Query         gi|254781090|ref|YP_003065503.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 71
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 23785
Date          Wed Jun  1 00:31:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781090.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3a1g_A RNA-directed RNA polyme  43.5      12 0.00049   19.0   2.4   25   21-45     52-76  (80)
  2 2xev_A YBGF; tetratricopeptide  20.4      53  0.0022   15.4   2.5   25   36-60     87-111 (129)
  3 3hsq_A Acyl-[acyl-carrier-prot  10.5 1.1E+02  0.0045   13.7   3.0   33   22-54    218-250 (259)
  4 1xri_A AT1G05000; structural g  10.0 1.1E+02  0.0047   13.6   2.0   27   13-39      6-33  (151)
  5 3oon_A Outer membrane protein    9.7 1.1E+02  0.0048   13.5   2.3   24   40-63     31-54  (123)
  6 1p9y_A Trigger factor, TF; alp   9.1 1.2E+02  0.0051   13.4   2.9   20   17-36     42-61  (121)
  7 2ckc_A Chromodomain-helicase-D   7.7 1.1E+02  0.0047   13.6   1.1   24   38-61     39-62  (80)
  8 1dbu_A HI1434, cysteinyl-tRNA(   7.5      91  0.0038   14.1   0.5   18    1-18      1-18  (158)
  9 2cka_A Chromodomain-helicase-D   7.4 1.2E+02   0.005   13.5   1.1   22   39-60     59-80  (95)
 10 3kos_A HTH-type transcriptiona   7.3 1.2E+02  0.0049   13.5   1.0   15   48-62     31-45  (219)

No 1  
>3a1g_A RNA-directed RNA polymerase catalytic subunit; influenza virus, RNA polymerase, nucleotide-binding, nucleotidyltransferase, nucleus, RNA replication; 1.70A {Influenza a virus} PDB: 2ztt_A
Probab=43.50  E-value=12  Score=19.02  Aligned_cols=25  Identities=28%  Similarity=0.624  Sum_probs=20.8

Q ss_pred             HHHCCCCCHHHHHHHHHHCCHHHHH
Q ss_conf             1233864378899898620116679
Q gi|254781090|r   21 GYRSGKTSKDKYQKIVKIGDHAESI   45 (71)
Q Consensus        21 gyrsgktskdkyqkivkigdhaesi   45 (71)
                      .|.||..+||.+.+|.||-...|..
T Consensus        52 d~esgr~~k~~f~~~mkicstieel   76 (80)
T 3a1g_A           52 DFESGRIKKEEFTEIMKICSTIEEL   76 (80)
T ss_dssp             HHHHTSSCHHHHHHHHHHHHHHHHH
T ss_pred             CHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             3121664489999999999889999


No 2  
>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}
Probab=20.45  E-value=53  Score=15.38  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=17.7

Q ss_pred             HHHCCHHHHHHHHHHHHHHCCCCCE
Q ss_conf             8620116679999999631888740
Q gi|254781090|r   36 VKIGDHAESIKTLADFIKDYPDCDL   60 (71)
Q Consensus        36 vkigdhaesiktladfikdypdcdl   60 (71)
                      ...|+..+++.++..+++.||+-+.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~yP~s~~  111 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVATQYPGSDA  111 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTSHH
T ss_pred             HHCCCHHHHHHHHHHHHHHCCCCHH
T ss_conf             9849999999999999988819999


No 3  
>3hsq_A Acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; L.interrogans LPXA, LPXA, LPXA acyltransferase; 2.10A {Leptospira interrogans} PDB: 3i3a_A* 3i3x_A*
Probab=10.48  E-value=1.1e+02  Score=13.71  Aligned_cols=33  Identities=24%  Similarity=0.545  Sum_probs=22.4

Q ss_pred             HHCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHH
Q ss_conf             233864378899898620116679999999631
Q gi|254781090|r   22 YRSGKTSKDKYQKIVKIGDHAESIKTLADFIKD   54 (71)
Q Consensus        22 yrsgktskdkyqkivkigdhaesiktladfikd   54 (71)
                      ||++..-++.-+.+-+-...-+.++.+.+|+++
T Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~  250 (259)
T 3hsq_A          218 YHSGISTRKALDELEASGNLIEQVKYIIKFFRD  250 (259)
T ss_dssp             HSSSSCHHHHHHHHHTTCCCCHHHHHHHHHHHH
T ss_pred             HCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             727998999999998645798999999999973


No 4  
>1xri_A AT1G05000; structural genomics, protein structure initiative, CESG, center for eukaryotic structural genomics, phosphoprotein phosphatase; 3.30A {Arabidopsis thaliana} SCOP: c.45.1.1 PDB: 2q47_A
Probab=10.02  E-value=1.1e+02  Score=13.61  Aligned_cols=27  Identities=26%  Similarity=0.616  Sum_probs=18.5

Q ss_pred             CEEEEEEEH-HHCCCCCHHHHHHHHHHC
Q ss_conf             012112311-233864378899898620
Q gi|254781090|r   13 VNFRFLLDG-YRSGKTSKDKYQKIVKIG   39 (71)
Q Consensus        13 vnfrflldg-yrsgktskdkyqkivkig   39 (71)
                      .||...-+| ||||..+....+.+-+.|
T Consensus         6 ~nF~~V~~~lyRs~~~~~~~~~~L~~lg   33 (151)
T 1xri_A            6 LNFSMVDNGIFRSGFPDSANFSFLQTLG   33 (151)
T ss_dssp             TTCEEEETTEEEESCCCHHHHHHHHHHT
T ss_pred             CCCCEECCCCEECCCCCHHHHHHHHHCC
T ss_conf             6323456884476998965399999879


No 5  
>3oon_A Outer membrane protein (TPN50); protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG; 1.79A {Borrelia burgdorferi}
Probab=9.68  E-value=1.1e+02  Score=13.54  Aligned_cols=24  Identities=13%  Similarity=0.379  Sum_probs=17.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEHH
Q ss_conf             116679999999631888740077
Q gi|254781090|r   40 DHAESIKTLADFIKDYPDCDLELE   63 (71)
Q Consensus        40 dhaesiktladfikdypdcdlele   63 (71)
                      +..+.+..+|.+++.+|++.++++
T Consensus        31 ~~~~~L~~ia~~l~~~~~~~I~I~   54 (123)
T 3oon_A           31 KEYKKIDLIAKLLEKFKKNNILIE   54 (123)
T ss_dssp             GGHHHHHHHHHHHHHSCSCCEEEE
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             899999999999986899569999


No 6  
>1p9y_A Trigger factor, TF; alpha-beta protein, isomerase; 2.15A {Escherichia coli} SCOP: d.241.2.1 PDB: 1oms_A*
Probab=9.07  E-value=1.2e+02  Score=13.40  Aligned_cols=20  Identities=25%  Similarity=0.375  Sum_probs=14.5

Q ss_pred             EEEEHHHCCCCCHHHHHHHH
Q ss_conf             12311233864378899898
Q gi|254781090|r   17 FLLDGYRSGKTSKDKYQKIV   36 (71)
Q Consensus        17 flldgyrsgktskdkyqkiv   36 (71)
                      .-+.|+|.||....-..+-.
T Consensus        42 ~~ipGFRkGKvP~~vi~k~y   61 (121)
T 1p9y_A           42 VRIDGLRKGKVPMNIVAQRY   61 (121)
T ss_dssp             CCCTTSCTTCSCHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHH
T ss_conf             88899788988999999998


No 7  
>2ckc_A Chromodomain-helicase-DNA-binding protein 7; protein-protein interaction, phosphorylation, disease mutation, nucleotide-binding; NMR {Homo sapiens} SCOP: d.76.2.1 PDB: 2v0e_A
Probab=7.72  E-value=1.1e+02  Score=13.58  Aligned_cols=24  Identities=25%  Similarity=0.515  Sum_probs=21.2

Q ss_pred             HCCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             201166799999996318887400
Q gi|254781090|r   38 IGDHAESIKTLADFIKDYPDCDLE   61 (71)
Q Consensus        38 igdhaesiktladfikdypdcdle   61 (71)
                      .|++|-+.+.|.++.+..|+....
T Consensus        39 ~G~~AP~~~~L~~WL~~hP~y~Vd   62 (80)
T 2ckc_A           39 VGEDAPKNKDLVEWLKLHPTYTVD   62 (80)
T ss_dssp             CTTSSCBHHHHHHHHHHCTTEEES
T ss_pred             CCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf             677797778999999988692871


No 8  
>1dbu_A HI1434, cysteinyl-tRNA(Pro) deacylase; structural genomics, YBAK, structure 2 function project, S2F, hydrolase; HET: MSE; 1.80A {Haemophilus influenzae} SCOP: d.116.1.1 PDB: 1dbx_A
Probab=7.51  E-value=91  Score=14.10  Aligned_cols=18  Identities=33%  Similarity=0.490  Sum_probs=15.9

Q ss_pred             CCCHHHHHHCCCCEEEEE
Q ss_conf             971323111346012112
Q gi|254781090|r    1 MKPIIHLLNGWGVNFRFL   18 (71)
Q Consensus         1 mkpiihllngwgvnfrfl   18 (71)
                      |.|.+.+|+.+|+.|+..
T Consensus         1 mT~a~~~L~~~~I~y~~~   18 (158)
T 1dbu_A            1 MTPAIDLLKKQKIPFILH   18 (158)
T ss_dssp             -CHHHHHHHHHTCCCEEE
T ss_pred             CCHHHHHHHHCCCCCEEE
T ss_conf             977999999879997898


No 9  
>2cka_A Chromodomain-helicase-DNA-binding protein 8; BRK domain, transcription elongation, chromatin remodeling, protein-protein interaction, transcription; NMR {Homo sapiens} SCOP: d.76.2.1
Probab=7.44  E-value=1.2e+02  Score=13.46  Aligned_cols=22  Identities=18%  Similarity=0.400  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCE
Q ss_conf             0116679999999631888740
Q gi|254781090|r   39 GDHAESIKTLADFIKDYPDCDL   60 (71)
Q Consensus        39 gdhaesiktladfikdypdcdl   60 (71)
                      |++|-..+.|.++.+..|+...
T Consensus        59 G~~AP~lk~L~~WL~~nP~Y~V   80 (95)
T 2cka_A           59 GEDAPRRAELEMWLQGHPEFAV   80 (95)
T ss_dssp             TTSSCBHHHHHHHHHHCTTEEE
T ss_pred             CCCCCCHHHHHHHHHHCCCCEE
T ss_conf             5679688899999998889688


No 10 
>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich, DNA-binding, transcription regulation; HET: MES; 1.83A {Citrobacter freundii} PDB: 3kot_A
Probab=7.33  E-value=1.2e+02  Score=13.50  Aligned_cols=15  Identities=47%  Similarity=0.988  Sum_probs=0.0

Q ss_pred             HHHHHHHCCCCCEEH
Q ss_conf             999963188874007
Q gi|254781090|r   48 LADFIKDYPDCDLEL   62 (71)
Q Consensus        48 ladfikdypdcdlel   62 (71)
                      |++|.+.||+-++++
T Consensus        31 L~~F~~~~P~i~v~l   45 (219)
T 3kos_A           31 LSDFKRSYPHIDLHI   45 (219)
T ss_dssp             HHHHHHHCTTEEEEE
T ss_pred             HHHHHHHCCCEEEEE
T ss_conf             999999883979999


Done!