Query         gi|254780509|ref|YP_003064922.1| hypothetical protein CLIBASIA_01980 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 112
No_of_seqs    141 out of 240
Neff          5.0 
Searched_HMMs 33803
Date          Wed Jun  1 16:50:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780509.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1q5z_A SIPA, SIPA; cell invas  58.9     9.8 0.00029   18.6   3.2   53    3-56     82-134 (177)
  2 >2qgu_A Probable signal peptid  48.1      20  0.0006   16.8   6.3   48   47-104    89-136 (155)
  3 >2k0n_A Mediator of RNA polyme  17.8      72  0.0021   13.8   5.4   35   37-71     28-69  (85)
  4 >2au3_A DNA primase; zinc ribb  15.7      53  0.0016   14.5   0.8   22   85-106    27-48  (48)
  5 >1v54_D Cytochrome C oxidase s  14.7      57  0.0017   14.4   0.7   14    1-14     19-32  (40)
  6 >3f2b_A DNA-directed DNA polym  10.6      56  0.0016   14.4  -0.4   22   53-74     53-74  (203)
  7 >3hvm_A Agmatine deiminase; hy  10.2      96  0.0028   13.1   0.8   25   83-107    36-60  (67)
  8 >2ztg_A Alanyl-tRNA synthetase   9.8 1.3E+02  0.0037   12.5   2.0   34   76-109    17-51  (71)
  9 >2inp_C Phenol hydroxylase com   9.5 1.3E+02  0.0038   12.4   1.5   26   85-110    87-112 (112)
 10 >2hnh_A DNA polymerase III alp   9.3      52  0.0015   14.6  -0.9   38   53-90     25-65  (111)

No 1  
>>1q5z_A SIPA, SIPA; cell invasion; 1.80A {Salmonella typhimurium} (A:)
Probab=58.89  E-value=9.8  Score=18.56  Aligned_cols=53  Identities=15%  Similarity=0.265  Sum_probs=32.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf             432466113554333688754432312078999998702285547999999999
Q gi|254780509|r    3 VLPISNISHSQSMGGNLAKISQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQ   56 (112)
Q Consensus         3 ~~pis~is~~~~M~gnla~is~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fE   56 (112)
                      |+|.+.|-+ ..+-..-+.+...+.--.....|+++-......++|.++|.||-
T Consensus        82 ILpnD~~ks-~alkaqcs~i~~~~eLk~k~~tLkeait~HPqrekLae~Alqf~  134 (177)
T 1q5z_A           82 ILPNDTIKS-AALKAQCSDIDKHPELKAKMETLKEVITHHPQKEKLAEIALQFA  134 (177)
T ss_dssp             HSCSSHHHH-HHHHHHHTTGGGCHHHHHHHHHHHHHHHTCTTHHHHHHHHHHHH
T ss_pred             CCCCCHHHH-HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             088620308-99999985048985787789999999806946999999999999


No 2  
>>2qgu_A Probable signal peptide protein; NESG, RSR89, Q8XV73, X-RAY, structural genomics, PSI-2, protein structure initiative; HET: MSE PEF; 1.50A {Ralstonia solanacearum GMI1000} (A:1-117,A:174-211)
Probab=48.05  E-value=20  Score=16.82  Aligned_cols=48  Identities=19%  Similarity=0.312  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             7999999999999999999995102112335753336899999999999999807987
Q gi|254780509|r   47 SVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQQRIT  104 (112)
Q Consensus        47 ~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~ggiG  104 (112)
                      .=++--++|-..|-+.++.+--..      +.....++|+    .+++..|+|+||.|
T Consensus        89 aS~eQr~~Fv~~F~~~Lv~tYa~~------L~~Y~~~~~~----~~~~~~~~~~~~~~  136 (155)
T 2qgu_A           89 ATPEQQQQIQDGFKSLLIRTYAGA------LANVRSETYK----NQFADVISKRGGVG  136 (155)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHH------HHTCSHHHHH----HHHHHHHHHHTSHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH------HHHCCHHHHH----HHHHHHHHHCCCHH
T ss_conf             599999999999999999999988------7624699999----99999998769999


No 3  
>>2k0n_A Mediator of RNA polymerase II transcription subunit 15; protein, activator, nucleus, phosphoprotein, transcription regulation; NMR {Saccharomyces cerevisiae} (A:)
Probab=17.85  E-value=72  Score=13.82  Aligned_cols=35  Identities=9%  Similarity=0.292  Sum_probs=24.6

Q ss_pred             HHHCC-CCHHHHHHHHHHHHHHHHH------HHHHHHHHHCC
Q ss_conf             98702-2855479999999999999------99999995102
Q gi|254780509|r   37 DVQEA-CDKSKSVPEMTQKLQGIMF------QYFIKSILPEE   71 (112)
Q Consensus        37 ~~~~~-~~~~~~l~~~a~~fEa~fl------~~~lksmr~~~   71 (112)
                      .+.-+ .+--+.++.-|++||+-..      +..+.+||...
T Consensus        28 ~iNGG~s~~~EKlk~~A~~FEaaLyaksSSK~eYmdsMr~ki   69 (85)
T 2k0n_A           28 TLNGGSSDTADKIRIHAKNFEAALFAKSSSKKEYMDSMNEKV   69 (85)
T ss_dssp             HHHSCSTTHHHHHHHHHHHHHHHHHHSCCSHHHHHHHHHHHH
T ss_pred             HCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             535875005999998899999999883163999999999999


No 4  
>>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} (A:1-19,A:67-95)
Probab=15.68  E-value=53  Score=14.55  Aligned_cols=22  Identities=18%  Similarity=0.172  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             9999999999999980798756
Q gi|254780509|r   85 WQEILAENISDVIVKQQRITLD  106 (112)
Q Consensus        85 ~~sMl~ee~a~~iAk~ggiGL~  106 (112)
                      |++.-+=|-|+.+||+-|+-||
T Consensus        27 ye~isyfeaa~~lakr~g~kl~   48 (48)
T 2au3_A           27 YEDISYFEAALELAKRYGKKLD   48 (48)
T ss_dssp             HHTCCHHHHHHHHHHHHTCCCC
T ss_pred             HHCCCHHHHHHHHHHHHCCCCC
T ss_conf             8299889999999997086520


No 5  
>>1v54_D Cytochrome C oxidase subunit IV isoform 1; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} (D:108-147)
Probab=14.66  E-value=57  Score=14.37  Aligned_cols=14  Identities=36%  Similarity=0.489  Sum_probs=8.6

Q ss_pred             CCCCCCCCCHHHHH
Q ss_conf             95432466113554
Q gi|254780509|r    1 MQVLPISNISHSQS   14 (112)
Q Consensus         1 ~~~~pis~is~~~~   14 (112)
                      |+++||.++++...
T Consensus        19 m~~nPi~G~sskWD   32 (40)
T 1v54_D           19 MKVAPIQGFSAKWD   32 (40)
T ss_dssp             TTSSTTTTSGGGEE
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             48999877200013


No 6  
>>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* (A:690-775,A:856-972)
Probab=10.55  E-value=56  Score=14.44  Aligned_cols=22  Identities=5%  Similarity=0.149  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999999995102112
Q gi|254780509|r   53 QKLQGIMFQYFIKSILPEETVK   74 (112)
Q Consensus        53 ~~fEa~fl~~~lksmr~~~~~~   74 (112)
                      =|||+-+.+.||+-+.|....+
T Consensus        53 fQ~eS~gmr~~L~~~~P~~f~d   74 (203)
T 3f2b_A           53 PEFGTRFVRQMLEETRPKTFSE   74 (203)
T ss_dssp             TTTTSHHHHHHHHHHCCCSHHH
T ss_pred             CCCCCHHHHHHHHHHCCCCHHH
T ss_conf             6423589999999848976677


No 7  
>>3hvm_A Agmatine deiminase; hydrolase; 2.10A {Helicobacter pylori J99} PDB: 2cmu_A (A:1-8,A:81-139)
Probab=10.24  E-value=96  Score=13.13  Aligned_cols=25  Identities=8%  Similarity=-0.040  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             6899999999999999807987564
Q gi|254780509|r   83 DFWQEILAENISDVIVKQQRITLDL  107 (112)
Q Consensus        83 d~~~sMl~ee~a~~iAk~ggiGL~~  107 (112)
                      .-|..-+|++++..|++.+.+|..+
T Consensus        36 gK~~~~~D~~v~~~ia~~~~~~~~~   60 (67)
T 3hvm_A           36 LKYPSNLDNQVNFKLKSLGFLKHPL   60 (67)
T ss_dssp             HTSCCTTGGGHHHHHHHTTCCCSCE
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCC
T ss_conf             6798403467999999974246876


No 8  
>>2ztg_A Alanyl-tRNA synthetase; class-II aminoacyl-tRNA synthetase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: A5A; 2.20A {Archaeoglobus fulgidus} (A:424-494)
Probab=9.78  E-value=1.3e+02  Score=12.48  Aligned_cols=34  Identities=9%  Similarity=0.159  Sum_probs=21.4

Q ss_pred             CCCCCHHHHHHHH-HHHHHHHHHHHCCCCCCCCHH
Q ss_conf             3575333689999-999999999980798756401
Q gi|254780509|r   76 LGGGFNGDFWQEI-LAENISDVIVKQQRITLDLPE  109 (112)
Q Consensus        76 lggg~a~d~~~sM-l~ee~a~~iAk~ggiGL~~~~  109 (112)
                      +-|..+-..|.+. +--++-..||+..|+.+|+|+
T Consensus        17 l~g~~af~LydTyGfP~dlt~~ia~e~g~~vD~~~   51 (71)
T 2ztg_A           17 LEKDDLIELYDSHGIPVELAVGIAAEKGAEVEXPK   51 (71)
T ss_dssp             CCHHHHHHHHHHHCCCHHHHHHHHHHTTCBCCCCT
T ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHH
T ss_conf             77788875875069888999999987403212417


No 9  
>>2inp_C Phenol hydroxylase component PHL; DIIRON, four-helix bundle, regulatory protein, oxidoreductase; 2.30A {Pseudomonas stutzeri} PDB: 2inn_C (C:217-328)
Probab=9.48  E-value=1.3e+02  Score=12.42  Aligned_cols=26  Identities=12%  Similarity=0.146  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             99999999999999807987564010
Q gi|254780509|r   85 WQEILAENISDVIVKQQRITLDLPEI  110 (112)
Q Consensus        85 ~~sMl~ee~a~~iAk~ggiGL~~~~~  110 (112)
                      +.+-+++-.+..-....+|||.+|-+
T Consensus        87 ~~~a~~~a~~~~~~~~~~~GL~~~~~  112 (112)
T 2inp_C           87 GIDGLNEARAELSARLKKFELQSRGV  112 (112)
T ss_dssp             CTHHHHHHHHHHHHHHHTTTCCCC--
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             65189999999999999669998989


No 10 
>>2hnh_A DNA polymerase III alpha subunit; DNA replication, nucleotidyltransferase, POL beta, PHP; HET: DNA; 2.30A {Escherichia coli} PDB: 2hqa_A* (A:585-671,A:755-778)
Probab=9.34  E-value=52  Score=14.59  Aligned_cols=38  Identities=13%  Similarity=0.091  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC---CCCHHHHHHHHHH
Q ss_conf             9999999999999995102112335---7533368999999
Q gi|254780509|r   53 QKLQGIMFQYFIKSILPEETVKSLG---GGFNGDFWQEILA   90 (112)
Q Consensus        53 ~~fEa~fl~~~lksmr~~~~~~~lg---gg~a~d~~~sMl~   90 (112)
                      =|||+-..+++|+.++|....+..-   =-.-|.++..|.+
T Consensus        25 FQlES~gmr~~l~~~~P~~fedlva~~aL~RPGp~~~g~i~   65 (111)
T 2hnh_A           25 FQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVD   65 (111)
T ss_dssp             TTCCSHHHHHHHHHHCCCSHHHHHHHHHHSSHHHHTTTHHH
T ss_pred             CCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             65687689999985699769999999875044321010316


Done!