Query         gi|255764484|ref|YP_003065144.2| hypothetical protein CLIBASIA_03090 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 43
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 33803
Date          Wed Jun  1 14:10:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764484.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1jb0_B Photosystem I P700 chl  53.9      14 0.00043   18.5   3.4   22    3-24      8-29  (131)
  2 >1r5q_A KAI A, circadian oscil  13.4      72  0.0021   14.8   1.0   17   25-41     36-52  (102)
  3 >1v2z_A Circadian clock protei  12.9      80  0.0024   14.6   1.1   17   25-41     43-59  (111)
  4 >1r8j_A KAIA; circadian clock   12.4      81  0.0024   14.6   1.0   17   25-41     43-59  (111)
  5 >1v54_I STA, cytochrome C oxid   8.6 1.7E+02   0.005   13.0   4.6   34    4-37     21-54  (73)
  6 >1ji6_A Pesticidial crystal pr   6.7 2.1E+02  0.0061   12.5   2.6   16    6-21      3-18  (96)
  7 >1jb0_B Photosystem I P700 chl   4.4   3E+02  0.0087   11.7   1.3   10   15-24     65-74  (80)
  8 >3h6n_A Plexin-D1; structural    4.2 3.1E+02  0.0091   11.6   1.2   14   25-38     32-45  (127)
  9 >3kuz_A Plexin-C1; structural    4.1 3.1E+02  0.0093   11.6   1.6   14   25-38     54-67  (126)
 10 >1twf_B DNA-directed RNA polym   4.1 3.1E+02  0.0093   11.6   1.0    6   30-35     34-39  (175)

No 1  
>>1jb0_B Photosystem I P700 chlorophyll A apoprotein A2; membrane protein, multiprotein-pigment complex, photosynthesis; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} (B:33-163)
Probab=53.94  E-value=14  Score=18.46  Aligned_cols=22  Identities=41%  Similarity=0.807  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999865899999999866
Q gi|255764484|r    3 RLIEILLLSSFAVIAIIFLWAD   24 (43)
Q Consensus         3 rlieilllssfaviaiiflwad   24 (43)
                      ++-.-+..|.|+-+||||+|..
T Consensus         8 ~l~~KIFssHfghLaiIflW~s   29 (131)
T 1jb0_B            8 NLYQKIFASHFGHLAIIFLWVS   29 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999874137899999960


No 2  
>>1r5q_A KAI A, circadian oscillation regulator; four-helix-bundle, gene regulation; 2.00A {Nostoc SP} (A:)
Probab=13.42  E-value=72  Score=14.85  Aligned_cols=17  Identities=24%  Similarity=0.358  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHCCHHH
Q ss_conf             65776999985432564
Q gi|255764484|r   25 IREKSISAFFRDIPIAL   41 (43)
Q Consensus        25 ireksisaffrdipial   41 (43)
                      |.+---.|||-|||+.-
T Consensus        36 id~fVn~aFfadi~v~~   52 (102)
T 1r5q_A           36 IDKFINAVFCANIPVPE   52 (102)
T ss_dssp             HHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHCCCCHHH
T ss_conf             99999999981784789


No 3  
>>1v2z_A Circadian clock protein KAIA homolog; all alpha, riken structural genomics/proteomics initiative, RSGI, structural genomics; 1.80A {Thermosynechococcus elongatus bp-1} (A:)
Probab=12.92  E-value=80  Score=14.62  Aligned_cols=17  Identities=41%  Similarity=0.565  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHCCHHH
Q ss_conf             65776999985432564
Q gi|255764484|r   25 IREKSISAFFRDIPIAL   41 (43)
Q Consensus        25 ireksisaffrdipial   41 (43)
                      |.+---.|||-|||+.-
T Consensus        43 id~FVn~aFfadi~v~~   59 (111)
T 1v2z_A           43 IDEFVSKAFFADISVSQ   59 (111)
T ss_dssp             HHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHCCCCHHH
T ss_conf             99999999971774889


No 4  
>>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc 7942} (A:179-289)
Probab=12.40  E-value=81  Score=14.60  Aligned_cols=17  Identities=35%  Similarity=0.567  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHCCHHH
Q ss_conf             65776999985432564
Q gi|255764484|r   25 IREKSISAFFRDIPIAL   41 (43)
Q Consensus        25 ireksisaffrdipial   41 (43)
                      |.+---.|||-|||+.-
T Consensus        43 id~FVn~aFfadi~v~~   59 (111)
T 1r8j_A           43 IDNFVNMAFFADVPVTK   59 (111)
T ss_dssp             HHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHCCCCHHH
T ss_conf             99999988853784779


No 5  
>>1v54_I STA, cytochrome C oxidase polypeptide VIC; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} (I:)
Probab=8.56  E-value=1.7e+02  Score=12.96  Aligned_cols=34  Identities=21%  Similarity=0.322  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999998658999999998666577699998543
Q gi|255764484|r    4 LIEILLLSSFAVIAIIFLWADIREKSISAFFRDI   37 (43)
Q Consensus         4 lieilllssfaviaiiflwadireksisaffrdi   37 (43)
                      ++.-+.+|-.+..+.-|++++-|.+.-..|++.-
T Consensus        21 l~~a~~lsl~~~~~~k~~v~~pRKkaYadFYknY   54 (73)
T 1v54_I           21 IVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNY   54 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC
T ss_conf             9999999999999999872447578999999812


No 6  
>>1ji6_A Pesticidial crystal protein CRY3BB; toxin; 2.40A {Bacillus thuringiensis} (A:126-221)
Probab=6.74  E-value=2.1e+02  Score=12.49  Aligned_cols=16  Identities=38%  Similarity=0.557  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999865899999999
Q gi|255764484|r    6 EILLLSSFAVIAIIFL   21 (43)
Q Consensus         6 eilllssfaviaiifl   21 (43)
                      |+++|+.||..|-..|
T Consensus         3 e~~lLp~yaq~AnlHL   18 (96)
T 1ji6_A            3 EVLFLPTYAQAANTHL   18 (96)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             1004899999999999


No 7  
>>1jb0_B Photosystem I P700 chlorophyll A apoprotein A2; membrane protein, multiprotein-pigment complex, photosynthesis; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} (B:164-218,B:269-293)
Probab=4.42  E-value=3e+02  Score=11.70  Aligned_cols=10  Identities=40%  Similarity=0.737  Sum_probs=7.4

Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999866
Q gi|255764484|r   15 VIAIIFLWAD   24 (43)
Q Consensus        15 viaiiflwad   24 (43)
                      .|++.|+||.
T Consensus        65 a~~vlf~~a~   74 (80)
T 1jb0_B           65 AIAVLFIVAG   74 (80)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
T ss_conf             9999999875


No 8  
>>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens} (A:)
Probab=4.22  E-value=3.1e+02  Score=11.61  Aligned_cols=14  Identities=36%  Similarity=0.904  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             65776999985432
Q gi|255764484|r   25 IREKSISAFFRDIP   38 (43)
Q Consensus        25 ireksisaffrdip   38 (43)
                      ..||-+.|++|..|
T Consensus        32 vKeKiLDavYk~~p   45 (127)
T 3h6n_A           32 VKEKILEAFCKNVP   45 (127)
T ss_dssp             HHHHHHHHHSTTSC
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999999972388


No 9  
>>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens} (A:)
Probab=4.10  E-value=3.1e+02  Score=11.56  Aligned_cols=14  Identities=29%  Similarity=0.368  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             65776999985432
Q gi|255764484|r   25 IREKSISAFFRDIP   38 (43)
Q Consensus        25 ireksisaffrdip   38 (43)
                      ..||-+.|+||..|
T Consensus        54 VKeKILDavYk~~p   67 (126)
T 3kuz_A           54 AKEKIFQAFLSKNG   67 (126)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999980289


No 10 
>>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (B:1-42,B:542-549,B:630-754)
Probab=4.10  E-value=3.1e+02  Score=11.56  Aligned_cols=6  Identities=100%  Similarity=1.514  Sum_probs=0.0

Q ss_pred             HHHHHH
Q ss_conf             999985
Q gi|255764484|r   30 ISAFFR   35 (43)
Q Consensus        30 isaffr   35 (43)
                      ||+||+
T Consensus        34 is~~f~   39 (175)
T 1twf_B           34 ISAFFR   39 (175)
T ss_dssp             HHHHHH
T ss_pred             HHHHHC
T ss_conf             999868


Done!