Query         gi|254780990|ref|YP_003065403.1| hypothetical protein CLIBASIA_04455 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 66
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 23785
Date          Tue May 31 23:23:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780990.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3do5_A HOM, homoserine dehydro  12.1      93  0.0039   14.0   3.1   61    4-66    233-293 (327)
  2 1np3_A Ketol-acid reductoisome   9.0 1.2E+02  0.0051   13.4   2.0   40    1-41     77-116 (338)
  3 3pvi_A Protein (pvuii endonucl   8.7      76  0.0032   14.4   0.5   16   51-66     90-105 (157)
  4 3ksk_A Type-2 restriction enzy   5.1 1.6E+02  0.0067   12.8   0.6   14   52-65    250-263 (324)
  5 2qj2_A Hepatocyte growth facto   4.2   2E+02  0.0082   12.3   0.6   12   17-28     61-72  (184)
  6 3kks_A Integrase, IN; beta-str   3.9 2.5E+02   0.011   11.8   0.9   10   32-41      3-12  (152)
  7 1h95_A CSD, Y-box binding prot   3.5 1.4E+02  0.0058   13.1  -0.7   12    2-13     24-35  (79)
  8 2k5n_A Putative cold-shock pro   3.4 1.5E+02  0.0063   12.9  -0.6   11    2-13     18-28  (74)
  9 3lk3_T Carmil homolog, leucine   3.3   2E+02  0.0083   12.3  -0.1   16    6-21     60-75  (115)
 10 3hn4_A Hepatocyte growth facto   3.2 2.4E+02    0.01   11.9   0.3   13   48-60     10-22  (264)

No 1  
>3do5_A HOM, homoserine dehydrogenase; NP_069768.1, putative homoserine dehydrogenase, structural genomics, joint center for structural genomics; 2.20A {Archaeoglobus fulgidus}
Probab=12.13  E-value=93  Score=13.99  Aligned_cols=61  Identities=20%  Similarity=0.198  Sum_probs=42.8

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCCCCCCCCEEEEEC
Q ss_conf             456434567775545413895218986502221345441052210076520002463465429
Q gi|254780990|r    4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEINCALLRRRHPINKYEKTDNFFALYT   66 (66)
Q Consensus         4 vpddgiddlfeedlfqydankselvlisslwsidffeincallrrrhpinkyektdnffalyt   66 (66)
                      |+-.||+.+..+|+-+-.....-+-++.+..... ..+.-.++-..||.. -..++|.+.++|
T Consensus       233 v~~~gi~~~~~~~~~~a~~~g~~lrlv~~~~~~~-~~V~~~~v~~~~pla-~~g~~N~v~i~t  293 (327)
T 3do5_A          233 VEVTGITQITPEAFQVAAEKGYTIRLIAEVSREK-LKVSPRLVPFHHPLA-IKGTMNAAMFKT  293 (327)
T ss_dssp             SEECCSTTCCHHHHHHHHTTTEEEEEEEEESSSC-EEEEEEEEETTSGGG-CCSSCEEEEEEE
T ss_pred             HCCCCCCCCCHHHHHHHHHCCCEEEEEEEEECCE-EEEEEEEECCCCCCE-ECCCCEEEEEEE
T ss_conf             0415854468899999986497799987852766-999999967999713-789855999984


No 2  
>1np3_A Ketol-acid reductoisomerase; A DEEP figure-OF-eight knot, C-terminal alpha-helical domain, oxidoreductase; 2.00A {Pseudomonas aeruginosa} SCOP: a.100.1.2 c.2.1.6
Probab=8.99  E-value=1.2e+02  Score=13.38  Aligned_cols=40  Identities=23%  Similarity=0.383  Sum_probs=29.8

Q ss_pred             CEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEE
Q ss_conf             93345643456777554541389521898650222134544
Q gi|254780990|r    1 MFLVPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEI   41 (66)
Q Consensus         1 mflvpddgiddlfeedlfqydankselvlisslwsidffei   41 (66)
                      |+|+||...-+++++++.++=...+-|. .|.=.+|.|-.|
T Consensus        77 ~~L~pD~~q~~~y~~~i~p~l~~g~~l~-faHGf~i~~~~i  116 (338)
T 1np3_A           77 MILTPDEFQGRLYKEEIEPNLKKGATLA-FAHGFSIHYNQV  116 (338)
T ss_dssp             EECSCHHHHHHHHHHHTGGGCCTTCEEE-ESCCHHHHTTSS
T ss_pred             EEECCHHHHHHHHHHHHHHHCCCCCEEE-ECCCCEEEECCE
T ss_conf             6508877779999876664358887798-625540420330


No 3  
>3pvi_A Protein (pvuii endonuclease); complex (restriction endonuclease/DNA), mutant, protein/DNA, hydrolase/DNA complex; HET: DNA; 1.59A {Proteus vulgaris} SCOP: c.52.1.6 PDB: 1eyu_A* 1f0o_A 1pvi_A* 1ni0_A 1k0z_A 1h56_A 1pvu_A 2pvi_A*
Probab=8.68  E-value=76  Score=14.42  Aligned_cols=16  Identities=38%  Similarity=0.636  Sum_probs=13.5

Q ss_pred             CCCCCCCCCCEEEEEC
Q ss_conf             6520002463465429
Q gi|254780990|r   51 PINKYEKTDNFFALYT   66 (66)
Q Consensus        51 pinkyektdnffalyt   66 (66)
                      -|.||.|.|-+||.|.
T Consensus        90 Ii~KYRkV~WiFA~y~  105 (157)
T 3pvi_A           90 IIAKYRQVPWIFAIYR  105 (157)
T ss_dssp             HHHHHHTSCEEEEEEE
T ss_pred             HHHHHHCCCEEEEEEC
T ss_conf             9988735776876534


No 4  
>3ksk_A Type-2 restriction enzyme pvuii; single chain restriction endonuclease, DNA-binding protein, endonuclease, hydrolase, magnesium, metal-binding; 2.35A {Proteus vulgaris}
Probab=5.10  E-value=1.6e+02  Score=12.79  Aligned_cols=14  Identities=43%  Similarity=0.793  Sum_probs=7.0

Q ss_pred             CCCCCCCCCEEEEE
Q ss_conf             52000246346542
Q gi|254780990|r   52 INKYEKTDNFFALY   65 (66)
Q Consensus        52 inkyektdnffaly   65 (66)
                      |.||.|.|-+||.|
T Consensus       250 i~KYRkV~WiFA~y  263 (324)
T 3ksk_A          250 IAKYRQVPWIFAIY  263 (324)
T ss_dssp             HHHHTTSCEEEEEE
T ss_pred             HHHHHCCCEEEEEE
T ss_conf             98763577688752


No 5  
>2qj2_A Hepatocyte growth factor; HGF/SF, hormone/growth factor; 1.81A {Homo sapiens} SCOP: g.10.1.1 g.14.1.1 PDB: 1nk1_A 3mkp_A* 1gmn_A* 1gmo_A* 1bht_A* 1gp9_A* 2qj4_A
Probab=4.24  E-value=2e+02  Score=12.33  Aligned_cols=12  Identities=17%  Similarity=0.506  Sum_probs=4.7

Q ss_pred             HHHHCCCCCEEE
Q ss_conf             454138952189
Q gi|254780990|r   17 LFQYDANKSELV   28 (66)
Q Consensus        17 lfqydankselv   28 (66)
                      -|+|+.....-+
T Consensus        61 aF~~~~~~~~C~   72 (184)
T 2qj2_A           61 AFVFDKARKQCL   72 (184)
T ss_dssp             EEEEETTTTEEE
T ss_pred             CCCCCCCCCCEE
T ss_conf             243157457048


No 6  
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus R29} PDB: 3kkr_A
Probab=3.85  E-value=2.5e+02  Score=11.78  Aligned_cols=10  Identities=30%  Similarity=0.624  Sum_probs=4.0

Q ss_pred             ECCCEEEEEE
Q ss_conf             0222134544
Q gi|254780990|r   32 SLWSIDFFEI   41 (66)
Q Consensus        32 slwsidffei   41 (66)
                      -+|.+|+..+
T Consensus         3 h~W~~D~t~~   12 (152)
T 3kks_A            3 HLWQMDNTHW   12 (152)
T ss_dssp             CEEEEEEEEE
T ss_pred             CEEEEEEEEE
T ss_conf             1000516266


No 7  
>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5
Probab=3.50  E-value=1.4e+02  Score=13.12  Aligned_cols=12  Identities=33%  Similarity=0.739  Sum_probs=0.0

Q ss_pred             EECCCCCHHHHH
Q ss_conf             334564345677
Q gi|254780990|r    2 FLVPDDGIDDLF   13 (66)
Q Consensus         2 flvpddgiddlf   13 (66)
                      |..||||-.|+|
T Consensus        24 FI~~ddg~~DvF   35 (79)
T 1h95_A           24 FINRNDTKEDVF   35 (79)
T ss_dssp             EEEEGGGTEEEE
T ss_pred             EEEECCCCEEEE
T ss_conf             998589970499


No 8  
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum}
Probab=3.36  E-value=1.5e+02  Score=12.92  Aligned_cols=11  Identities=27%  Similarity=0.869  Sum_probs=0.0

Q ss_pred             EECCCCCHHHHH
Q ss_conf             334564345677
Q gi|254780990|r    2 FLVPDDGIDDLF   13 (66)
Q Consensus         2 flvpddgiddlf   13 (66)
                      |+.++|| +|+|
T Consensus        18 FI~~~~G-~DvF   28 (74)
T 2k5n_A           18 FIKDENG-DNRY   28 (74)
T ss_dssp             EEEESSS-CEEE
T ss_pred             EEEECCC-CCEE
T ss_conf             9874699-8399


No 9  
>3lk3_T Carmil homolog, leucine-rich repeat-containing protein 16A; CAPZ, actin filaments, uncapping, actin-filament regulators, protein-protein complex; 2.68A {Homo sapiens}
Probab=3.27  E-value=2e+02  Score=12.31  Aligned_cols=16  Identities=31%  Similarity=0.848  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHC
Q ss_conf             6434567775545413
Q gi|254780990|r    6 DDGIDDLFEEDLFQYD   21 (66)
Q Consensus         6 ddgiddlfeedlfqyd   21 (66)
                      |.|+|+.|..-+.+.|
T Consensus        60 dEGld~FFskkv~~~~   75 (115)
T 3lk3_T           60 DEGVDEFFTKKVTKMD   75 (115)
T ss_dssp             CTTHHHHTTCCCC---
T ss_pred             CCCHHHHHHCCCCCCC
T ss_conf             2357867530324465


No 10 
>3hn4_A Hepatocyte growth factor; HGF/SF, hormone/growth factor, alternative splicing, disulfi glycoprotein, kringle, serine protease homol hormone; HET: EPE; 2.60A {Homo sapiens}
Probab=3.17  E-value=2.4e+02  Score=11.87  Aligned_cols=13  Identities=31%  Similarity=0.733  Sum_probs=0.0

Q ss_pred             HCCCCCCCCCCCC
Q ss_conf             0076520002463
Q gi|254780990|r   48 RRHPINKYEKTDN   60 (66)
Q Consensus        48 rrhpinkyektdn   60 (66)
                      +|.|++.|.||++
T Consensus        10 ~~~~l~~~~~~~~   22 (264)
T 3hn4_A           10 RRNTIHEFKKSAK   22 (264)
T ss_dssp             CCCCGGGEEEEEE
T ss_pred             CCCHHHHHHHCCC
T ss_conf             6455777642478


Done!