12.6

Q ss_pred             HHHHHCCCCCCCCEEE
Q ss_conf             3656379998766057
Q gi|254780122|r   16 FYFHSHPNADPDISIE   31 (123)
Q Consensus        16 ~~F~S~~N~~P~~~~E   31 (123)
                      .|+++||-.||+-|--
T Consensus         4 ~yL~~AP~~D~dGn~~   19 (57)
T d1yuaa2           4 RYLADAPQQDPEGNKT   19 (57)
T ss_dssp             HHHHHSCSSCTTCCCE
T ss_pred             EHHHCCCCCCCCCCEE
T ss_conf             2522398659999976


No 5  
>d1j7qa_ a.39.1.5 (A:) Calcium vector protein {Amphioxus (Branchiostoma lanceolatum) [TaxId: 7740]}
Probab=7.81  E-value=59  Score=11.78  Aligned_cols=49  Identities=33%  Similarity=0.495  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             999975889999875577888799999999999999998-7888999999997
Q gi|254780122|r   43 EEISQCNAVVDVFKRSDSTILDKLDAMDDLKTYISLLQA-TAKNLKSLLKEYW   94 (123)
Q Consensus        43 ~~i~~~~~~v~~~~Rs~~T~l~~~D~~~~~~~~I~L~~A-~~k~L~~~l~E~W   94 (123)
                      ++-..|-++.|.|+|....|-..-|.||-+..   |-|. ++|.-+...+|.-
T Consensus        11 eekdecmkifdifdrnaeniapvsdtmdmltk---lgqtytkreteaimkear   60 (86)
T d1j7qa_          11 EEKDECMKIFDIFDRNAENIAPVSDTMDMLTK---LGQTYTKRETEAIMKEAR   60 (86)
T ss_dssp             THHHHHHHHHHHHSTTTTSCBCHHHHHHHHHH---TSCCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHHHHHC
T ss_conf             25778999999970352115771028999999---614776888999999800


No 6  
>d1tbua1 d.38.1.3 (A:13-116) Peroxisomal long-chain acyl-CoA thioesterase 1, TES1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=6.46  E-value=69  Score=11.38  Aligned_cols=24  Identities=21%  Similarity=0.261  Sum_probs=18.6

Q ss_pred             HHHHHHCCCCCCCCEEEEEEECHH
Q ss_conf             136563799987660576650003
Q gi|254780122|r   15 NFYFHSHPNADPDISIEMQISENQ   38 (123)
Q Consensus        15 N~~F~S~~N~~P~~~~E~~i~E~~   38 (123)
                      .-||+...+++..+-|+|+++-.-
T Consensus        55 h~~Fl~pg~~~~pi~~~Ve~lrdG   78 (104)
T d1tbua1          55 HSYFIKGGDPRTKITYHVQNLRNG   78 (104)
T ss_dssp             EEEECSCCCTTSCCEEEEEEEEEC
T ss_pred             EEEEECCCCCCCEEEEEEEEEECC
T ss_conf             899854889983099998752279


No 7  
>d2f1fa1 d.58.18.6 (A:2-77) Acetolactate synthase small subunit,  IlvH {Escherichia coli [TaxId: 562]}
Probab=6.29  E-value=62  Score=11.67  Aligned_cols=36  Identities=28%  Similarity=0.539  Sum_probs=24.6

Q ss_pred             CCCCCCCCE-EEEEEECHHHHHHHHHHHHHHHHHHHH
Q ss_conf             799987660-576650003689999997588999987
Q gi|254780122|r   21 HPNADPDIS-IEMQISENQRYLDEEISQCNAVVDVFK   56 (123)
Q Consensus        21 ~~N~~P~~~-~E~~i~E~~~~L~~~i~~~~~~v~~~~   56 (123)
                      .|..+|.+| +-+-+.....-++.-++|-+|+++|.+
T Consensus        35 ~~te~~~iSR~tivv~~~~~~i~qi~kQL~KlidV~~   71 (76)
T d2f1fa1          35 APTDDPTLSRMTIQTVGDEKVLEQIEKQLHKLVDVLR   71 (76)
T ss_dssp             EECSCSSEEEEEEEEESCHHHHHHHHHHHHHSTTEEE
T ss_pred             CCCCCCCEEEEEEEEECCHHHHHHHHHHHHCCCCEEE
T ss_conf             0457998129999997888899999999857878799


No 8  
>d2oqma1 a.213.1.3 (A:1-171) Hypothetical protein Sden0562 {Shewanella denitrificans [TaxId: 192073]}
Probab=5.72  E-value=76  Score=11.12  Aligned_cols=13  Identities=15%  Similarity=0.460  Sum_probs=4.2

Q ss_pred             CCCCEEEEEEECH
Q ss_conf             8766057665000
Q gi|254780122|r   25 DPDISIEMQISEN   37 (123)
Q Consensus        25 ~P~~~~E~~i~E~   37 (123)
                      +|+.-.+.+..+.
T Consensus        34 ~~~~ll~~rL~~D   46 (171)
T d2oqma1          34 DMDVLLNSRLAAD   46 (171)
T ss_dssp             CHHHHHTCCSSTT
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9999998552245


No 9  
>d1ayia_ a.28.2.1 (A:) ImmE7 protein (Im7) {Escherichia coli [TaxId: 562]}
Probab=5.41  E-value=80  Score=11.00  Aligned_cols=10  Identities=50%  Similarity=0.740  Sum_probs=5.7

Q ss_pred             HHHHHCCCHH
Q ss_conf             3567386756
Q gi|254780122|r  104 EEIYEHPDQE  113 (123)
Q Consensus       104 E~~~EHPDQE  113 (123)
                      +.+.|||+.-
T Consensus        42 ~~iteHP~gs   51 (86)
T d1ayia_          42 VKITEHPDGT   51 (86)
T ss_dssp             HHHHCCTTTT
T ss_pred             HHHHCCCCCC
T ss_conf             9997089988


No 10 
>d1jnra3 d.168.1.1 (A:257-401) Adenylylsulfate reductase A subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
Probab=5.22  E-value=82  Score=10.92  Aligned_cols=23  Identities=35%  Similarity=0.445  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99987888999999997543138
Q gi|254780122|r   78 LLQATAKNLKSLLKEYWEESLDG  100 (123)
Q Consensus        78 L~~A~~k~L~~~l~E~WE~~~D~  100 (123)
                      ++.+.++.+|.+-.|-||.-||-
T Consensus        87 ~~~~~~k~~k~le~eawedfLdM  109 (145)
T d1jnra3          87 LAGGDKKKLKHIYEEAFEDFLDM  109 (145)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             75411667788899999998647


Done!