Query         gi|254780984|ref|YP_003065397.1| hypothetical protein CLIBASIA_04425 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 125
No_of_seqs    2 out of 4
Neff          1.1 
Searched_HMMs 13730
Date          Wed Jun  1 10:58:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780984.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 d1xeqa1 a.16.1.1 (A:15-103) N-  13.2      39  0.0029   13.1   4.2   52   45-96     31-82  (89)
  2 d2ifxa1 d.58.4.19 (A:1-108) Hy  12.4      41   0.003   13.0   1.8   19   73-91     80-98  (108)
  3 d1hhsa_ e.8.1.6 (A:) dsRNA pha  10.3      18  0.0013   15.1  -0.9   18  108-125   182-206 (664)
  4 d2c0ga1 a.71.1.1 (A:1146-1251)  10.0      50  0.0036   12.5   2.4   21   17-37      5-25  (106)
  5 d2ao9a1 a.4.1.17 (A:13-132) Ph   9.3      53  0.0039   12.3   1.2   46   46-91     17-74  (120)
  6 d1j5wa_ d.104.1.1 (A:) Glycyl-   9.2      54  0.0039   12.3   2.0   13   12-24    167-179 (281)
  7 d2g7ja1 d.198.5.1 (A:1-112) Pu   6.6      38  0.0028   13.2  -0.5   28   24-51     75-103 (112)
  8 d1sbqa_ c.124.1.6 (A:) 5,10-me   5.4      79  0.0058   11.3   0.5   12  112-123   116-127 (164)
  9 d1xhca3 d.87.1.1 (A:290-351) N   4.4      15  0.0011   15.6  -3.8   14   74-87     34-47  (62)
 10 d1xs8a_ d.279.1.1 (A:) Hypothe   4.2   1E+02  0.0074   10.7   1.2   26    2-27     40-65  (91)

No 1  
>d1xeqa1 a.16.1.1 (A:15-103) N-terminal, RNA-binding domain of nonstructural protein NS1 {Influenza B virus [TaxId: 11520]}
Probab=13.15  E-value=39  Score=13.12  Aligned_cols=52  Identities=29%  Similarity=0.241  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             6799999630079999999999987624836789999878777751686732
Q gi|254780984|r   45 SSRLAQLCAENEKRLKEFDKITRELNTLSENEKKAFFEHEKKVTSNLNYNAR   96 (125)
Q Consensus        45 ssrlaqlcaenekrlkefdkITR~~~~L~~~~KKAFF~HEKKV~~~LNYNA~   96 (125)
                      ..||..|-..-+.+.|.-.||.-+..|.|-.++||.=-.--||---.|-.||
T Consensus        31 q~rl~rlk~kl~s~ikt~nk~epe~kr~sle~~kaigvkm~k~llf~~psag   82 (89)
T d1xeqa1          31 QDRLHRLKRKLESRIKTHNKSEPENKRMSLEERKAIGVKMMKVLLFMDPSAG   82 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCGGGCCCHHHHHHHHHHHHHHHTTCCCCSS
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCCC
T ss_conf             5589999999997535887677104342378764342767766423366557


No 2  
>d2ifxa1 d.58.4.19 (A:1-108) Hypothetical protein Reut_A1503 {Ralstonia eutropha [TaxId: 106590]}
Probab=12.41  E-value=41  Score=12.99  Aligned_cols=19  Identities=37%  Similarity=0.639  Sum_probs=13.9

Q ss_pred             CHHHHHHHHHHHHHHHHHC
Q ss_conf             8367899998787777516
Q gi|254780984|r   73 SENEKKAFFEHEKKVTSNL   91 (125)
Q Consensus        73 ~~~~KKAFF~HEKKV~~~L   91 (125)
                      ..|-.||+|+|.|-....|
T Consensus        80 ~sdirkawfehgk~figql   98 (108)
T d2ifxa1          80 ASDIRKAWFEHGKTFIGQL   98 (108)
T ss_dssp             HCHHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHCCEEEEEC
T ss_conf             9889999997260622202


No 3  
>d1hhsa_ e.8.1.6 (A:) dsRNA phage RNA-dependent RNA-polymerase {Bacteriophage PHI-6 [TaxId: 10879]}
Probab=10.31  E-value=18  Score=15.07  Aligned_cols=18  Identities=44%  Similarity=0.923  Sum_probs=11.4

Q ss_pred             HHCCEE-------CCCCHHHHHCCC
Q ss_conf             201501-------167112100149
Q gi|254780984|r  108 ARGKYR-------YGNGYYRNYRSQ  125 (125)
Q Consensus       108 AR~KYR-------ygngyyrnyrsq  125 (125)
                      +.|+|+       +|.-||+.||.|
T Consensus       182 ~kg~y~~af~~~d~~g~yY~~y~~q  206 (664)
T d1hhsa_         182 LQGKFDDAYQLHQMGGAYYVVYRAQ  206 (664)
T ss_dssp             HTTCHHHHHHHHCCCSCEEEEEEEE
T ss_pred             HCCCHHHHHHHCCCCCCEEEEHHHC
T ss_conf             2341466565302465257651321


No 4  
>d2c0ga1 a.71.1.1 (A:1146-1251) Windbeutel, C-terminal domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}
Probab=10.02  E-value=50  Score=12.51  Aligned_cols=21  Identities=5%  Similarity=0.316  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHCCCCCCHHHHH
Q ss_conf             777533332077766434556
Q gi|254780984|r   17 LNLYDAKARRFPTYGSEERIA   37 (125)
Q Consensus        17 lnlydakarrfptygseeria   37 (125)
                      +.-+|+-|..|-.-+.++|-+
T Consensus         5 i~~~D~La~eF~~a~~~er~~   25 (106)
T d2c0ga1           5 IKEFNEVLKNYANIPDAEQLK   25 (106)
T ss_dssp             CHHHHHHHTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCHHHHHH
T ss_conf             388999999998377888999


No 5  
>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}
Probab=9.32  E-value=53  Score=12.35  Aligned_cols=46  Identities=26%  Similarity=0.342  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHH------HHHHHHHHH----HC--CHHHHHHHHHHHHHHHHHC
Q ss_conf             7999996300799999------999999876----24--8367899998787777516
Q gi|254780984|r   46 SRLAQLCAENEKRLKE------FDKITRELN----TL--SENEKKAFFEHEKKVTSNL   91 (125)
Q Consensus        46 srlaqlcaenekrlke------fdkITR~~~----~L--~~~~KKAFF~HEKKV~~~L   91 (125)
                      -+-|++|++||---..      -|.|..+|.    +|  -+.+.|+|.+-..-|+|.+
T Consensus        17 ~~AA~~l~~Ne~~~~~~~ekktqeqiAeelGisr~tLyrWrt~dk~FI~y~nevAd~~   74 (120)
T d2ao9a1          17 IQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTKNQDFIAFKSEVADSF   74 (120)
T ss_dssp             HHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCHHCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_conf             9999998603001100033414999999958018889887606626999999999999


No 6  
>d1j5wa_ d.104.1.1 (A:) Glycyl-tRNA synthetase (GlyRS) alpha chain {Thermotoga maritima [TaxId: 2336]}
Probab=9.23  E-value=54  Score=12.33  Aligned_cols=13  Identities=23%  Similarity=0.434  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9987777753333
Q gi|254780984|r   12 LISNVLNLYDAKA   24 (125)
Q Consensus        12 lisnvlnlydaka   24 (125)
                      .|-+|-|.||-.-
T Consensus       167 ylQ~vd~v~Dl~w  179 (281)
T d1j5wa_         167 YLQGVDNVYEVQW  179 (281)
T ss_dssp             HHHTCSSGGGCEE
T ss_pred             HHHCCCHHEEEEC
T ss_conf             9848640403222


No 7  
>d2g7ja1 d.198.5.1 (A:1-112) Putative cytoplasmic protein YgaC {Salmonella typhimurium [TaxId: 90371]}
Probab=6.64  E-value=38  Score=13.19  Aligned_cols=28  Identities=32%  Similarity=0.420  Sum_probs=16.9

Q ss_pred             HHHCCCCCCHHHHHHHHC-CCHHHHHHHH
Q ss_conf             320777664345565407-7636799999
Q gi|254780984|r   24 ARRFPTYGSEERIATCAK-PGYSSRLAQL   51 (125)
Q Consensus        24 arrfptygseeriatcak-pgyssrlaql   51 (125)
                      -.+||-|-..|.-+.-.- -|+|||.+-.
T Consensus        75 Y~~FPlyl~g~~~~~yGIphGFsSR~~L~  103 (112)
T d2g7ja1          75 YQNFPLYLGGETHEHYGIPHGFSSRIALE  103 (112)
T ss_dssp             CCCSCCCCSSSSCCEEECEECCSCHHHHH
T ss_pred             HHCCCCCCCCCCHHHCCCCCCCCHHHHHH
T ss_conf             43177654655221117885623699999


No 8  
>d1sbqa_ c.124.1.6 (A:) 5,10-methenyltetrahydrofolate synthetase homolog MPN348 {Mycoplasma pneumoniae [TaxId: 2104]}
Probab=5.37  E-value=79  Score=11.33  Aligned_cols=12  Identities=42%  Similarity=1.090  Sum_probs=7.2

Q ss_pred             EECCCCHHHHHC
Q ss_conf             011671121001
Q gi|254780984|r  112 YRYGNGYYRNYR  123 (125)
Q Consensus       112 YRygngyyrnyr  123 (125)
                      --||.|||-.+-
T Consensus       116 LGyGgGyYDR~L  127 (164)
T d1sbqa_         116 LGFGKGYYDRYL  127 (164)
T ss_dssp             ECCSSCHHHHHG
T ss_pred             CCCCCCHHHHHH
T ss_conf             514658099999


No 9  
>d1xhca3 d.87.1.1 (A:290-351) NADH oxidase /nitrite reductase {Pyrococcus furiosus [TaxId: 2261]}
Probab=4.35  E-value=15  Score=15.58  Aligned_cols=14  Identities=36%  Similarity=0.724  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             36789999878777
Q gi|254780984|r   74 ENEKKAFFEHEKKV   87 (125)
Q Consensus        74 ~~~KKAFF~HEKKV   87 (125)
                      ..+.|+|++|||-|
T Consensus        34 d~~tK~Fy~d~Kii   47 (62)
T d1xhca3          34 EDNTKVFYENGKII   47 (62)
T ss_dssp             ETTEEEEC-----C
T ss_pred             CCCCEEEEECCCEE
T ss_conf             21132666679588


No 10 
>d1xs8a_ d.279.1.1 (A:) Hypothetical protein YggX {Salmonella typhimurium [TaxId: 90371]}
Probab=4.25  E-value=1e+02  Score=10.71  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             16899999999987777753333207
Q gi|254780984|r    2 KKYITLLTVLLISNVLNLYDAKARRF   27 (125)
Q Consensus         2 kkyitlltvllisnvlnlydakarrf   27 (125)
                      ..++..-|.|+--+-||+.|.++|.|
T Consensus        40 ~~Wl~~QtmLINE~rL~l~d~~~R~~   65 (91)
T d1xs8a_          40 AQWQHKQTMLINEKKLNMMNAEHRKL   65 (91)
T ss_dssp             HHHHHHHHHHHHHHCCCTTSHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf             99998527531203579799789999


Done!