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 23785
Date          Mon May 30 08:46:35 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780319.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2zjr_3 50S ribosomal protein L 100.0 3.1E-29 1.3E-33  162.0   6.3   65    1-66      1-65  (66)
  2 2j01_8 50S ribosomal protein L  99.9 1.2E-28 4.9E-33  159.2   3.0   64    1-65      1-64  (65)
  3 3ofq_3 50S ribosomal protein L  99.9 9.8E-27 4.1E-31  149.8   3.9   64    2-66      1-64  (64)
  4 3bbo_5 Ribosomal protein L35;   99.9 8.9E-25 3.7E-29  140.2   0.3   63    3-66     91-153 (159)
  5 3c8l_A FTSZ-like protein of un   7.7   1E+02  0.0043   12.7   0.9   14   52-66     67-80  (122)
  6 3jyw_M 60S ribosomal protein L   7.1      50  0.0021   14.2  -1.0   13   54-66     73-85  (178)
  7 2jra_A Protein RPA2121; domain   3.9 2.1E+02   0.009   11.2   1.7   18    7-24     48-65  (67)
  8 1vq8_J 50S ribosomal protein L   3.3 2.5E+02    0.01   10.8   1.2   11   55-65     79-89  (145)
  9 3heq_A Major prion protein; ce   2.5 2.6E+02   0.011   10.8  -0.3   41   25-67      1-41  (142)
 10 2v1y_A Phosphatidylinositol-4,   2.3 3.3E+02   0.014   10.2   0.4    6   62-67     25-30  (108)

No 1  
>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 1voy_5 1vp0_5
Probab=99.95  E-value=3.1e-29  Score=162.02  Aligned_cols=65  Identities=45%  Similarity=0.581  Sum_probs=63.6

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~sGKv~r~~a~k~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~-lLPyg   65 (66)
T 2zjr_3            1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG   65 (66)
T ss_pred             CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997543122352057768987865537776665558888998657985478999999999-67899


No 2  
>2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.301.1.1 PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ...
Probab=99.94  E-value=1.2e-28  Score=159.23  Aligned_cols=64  Identities=47%  Similarity=0.612  Sum_probs=62.6

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCC
Q ss_conf             98732330121225775998097032488525415880465414698683777899999985868
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPN   65 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPY   65 (67)
                      |||||||+||+|||++||||||++++||++|+++++|.+++|+|+++.+|+++|.++|.+ ||||
T Consensus         1 MPKmKT~k~a~KRfkvT~sGKi~r~~ag~~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~-lLPY   64 (65)
T 2j01_8            1 MPKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKL-LLPY   64 (65)
T ss_dssp             -CCCCCCHHHHHHCEECSSSCEEECCTTTTTCSSCSCCSTTTSCSCEECCSSHHHHHHTT-TTTC
T ss_pred             CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCC
T ss_conf             997643211351157768987874416777765448888898657985587999999998-3899


No 3  
>3ofq_3 50S ribosomal protein L35; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ...
Probab=99.93  E-value=9.8e-27  Score=149.82  Aligned_cols=64  Identities=33%  Similarity=0.449  Sum_probs=62.3

Q ss_pred             CCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             87323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    2 PKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         2 PKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      ||||||+||+|||++||||+|++++||++|++++||.+++|+|+++++|+++|.++|.+ ||||.
T Consensus         1 PKmKT~k~akKRfk~T~sGKikr~~a~~~H~l~~Ks~k~kR~lr~~~~v~~~~~k~vkk-lLPYa   64 (64)
T 3ofq_3            1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA-CLPYA   64 (64)
T ss_dssp             CCCCCCTTGGGSCCCCSSSCCCCCCSSCSSCCSSSCHHHHHHHSSCCCCCHHHHHHHHH-HCSCC
T ss_pred             CCCCCCHHHHHCEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             98764123463046778997864417777665458988998767982478999999998-68899


No 4  
>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=99.89  E-value=8.9e-25  Score=140.24  Aligned_cols=63  Identities=35%  Similarity=0.456  Sum_probs=60.9

Q ss_pred             CCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             7323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    3 KMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         3 KmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|.++|.+ ||||-
T Consensus        91 KMKThKgAkKRFKvTgsGKvkR~rAgkrHll~kKS~krKRrLRk~~~Vs~sd~K~Ikk-lLPY~  153 (159)
T 3bbo_5           91 KMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIG-ALPYL  153 (159)
T ss_dssp             CCCCCHHHHTTCCBCSSSCBEEECSSCTTCCSSCCSSCTTSCSEEECCSTHHHHTTTT-TTTC-
T ss_pred             CCCCCHHHHCEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             6455331241158757975866527777665458998998657985477999999998-57983


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}
Probab=7.67  E-value=1e+02  Score=12.69  Aligned_cols=14  Identities=29%  Similarity=0.413  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHCCCC
Q ss_conf             778999999858688
Q gi|254780319|r   52 SADAKKVIRNYLPNG   66 (67)
Q Consensus        52 ~~~~~~i~r~llPYg   66 (67)
                      .-|...+ +..||||
T Consensus        67 ~VD~~~v-~~~lPyG   80 (122)
T 3c8l_A           67 QVREEEV-LAVLPFG   80 (122)
T ss_dssp             GCCHHHH-HTTSCSS
T ss_pred             HHCHHHH-HHHCCCC
T ss_conf             2048889-9768877


No 6  
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M
Probab=7.14  E-value=50  Score=14.23  Aligned_cols=13  Identities=15%  Similarity=0.133  Sum_probs=8.7

Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             8999999858688
Q gi|254780319|r   54 DAKKVIRNYLPNG   66 (67)
Q Consensus        54 ~~~~i~r~llPYg   66 (67)
                      -.++.++.||||.
T Consensus        73 Il~rAVrGMLP~K   85 (178)
T 3jyw_M           73 IFYKALRGMVSHK   85 (178)
T ss_dssp             HHHHHTTSSSCSS
T ss_pred             HHHHHHHCCCCCC
T ss_conf             9999984568999


No 7  
>2jra_A Protein RPA2121; domain-swapped dimer, structural genomics, PSI, protein structure initiative; NMR {Rhodopseudomonas palustris CGA009}
Probab=3.92  E-value=2.1e+02  Score=11.15  Aligned_cols=18  Identities=17%  Similarity=0.333  Sum_probs=12.9

Q ss_pred             CCHHHEEEEECCCCEEEE
Q ss_conf             301212257759980970
Q gi|254780319|r    7 NSSSKKRFSITATGKVRA   24 (67)
Q Consensus         7 ~k~akKRFk~T~sGKvkr   24 (67)
                      |-|.-=|.++|..||++-
T Consensus        48 H~g~~Y~LR~Tr~gKLIL   65 (67)
T 2jra_A           48 HGDDRYRLRLTSQNKLIL   65 (67)
T ss_dssp             ETTEEEEEEECTTSCEEE
T ss_pred             ECCCEEEEEECCCCCEEE
T ss_conf             799089978835896786


No 8  
>1vq8_J 50S ribosomal protein L13P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Probab=3.25  E-value=2.5e+02  Score=10.82  Aligned_cols=11  Identities=45%  Similarity=0.766  Sum_probs=7.8

Q ss_pred             HHHHHHHHCCC
Q ss_conf             99999985868
Q gi|254780319|r   55 AKKVIRNYLPN   65 (67)
Q Consensus        55 ~~~i~r~llPY   65 (67)
                      ..+.++.||||
T Consensus        79 l~raVrGMLP~   89 (145)
T 1vq8_J           79 FKRTIRGMLPH   89 (145)
T ss_dssp             HHHHHHTTTTT
T ss_pred             HHHHHHCCCCC
T ss_conf             99998415899


No 9  
>3heq_A Major prion protein; cell membrane, disease mutation, disulfide bond, glycoprotein, golgi apparatus, GPI-anchor, lipoprotein, membrane, polymorphism; 1.80A {Homo sapiens} PDB: 2k1d_A 1fkc_A 1fo7_A 3haf_A 3hj5_A 1qm0_A 1qm1_A 3hes_A 3her_A 1b10_A 2joh_A 2fj3_A 2jom_A 2kfo_A 2k5o_A 2kfm_A 2kfl_A
Probab=2.47  E-value=2.6e+02  Score=10.77  Aligned_cols=41  Identities=20%  Similarity=0.123  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCCC
Q ss_conf             3248852541588046541469868377789999998586889
Q gi|254780319|r   25 QAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI   67 (67)
Q Consensus        25 ~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg~   67 (67)
                      .+.|..|....|.+|.+-.+......+.+-+  |.-.+.-|+|
T Consensus         1 ~~gg~~~~q~~kppK~ktn~K~va~aAaaGA--v~G~~~GY~l   41 (142)
T 3heq_A            1 GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA--VVGGLGGYML   41 (142)
T ss_dssp             --------------------------------------CCCEE
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH--HHHCCHHHHH
T ss_conf             9988777777899998321999998876533--5413201311


No 10 
>2v1y_A Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform; cancer, SH2 domain, SH3 domain, transferase, oncogenic mutations, HOST-virus interaction; 2.4A {Bos taurus}
Probab=2.32  E-value=3.3e+02  Score=10.24  Aligned_cols=6  Identities=67%  Similarity=1.359  Sum_probs=0.0

Q ss_pred             HCCCCC
Q ss_conf             586889
Q gi|254780319|r   62 YLPNGI   67 (67)
Q Consensus        62 llPYg~   67 (67)
                      |||+|+
T Consensus        25 LLPnGi   30 (108)
T 2v1y_A           25 LLPNGM   30 (108)
T ss_dssp             ECTTSC
T ss_pred             ECCCEE
T ss_conf             868605


Done!