Query         gi|254780319|ref|YP_003064732.1| 50S ribosomal protein L35 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 67
No_of_seqs    108 out of 707
Neff          5.0 
Searched_HMMs 33803
Date          Wed Jun  1 11:58:41 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780319.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2zjr_3 50S ribosomal protein  100.0   1E-28   3E-33  160.3   6.1   65    1-66      1-65  (66)
  2 >3i1n_3 50S ribosomal protein   99.9 5.5E-29 1.6E-33  161.6   3.6   65    1-66      1-65  (65)
  3 >2j01_8 50S ribosomal protein   99.9 2.1E-28 6.3E-33  158.7   3.0   65    1-66      1-65  (65)
  4 >3bbo_5 Ribosomal protein L35;  99.9 2.8E-25 8.4E-30  143.4   0.3   65    1-66     89-153 (159)
  5 >3c8l_A FTSZ-like protein of u   6.5 1.8E+02  0.0054   12.2   0.9   13   53-66     68-80  (122)
  6 >3gqw_A Fatty acid AMP ligase;   6.1 1.1E+02  0.0033   13.3  -0.5   14   13-26     62-75  (95)
  7 >3c5e_A Acyl-coenzyme A synthe   5.1 1.3E+02  0.0038   13.0  -0.6   13   14-26     88-100 (115)
  8 >3ipl_A 2-succinylbenzoate--CO   4.5   2E+02  0.0058   12.1   0.0   13   14-26     80-92  (103)
  9 >2jra_A Protein RPA2121; domai   4.5 2.7E+02   0.008   11.4   1.7   17    7-23     48-64  (67)
 10 >3hrz_C Cobra venom factor; se   4.4 1.7E+02  0.0049   12.4  -0.4    8   14-21     48-55  (67)

No 1  
>>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (3:)
Probab=99.95  E-value=1e-28  Score=160.28  Aligned_cols=65  Identities=45%  Similarity=0.581  Sum_probs=63.4

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++||+|+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ |||||
T Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~k~kR~Lr~~~~v~~~~~k~ik~-~Lpy~   65 (66)
T 2zjr_3            1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG   65 (66)
T ss_pred             CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997643221353136778987860627776455337988998667985577999999999-67899


No 2  
>>3i1n_3 50S ribosomal protein L35; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_3 1vs6_3 3i1p_3 3i1r_3 3i1t_3 3i20_3 3i22_3 2qam_3* 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* ... (3:)
Probab=99.95  E-value=5.5e-29  Score=161.57  Aligned_cols=65  Identities=34%  Similarity=0.464  Sum_probs=63.5

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++||||+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ |||||
T Consensus         1 MPKmKT~k~akKRFkvT~sGKi~r~~agk~H~~~~Ks~k~kR~L~~~~~v~~~~~k~ik~-~LPy~   65 (65)
T 3i1n_3            1 MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA-CLPYA   65 (65)
T ss_dssp             -CCCCCCTTGGGTCCCCTTSCCCEECSSCSSCCTTSCHHHHHHHSSEECCCHHHHHHHHH-TCTTC
T ss_pred             CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997642043564125778998862538876144247988898578984468999999998-68899


No 3  
>>2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (8:)
Probab=99.94  E-value=2.1e-28  Score=158.71  Aligned_cols=65  Identities=46%  Similarity=0.599  Sum_probs=63.2

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++|++|+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ ||||.
T Consensus         1 MPKmKT~k~a~KRFk~T~sGKikr~~a~k~H~l~~Ks~krkR~Lr~~~~v~~~~~k~ikk-~LPy~   65 (65)
T 2j01_8            1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKL-LLPYE   65 (65)
T ss_dssp             -CCCCCCHHHHHHCEECSSSCEEECCTTTTTCSSCSCCSTTTSCSCEECCSSHHHHHHTT-TTTC-
T ss_pred             CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997643212353046778987864306787765548888898647983367999999998-28999


No 4  
>>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (5:)
Probab=99.90  E-value=2.8e-25  Score=143.41  Aligned_cols=65  Identities=34%  Similarity=0.408  Sum_probs=62.8

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++|++|+|+|++||++|++++||.+++|+|+++.+|+++|.+.|.+ ||||.
T Consensus        89 ~~KmKT~k~a~KRFk~t~~Gk~~r~~agk~H~~~kKs~~~krrLr~~~~v~~~~~~~i~k-~lpy~  153 (159)
T 3bbo_5           89 GYKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIG-ALPYL  153 (159)
T ss_dssp             --CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTT-TTTC-
T ss_pred             CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCH
T ss_conf             766564341240047767975855417776564448998998657985467989999999-57971


No 5  
>>3c8l_A FTSZ-like protein of unknown function; ZP_00109722.1, conserved hypothetical protein (LIN0512_FAM), structural genomics; HET: MSE; 1.22A {Nostoc punctiforme pcc 73102} (A:)
Probab=6.49  E-value=1.8e+02  Score=12.23  Aligned_cols=13  Identities=31%  Similarity=0.440  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             78999999858688
Q gi|254780319|r   53 ADAKKVIRNYLPNG   66 (67)
Q Consensus        53 ~~~~~i~r~llPYg   66 (67)
                      -|...+ +..||||
T Consensus        68 vD~~~v-~~~lPyG   80 (122)
T 3c8l_A           68 VREEEV-LAVLPFG   80 (122)
T ss_dssp             CCHHHH-HTTSCSS
T ss_pred             CCHHHH-HHHCCCC
T ss_conf             259999-9768877


No 6  
>>3gqw_A Fatty acid AMP ligase; FAAL, E. coli, ATP-dependent AMP-binding enzyme family,, structural genomics, PSI-2, protein structure initiative; HET: ZZ9; 3.00A {Escherichia coli O6} (A:482-576)
Probab=6.07  E-value=1.1e+02  Score=13.31  Aligned_cols=14  Identities=21%  Similarity=0.252  Sum_probs=9.0

Q ss_pred             EEEECCCCEEEECC
Q ss_conf             25775998097032
Q gi|254780319|r   13 RFSITATGKVRAQA   26 (67)
Q Consensus        13 RFk~T~sGKvkr~~   26 (67)
                      .|=.|+||||.|..
T Consensus        62 ~lP~T~sGKi~R~~   75 (95)
T 3gqw_A           62 SIPRTSSGKPARAE   75 (95)
T ss_dssp             CSCBCTTSSBCHHH
T ss_pred             CCCCCCCCCHHHHH
T ss_conf             43669986663999


No 7  
>>3c5e_A Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor; middle-chain acyl-COA synthetase, xenobiotic/medium-chain fatty acid-COA ligase; HET: ATP; 1.60A {Homo sapiens} PDB: 2vze_A 3b7w_A* 3day_A* 3eq6_A* 3eyn_A* 3gpc_A* 2wd9_A* (A:456-570)
Probab=5.08  E-value=1.3e+02  Score=12.99  Aligned_cols=13  Identities=31%  Similarity=0.478  Sum_probs=8.4

Q ss_pred             EEECCCCEEEECC
Q ss_conf             5775998097032
Q gi|254780319|r   14 FSITATGKVRAQA   26 (67)
Q Consensus        14 Fk~T~sGKvkr~~   26 (67)
                      |=.|+||||-|..
T Consensus        88 lP~T~sGKidR~~  100 (115)
T 3c5e_A           88 LPKTVTGKIQRAK  100 (115)
T ss_dssp             CCBCTTCCBCHHH
T ss_pred             CCCCCCCCCCHHH
T ss_conf             7879887754898


No 8  
>>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein synthetase, PSI-2, protein structure initiative; 2.30A {Staphylococcus aureus subsp} (A:399-501)
Probab=4.54  E-value=2e+02  Score=12.09  Aligned_cols=13  Identities=31%  Similarity=0.529  Sum_probs=8.7

Q ss_pred             EEECCCCEEEECC
Q ss_conf             5775998097032
Q gi|254780319|r   14 FSITATGKVRAQA   26 (67)
Q Consensus        14 Fk~T~sGKvkr~~   26 (67)
                      |=.|+|||+.|..
T Consensus        80 lP~t~sGKi~r~~   92 (103)
T 3ipl_A           80 LPYTSTGKLQRNK   92 (103)
T ss_dssp             CC-----------
T ss_pred             CCCCCCCCCCHHH
T ss_conf             7869886826899


No 9  
>>2jra_A Protein RPA2121; domain-swapped dimer, structural genomics, PSI, protein structure initiative; NMR {Rhodopseudomonas palustris CGA009} (A:)
Probab=4.52  E-value=2.7e+02  Score=11.41  Aligned_cols=17  Identities=18%  Similarity=0.376  Sum_probs=0.0

Q ss_pred             CCHHHEEEEECCCCEEE
Q ss_conf             30121225775998097
Q gi|254780319|r    7 NSSSKKRFSITATGKVR   23 (67)
Q Consensus         7 ~k~akKRFk~T~sGKvk   23 (67)
                      |-|.-=|.++|..||++
T Consensus        48 H~G~~Y~LR~Tr~GKLI   64 (67)
T 2jra_A           48 HGDDRYRLRLTSQNKLI   64 (67)
T ss_dssp             ETTEEEEEEECTTSCEE
T ss_pred             ECCEEEEEEECCCCCEE
T ss_conf             79918997882479577


No 10 
>>3hrz_C Cobra venom factor; serine protease, glycosilated, multi-domain, complement system, convertase, complement alternate pathway, complement pathway; HET: NAG P6G; 2.20A {Naja kaouthia} PDB: 3frp_B* 3hs0_C* (C:1-67)
Probab=4.42  E-value=1.7e+02  Score=12.45  Aligned_cols=8  Identities=38%  Similarity=0.796  Sum_probs=0.0

Q ss_pred             EEECCCCE
Q ss_conf             57759980
Q gi|254780319|r   14 FSITATGK   21 (67)
Q Consensus        14 Fk~T~sGK   21 (67)
                      |.|||+|+
T Consensus        48 f~VtA~G~   55 (67)
T 3hrz_C           48 ITVTASGD   55 (67)
T ss_dssp             EEEEEEES
T ss_pred             EEEEEEEE
T ss_conf             99999988


Done!