Query         gi|254781132|ref|YP_003065545.1| hypothetical protein CLIBASIA_05170 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 31
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 04:55:48 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781132.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam06884 DUF1264 Protein of u  19.6      26 0.00067   17.9  -0.3   14    2-15     73-86  (171)
  2 pfam08958 DUF1871 Domain of un  19.1      65  0.0016   16.2   1.6   22    3-24     11-33  (79)
  3 KOG4389 consensus               11.1 1.8E+02  0.0046   14.2   2.1   23    3-25    478-500 (601)
  4 pfam09809 MRP-L27 Mitochondria  10.6 1.5E+02  0.0038   14.5   1.5   18   14-31     73-90  (113)
  5 pfam08469 NPHI_C Nucleoside tr   9.9      85  0.0022   15.6   0.1   10    3-12     97-106 (148)
  6 pfam10183 ESSS ESSS subunit of   9.1 1.4E+02  0.0037   14.6   1.0   18    2-19     66-83  (151)
  7 COG3664 XynB Beta-xylosidase [   8.5 1.9E+02  0.0048   14.1   1.4   25    4-28     34-58  (428)
  8 pfam11757 RSS_P20 Suppressor o   8.1 1.8E+02  0.0047   14.1   1.2   25    4-28     96-120 (137)
  9 KOG1024 consensus                7.7   1E+02  0.0026   15.3  -0.3   12   20-31    440-451 (563)
 10 KOG0738 consensus                5.5 3.4E+02  0.0087   12.9   2.3   26    2-30    181-206 (491)

No 1  
>pfam06884 DUF1264 Protein of unknown function (DUF1264). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=19.56  E-value=26  Score=17.95  Aligned_cols=14  Identities=50%  Similarity=0.987  Sum_probs=10.5

Q ss_pred             CCCCCCCCCCCHHH
Q ss_conf             88841321113468
Q gi|254781132|r    2 ENPLWYSHEYDDEA   15 (31)
Q Consensus         2 enplwysheyddea   15 (31)
                      |.+||-||+|.-..
T Consensus        73 EkklWHsH~~EVkS   86 (171)
T pfam06884        73 EKKLWHSHEYEVKS   86 (171)
T ss_pred             HHHCCCCCCCEEEC
T ss_conf             88614642011003


No 2  
>pfam08958 DUF1871 Domain of unknown function (DUF1871). This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus.
Probab=19.09  E-value=65  Score=16.18  Aligned_cols=22  Identities=41%  Similarity=0.661  Sum_probs=15.8

Q ss_pred             CCCCCCC-CCCHHHHHHHHHHHH
Q ss_conf             8841321-113468999999766
Q gi|254781132|r    3 NPLWYSH-EYDDEAKDLVSAVSR   24 (31)
Q Consensus         3 nplwysh-eyddeakdlvsavsr   24 (31)
                      +|.-|.. -||.||-|.|.||+.
T Consensus        11 DPF~~G~d~YetEa~dvv~Av~~   33 (79)
T pfam08958        11 DPFQYGEDFYETEAADVVQAVYD   33 (79)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             96456854112379999999980


No 3  
>KOG4389 consensus
Probab=11.07  E-value=1.8e+02  Score=14.15  Aligned_cols=23  Identities=39%  Similarity=0.491  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             88413211134689999997667
Q gi|254781132|r    3 NPLWYSHEYDDEAKDLVSAVSRD   25 (31)
Q Consensus         3 nplwysheyddeakdlvsavsrd   25 (31)
                      -|||||..|.+|.|+|-+.+-|-
T Consensus       478 ~PL~~s~nYt~~E~~ls~rim~~  500 (601)
T KOG4389         478 IPLNYSRNYTKEEKILSRRIMRY  500 (601)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             63563446468999999999999


No 4  
>pfam09809 MRP-L27 Mitochondrial ribosomal protein L27. Members of this family of proteins are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation.
Probab=10.64  E-value=1.5e+02  Score=14.55  Aligned_cols=18  Identities=50%  Similarity=0.565  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHCCC
Q ss_conf             689999997667653169
Q gi|254781132|r   14 EAKDLVSAVSRDLITKDY   31 (31)
Q Consensus        14 eakdlvsavsrdlitkdy   31 (31)
                      .|+||.+++-..-|.+||
T Consensus        73 ta~~lf~~~~a~~i~~df   90 (113)
T pfam09809        73 TAKDLFNAVYAPKIFKDF   90 (113)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             789999988879999886


No 5  
>pfam08469 NPHI_C Nucleoside triphosphatase I C-terminal. This viral domain is found to the C-terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I) together with the helicase conserved C-terminal domain (pfam00271).
Probab=9.91  E-value=85  Score=15.63  Aligned_cols=10  Identities=40%  Similarity=1.169  Sum_probs=7.9

Q ss_pred             CCCCCCCCCC
Q ss_conf             8841321113
Q gi|254781132|r    3 NPLWYSHEYD   12 (31)
Q Consensus         3 nplwysheyd   12 (31)
                      .|.|||+.++
T Consensus        97 ~nIwYs~s~~  106 (148)
T pfam08469        97 QNIWYSKSYR  106 (148)
T ss_pred             CEEEEECCCH
T ss_conf             7058984411


No 6  
>pfam10183 ESSS ESSS subunit of NADH:ubiquinone oxidoreductase (complex I). This subunit is part of the mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences.
Probab=9.07  E-value=1.4e+02  Score=14.59  Aligned_cols=18  Identities=22%  Similarity=0.087  Sum_probs=12.3

Q ss_pred             CCCCCCCCCCCHHHHHHH
Q ss_conf             888413211134689999
Q gi|254781132|r    2 ENPLWYSHEYDDEAKDLV   19 (31)
Q Consensus         2 enplwysheyddeakdlv   19 (31)
                      .|+.||.-.|+|+..|.-
T Consensus        66 Knw~s~Gf~~~D~~~D~~   83 (151)
T pfam10183        66 KNWDSHGYDYKDPKEDRW   83 (151)
T ss_pred             CCCCCCCCCCCCHHHHHH
T ss_conf             186102778888266677


No 7  
>COG3664 XynB Beta-xylosidase [Carbohydrate transport and metabolism]
Probab=8.45  E-value=1.9e+02  Score=14.08  Aligned_cols=25  Identities=36%  Similarity=0.531  Sum_probs=20.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             8413211134689999997667653
Q gi|254781132|r    4 PLWYSHEYDDEAKDLVSAVSRDLIT   28 (31)
Q Consensus         4 plwysheyddeakdlvsavsrdlit   28 (31)
                      -+||+-+|+||--|..+...+|+|-
T Consensus        34 ~~~~~~t~~d~i~d~~~~~~~~~ie   58 (428)
T COG3664          34 KLFYPFTYIDEIIDTLLDLGLDLIE   58 (428)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHH
T ss_conf             0458747777887878772557999


No 8  
>pfam11757 RSS_P20 Suppressor of RNA silencing P21-like. This is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins.
Probab=8.07  E-value=1.8e+02  Score=14.13  Aligned_cols=25  Identities=28%  Similarity=0.215  Sum_probs=20.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             8413211134689999997667653
Q gi|254781132|r    4 PLWYSHEYDDEAKDLVSAVSRDLIT   28 (31)
Q Consensus         4 plwysheyddeakdlvsavsrdlit   28 (31)
                      +.=||+-+.+.-|-.++||-+||+.
T Consensus        96 ~~~~s~i~~~kvk~~~~aVl~dlS~  120 (137)
T pfam11757        96 HVPFSEVMRTKLKLVVKAVISDLSR  120 (137)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9987999987117889999999889


No 9  
>KOG1024 consensus
Probab=7.67  E-value=1e+02  Score=15.26  Aligned_cols=12  Identities=67%  Similarity=0.958  Sum_probs=0.0

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             997667653169
Q gi|254781132|r   20 SAVSRDLITKDY   31 (31)
Q Consensus        20 savsrdlitkdy   31 (31)
                      ||.||||...||
T Consensus       440 saLSRDLFP~DY  451 (563)
T KOG1024         440 SALSRDLFPGDY  451 (563)
T ss_pred             CHHCCCCCCCCC
T ss_conf             311114376653


No 10 
>KOG0738 consensus
Probab=5.51  E-value=3.4e+02  Score=12.90  Aligned_cols=26  Identities=38%  Similarity=0.668  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             88841321113468999999766765316
Q gi|254781132|r    2 ENPLWYSHEYDDEAKDLVSAVSRDLITKD   30 (31)
Q Consensus         2 enplwysheyddeakdlvsavsrdlitkd   30 (31)
                      +.+.+-+-+||   ++||.++.||.+..+
T Consensus       181 ~~~~f~~~~~d---~~Lve~lerdIl~~n  206 (491)
T KOG0738         181 EDKKFDSLGYD---ADLVEALERDILQRN  206 (491)
T ss_pred             CCCCCCCCCCH---HHHHHHHHHHHHCCC
T ss_conf             66778753104---899999988886059


Done!