Query         gi|254781125|ref|YP_003065538.1| hypothetical protein CLIBASIA_05135 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 59
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 23785
Date          Wed Jun  1 00:59:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781125.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2o0j_A Terminase, DNA packagin  13.2      43  0.0018   15.5   0.5   12    4-15    132-143 (385)
  2 1mg7_A Early switch protein XO  10.1      43  0.0018   15.5  -0.3   25    2-27     22-48  (417)
  3 3cpe_A Terminase, DNA packagin   9.1      87  0.0037   13.8   1.0   11    4-14    132-142 (592)
  4 1xrs_A D-lysine 5,6-aminomutas   8.6      26  0.0011   16.6  -1.9   20   19-38    256-277 (516)
  5 1b34_B Protein (small nuclear    8.2 1.3E+02  0.0053   13.0   1.6   21   18-38     55-75  (118)
  6 3kfu_G Glutamyl-tRNA(Gln) amid   7.1 1.2E+02   0.005   13.1   0.9   30    2-35     35-64  (92)
  7 3kwr_A Putative RNA-binding pr   7.0 1.3E+02  0.0056   12.8   1.2   13   23-35      8-20  (97)
  8 3kp1_A D-ornithine aminomutase   5.8      31  0.0013   16.3  -2.7   17   19-35    180-196 (763)
  9 2yxy_A Hypothetical conserved    5.6 1.7E+02  0.0073   12.2   1.3   12   48-59     46-57  (115)
 10 3eap_A RHO GTPase-activating p   5.2      81  0.0034   14.0  -0.8   10   33-42     82-91  (271)

No 1  
>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*
Probab=13.20  E-value=43  Score=15.52  Aligned_cols=12  Identities=25%  Similarity=0.556  Sum_probs=8.6

Q ss_pred             HHHHHHHCCCCC
Q ss_conf             899998507864
Q gi|254781125|r    4 ILEYIRCLNDPN   15 (59)
Q Consensus         4 ileyirclndpn   15 (59)
                      |.||++|.+||-
T Consensus       132 ~~e~~kc~~dp~  143 (385)
T 2o0j_A          132 VEEWKKCRDDIV  143 (385)
T ss_dssp             HHHHHHHHHCHH
T ss_pred             HHHHHHHHCCHH
T ss_conf             999999841989


No 2  
>1mg7_A Early switch protein XOL-1 2.2K splice form; alpha-beta, gene regulation; 1.55A {Caenorhabditis elegans} SCOP: d.14.1.6 d.58.26.6
Probab=10.08  E-value=43  Score=15.50  Aligned_cols=25  Identities=44%  Similarity=0.757  Sum_probs=16.7

Q ss_pred             CHHHHHHHHCCCCCE--EEEECCCCCEE
Q ss_conf             248999985078641--47302587503
Q gi|254781125|r    2 SPILEYIRCLNDPNR--YRLSAKDPHYN   27 (59)
Q Consensus         2 spileyirclndpnr--yrlsakdphyn   27 (59)
                      +|.+.|..|+||||-  -|+.+ .||--
T Consensus        22 ~~~~t~~e~~~~~~~~~~~~~~-APHvV   48 (417)
T 1mg7_A           22 SPVLTYMETEDDPNFRNSKLAA-APHTV   48 (417)
T ss_dssp             CHHHHTC----------CEEEE-EEEEE
T ss_pred             CCCEEEEEECCCCCCCCCCCCC-CCEEE
T ss_conf             7622688731687766653467-87177


No 3  
>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*
Probab=9.08  E-value=87  Score=13.81  Aligned_cols=11  Identities=27%  Similarity=0.673  Sum_probs=6.8

Q ss_pred             HHHHHHHCCCC
Q ss_conf             89999850786
Q gi|254781125|r    4 ILEYIRCLNDP   14 (59)
Q Consensus         4 ileyirclndp   14 (59)
                      |.||.+|.+||
T Consensus       132 ~~e~~kc~~d~  142 (592)
T 3cpe_A          132 VEEWKKCRDDI  142 (592)
T ss_dssp             HHHHHHHHTCH
T ss_pred             HHHHHHHHCCH
T ss_conf             99999874088


No 4  
>1xrs_A D-lysine 5,6-aminomutase alpha subunit; TIM barrel, rossmann domain, PLP, cobalamin, 5'- deoxyadenosine, radical, adenosylcobalamin; HET: B12 PLP 5AD; 2.80A {Clostridium sticklandii} SCOP: c.1.19.4
Probab=8.57  E-value=26  Score=16.64  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=14.2

Q ss_pred             EECCCCCEEEEEECCCH--HHH
Q ss_conf             30258750378711143--778
Q gi|254781125|r   19 LSAKDPHYNVIFRDEVP--SFI   38 (59)
Q Consensus        19 lsakdphynvifrdevp--sfi   38 (59)
                      .--.||.||++|||--+  ||+
T Consensus       256 ~~lnD~~YgILfRdINm~Rtfv  277 (516)
T 1xrs_A          256 VMLNDALYGILFRDINMQRTMI  277 (516)
T ss_dssp             EEECCSSHHHHHHCBCHHHHHH
T ss_pred             HHHCCHHHCHHCCCCCHHHHHH
T ss_conf             2220223320003664355688


No 5  
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemic lupus erythematosus, SLE; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 3cw1_C
Probab=8.17  E-value=1.3e+02  Score=12.95  Aligned_cols=21  Identities=24%  Similarity=0.408  Sum_probs=16.5

Q ss_pred             EEECCCCCEEEEEECCCHHHH
Q ss_conf             730258750378711143778
Q gi|254781125|r   18 RLSAKDPHYNVIFRDEVPSFI   38 (59)
Q Consensus        18 rlsakdphynvifrdevpsfi   38 (59)
                      .|.|-|.|.|.+..|-.-.+.
T Consensus        55 ~L~afD~h~NlVL~d~~E~~~   75 (118)
T 1b34_B           55 RVKAFDRHCNMVLENVKEMWT   75 (118)
T ss_dssp             EEEEECTTCCEEEEEEEEC--
T ss_pred             EEEEECCCCEEEEECEEEEEE
T ss_conf             999862210666402068885


No 6  
>3kfu_G Glutamyl-tRNA(Gln) amidotransferase subunit C; ASPRS, gatcab, ATP-binding, aminoacyl-tRNA synthetase, ligas nucleotide-binding, protein biosynthesis, ligase-RNA comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Probab=7.12  E-value=1.2e+02  Score=13.09  Aligned_cols=30  Identities=17%  Similarity=0.396  Sum_probs=21.6

Q ss_pred             CHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCH
Q ss_conf             2489999850786414730258750378711143
Q gi|254781125|r    2 SPILEYIRCLNDPNRYRLSAKDPHYNVIFRDEVP   35 (59)
Q Consensus         2 spileyirclndpnryrlsakdphynvifrdevp   35 (59)
                      +-||+|+..|+.-+   .+.-.|-+|+ +|+.++
T Consensus        35 ~~Il~~~~~L~~vd---t~~v~p~~~~-lReD~~   64 (92)
T 3kfu_G           35 KRILDFVDALPRVE---EGGAEEALGR-LREDEP   64 (92)
T ss_dssp             HHHHHHHHTCCCCC---CCCCCCCCCC-CBCSCC
T ss_pred             HHHHHHHHHHHCCC---CCCCCCCCCC-CCCCCC
T ss_conf             99999999983246---5788744457-889968


No 7  
>3kwr_A Putative RNA-binding protein; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: GOL; 1.45A {Lactobacillus plantarum}
Probab=7.05  E-value=1.3e+02  Score=12.81  Aligned_cols=13  Identities=46%  Similarity=0.751  Sum_probs=8.8

Q ss_pred             CCCEEEEEECCCH
Q ss_conf             8750378711143
Q gi|254781125|r   23 DPHYNVIFRDEVP   35 (59)
Q Consensus        23 dphynvifrdevp   35 (59)
                      .-.|-.|||||-.
T Consensus         8 evkypaifrdegt   20 (97)
T 3kwr_A            8 EVKYPAIFRDEGT   20 (97)
T ss_dssp             CCEEEEEEEECSS
T ss_pred             EEECCEEEECCCC
T ss_conf             8754417814871


No 8  
>3kp1_A D-ornithine aminomutase E component; 5 aminomutase (OAM), metal binding protein; HET: PLP B12 5AD; 2.01A {Clostridium sticklandii} PDB: 3kow_A* 3koy_A* 3koz_A* 3kp0_A* 3kox_A*
Probab=5.77  E-value=31  Score=16.29  Aligned_cols=17  Identities=35%  Similarity=0.655  Sum_probs=10.5

Q ss_pred             EECCCCCEEEEEECCCH
Q ss_conf             30258750378711143
Q gi|254781125|r   19 LSAKDPHYNVIFRDEVP   35 (59)
Q Consensus        19 lsakdphynvifrdevp   35 (59)
                      .--.||.||++|||--+
T Consensus       180 ~~~~d~~y~il~r~in~  196 (763)
T 3kp1_A          180 GAHQDPQYNVLYRNINM  196 (763)
T ss_dssp             EEECCHHHHHHHHCBCH
T ss_pred             HHHCCHHHCCEECCCCH
T ss_conf             22202223301036642


No 9  
>2yxy_A Hypothetical conserved protein, GK0453; alpha and beta proteins (A+B) class, structural genomics, unknown function, NPPSFA; 2.20A {Geobacillus kaustophilus HTA426}
Probab=5.62  E-value=1.7e+02  Score=12.20  Aligned_cols=12  Identities=50%  Similarity=0.963  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHC
Q ss_conf             346888887519
Q gi|254781125|r   48 KRKMAVIRSYML   59 (59)
Q Consensus        48 krkmavirsyml   59 (59)
                      .||+++-+||++
T Consensus        46 erK~~mA~sYLv   57 (115)
T 2yxy_A           46 ERKIAMAKAYML   57 (115)
T ss_dssp             HHHHHHHHHTTS
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999999726


No 10 
>3eap_A RHO GTPase-activating protein 11A; GAP, structural genomics consortium, GTPase activation, phosphoprotein, polymorphism hydrolase activator, SGC; 2.30A {Homo sapiens}
Probab=5.20  E-value=81  Score=13.99  Aligned_cols=10  Identities=30%  Similarity=0.793  Sum_probs=5.3

Q ss_pred             CCHHHHHHHH
Q ss_conf             1437789861
Q gi|254781125|r   33 EVPSFIYETL   42 (59)
Q Consensus        33 evpsfiyetl   42 (59)
                      .||.++.+.+
T Consensus        82 ~IP~iv~~~i   91 (271)
T 3eap_A           82 HIPSFLVDAC   91 (271)
T ss_dssp             EEEHHHHHHH
T ss_pred             CCCHHHHHHH
T ss_conf             8796999999


Done!