Query         gi|254780475|ref|YP_003064888.1| 50S ribosomal protein L33 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 55
No_of_seqs    108 out of 436
Neff          4.1 
Searched_HMMs 23785
Date          Mon May 30 12:18:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780475.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_1 50S ribosomal protein L  99.9 3.3E-25 1.4E-29  151.2   6.7   54    1-54      1-55  (55)
  2 1nkw_1 50S ribosomal protein L  99.9   5E-25 2.1E-29  150.3   6.2   54    1-54     28-82  (82)
  3 2j01_6 50S ribosomal protein L  99.8   2E-23 8.2E-28  141.9  -1.7   54    1-54      1-54  (54)
  4 3ofq_1 50S ribosomal protein L  99.8 9.3E-23 3.9E-27  138.4   0.7   50    4-53      1-50  (50)
  5 3bbo_3 Ribosomal protein L33;   99.8 1.5E-22 6.3E-27  137.3  -0.7   53    1-53      1-65  (66)
  6 2ftc_P Mitochondrial ribosomal  99.8   3E-20 1.3E-24  125.2   5.8   51    1-53      2-52  (52)
  7 1vq8_3 50S ribosomal protein L  93.3   0.046 1.9E-06   30.2   2.9   21   35-55      6-26  (92)
  8 2zkr_4 60S ribosomal protein L  91.0    0.13 5.5E-06   27.8   2.9   22   34-55      6-27  (106)
  9 3cng_A Nudix hydrolase; struct  23.0      23 0.00097   16.1   1.1   13    9-21     24-36  (189)
 10 3kde_C Transposable element P   22.0      19 0.00079   16.5   0.4   12   37-48      1-12  (77)
 11 2con_A RUH-035 protein, NIN on  21.6      23 0.00095   16.1   0.8   32    8-51     13-44  (79)

No 1  
>2zjr_1 50S ribosomal protein L33; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.6 PDB: 1nwx_1* 1xbp_1* 2zjp_1* 2zjq_1 1nwy_1 3cf5_1* 3dll_1* 1pnu_1 1pny_1 1vor_3 1vou_3 1vow_3 1voy_3 1vp0_3
Probab=99.91  E-value=3.3e-25  Score=151.20  Aligned_cols=54  Identities=52%  Similarity=0.782  Sum_probs=52.7

Q ss_pred             CCC-CCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf             987-762699999517788759835488998333699413174463446688650
Q gi|254780475|r    1 MAK-AATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKI   54 (55)
Q Consensus         1 MaK-~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~Ki   54 (55)
                      ||| ++|++|+|+|+||+|++|+|+||++|+||||||+||||+||+||+|+|+||
T Consensus         1 MAKk~~rv~I~L~st~~t~~~Y~t~Kn~~~~~~kLel~Ky~p~~rkh~lhkE~Ki   55 (55)
T 2zjr_1            1 MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV   55 (55)
T ss_pred             CCCCCCEEEEEEEEECCCCCEEEEECCCCCCCHHEEEECCCCCCCCEEEEEEEEC
T ss_conf             9887780799999958989789771688999403179733878872561886309


No 2  
>1nkw_1 50S ribosomal protein L33; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB: 1sm1_1* 1yl3_6 2b66_6 2b9n_6 2b9p_6
Probab=99.91  E-value=5e-25  Score=150.28  Aligned_cols=54  Identities=52%  Similarity=0.782  Sum_probs=52.2

Q ss_pred             CCC-CCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf             987-762699999517788759835488998333699413174463446688650
Q gi|254780475|r    1 MAK-AATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKI   54 (55)
Q Consensus         1 MaK-~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~Ki   54 (55)
                      ||| ++|++|+|+||||+||+|+|+||++|+||||||+||||+||+||+|+|+||
T Consensus        28 MAKk~~Ri~IkL~Sta~tg~~Y~T~KNkrn~~eKLelkKYcp~crKHtlhkEtKi   82 (82)
T 1nkw_1           28 MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV   82 (82)
T ss_pred             CCCCCCCEEEEEEEECCCCCEEEECCCCCCCCHHCEEECCCCCCCCEEEEEEEEC
T ss_conf             1367882799999847889889762788899301068624877763450775209


No 3  
>2j01_6 50S ribosomal protein L33; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: g.41.8.6 PDB: 2hgq_5 2hgj_5 2hgu_5 2j03_6 2jl6_6 2jl8_6 2v47_6 2v49_6 2wdi_6 2wdj_6 2wdl_6 2wdn_6 2wh2_6 2wh4_6 2wrj_6 2wrl_6 2wro_6 2wrr_6 2x9s_6 2x9u_6 ...
Probab=99.85  E-value=2e-23  Score=141.93  Aligned_cols=54  Identities=37%  Similarity=0.442  Sum_probs=53.3

Q ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEE
Q ss_conf             987762699999517788759835488998333699413174463446688650
Q gi|254780475|r    1 MAKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKI   54 (55)
Q Consensus         1 MaK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~Ki   54 (55)
                      ||++.|+.|.|+|++|++++|+|+||++|+|+||||+||||+|++||+|+|+||
T Consensus         1 Ma~~~R~~I~L~Ctec~~rnY~T~KNkrn~p~rLelkKycp~c~kHt~hkE~Ki   54 (54)
T 2j01_6            1 MASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI   54 (54)
T ss_dssp             --------CCCCCCCTTSCCCCCCCCCTTSSCSSCCCCCCCSSSCCCCCCCC--
T ss_pred             CCCCCEEEEEEEECCCCCCCCEECCCCCCCCCEEEEECCCCCCCCEEEEEEEEC
T ss_conf             987753069999578778882497767889760579661878897434755019


No 4  
>3ofq_1 50S ribosomal protein L33; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 3fik_1 2wwq_4 3ofr_1* 3i1n_1 1vs8_1 1vs6_1 1vt2_1 3i1p_1 3i1r_1 3i1t_1 3i20_1 3i22_1 3kcr_1 3orb_1* 2gya_1 2gyc_1 2qam_1* 1p85_1 1p86_1 2awb_1 ...
Probab=99.84  E-value=9.3e-23  Score=138.40  Aligned_cols=50  Identities=56%  Similarity=0.832  Sum_probs=48.6

Q ss_pred             CCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             76269999951778875983548899833369941317446344668865
Q gi|254780475|r    4 AATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         4 ~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |.|++|+|+|+||+|++|+|+||++|+||||||+||||+|++||+|+|+|
T Consensus         1 gmR~~I~L~st~~tg~~Y~t~Kn~~~~~~rLel~Kycp~~~kHtlhkE~K   50 (50)
T 3ofq_1            1 GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK   50 (50)
T ss_dssp             CCSEEECCBCSSSCCCBCCEEECTTTCCSCCCCCEECTTTSSEECCBCCC
T ss_pred             CCCCEEEEEEECCCCCEEEECCCCCCCCCCEEEECCCCCCCCEEEEEECC
T ss_conf             98658999982788845976588899950247974388887157178439


No 5  
>3bbo_3 Ribosomal protein L33; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=99.83  E-value=1.5e-22  Score=137.32  Aligned_cols=53  Identities=28%  Similarity=0.351  Sum_probs=49.2

Q ss_pred             CCC--CCEEEEEEEECCCCCCE----------EEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             987--76269999951778875----------983548899833369941317446344668865
Q gi|254780475|r    1 MAK--AATIKIKLISSAGTGSF----------YVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         1 MaK--~~r~~I~L~st~~tg~~----------Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |||  +.|++|.|+|++|...+          |+|+||++|+||||||+||||+|++||+|+|+|
T Consensus         1 MAk~k~~R~~I~L~Ct~C~~~n~~k~~~~~~rY~T~KNkrn~p~RLElkKycp~c~kHtlhkE~K   65 (66)
T 3bbo_3            1 MAKGKDVRVKVILECTGCVRKSVNKGSRGVSRYITQKNRHNTPSRLELRKFCPYCYKHTIHGEIK   65 (66)
T ss_dssp             CCCSSSSCCCCEECCCCTTCCSSSCCSSSCCCSSCEECCTTSSCCSCCCCCCCSSSSCCCCCCCC
T ss_pred             CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCCCCEEEEEECC
T ss_conf             98777872789998266655665445788522586777788966068974187778730052024


No 6  
>2ftc_P Mitochondrial ribosomal protein L33 isoform A, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_P
Probab=99.80  E-value=3e-20  Score=125.25  Aligned_cols=51  Identities=37%  Similarity=0.627  Sum_probs=48.1

Q ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             98776269999951778875983548899833369941317446344668865
Q gi|254780475|r    1 MAKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         1 MaK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      .||+++++|+|+|+|+|||+|+|+||+  .|++|+|+||||++++||+|+|.|
T Consensus         2 KaK~~~i~ikL~StAgTG~~y~t~knr--~~~kl~l~KYDPvvrkhVlF~E~K   52 (52)
T 2ftc_P            2 KSKSKNILVRMVSEAGTGFCFNTKRNR--LREKLTLLHYDPVVKQRVLFVEKK   52 (52)
T ss_pred             CCCCCEEEEEEEEECCCCEEEEEECCC--CCCCCEEEECCCCCEEEEEEEECC
T ss_conf             877660899999927886599983489--875451785384630568898449


No 7  
>1vq8_3 50S ribosomal protein L44E; 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: g.41.8.3 PDB: 1jj2_2 1k73_4* 1k8a_4* 1k9m_4* 1kc8_4* 1kd1_4* 1kqs_2* 1m1k_4* 1m90_4* 1n8r_4* 1nji_4* 1q7y_4* 1q81_4* 1q82_4* 1q86_4* 1qvf_2 1qvg_2 1s72_3* 1vq4_3* 1vq5_3* ...
Probab=93.28  E-value=0.046  Score=30.19  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=17.0

Q ss_pred             EEEECCCCCCCEEEEEEEEEC
Q ss_conf             994131744634466886509
Q gi|254780475|r   35 VKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus        35 el~Ky~p~~~kHvl~~E~KiK   55 (55)
                      ..+-|||.|++|+.|+=+..|
T Consensus         6 ~~~tyCp~CkkHt~HkV~~~K   26 (92)
T 1vq8_3            6 RFNTYCPHCNEHQEHEVEKVR   26 (92)
T ss_dssp             EEEEEETTTTEEEEEEEEECC
T ss_pred             CCCCCCCCCCCCCCEEEEEEC
T ss_conf             010109364787436999852


No 8  
>2zkr_4 60S ribosomal protein L44E; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} SCOP: i.1.1.1 PDB: 1s1i_Z 3jyw_Z
Probab=90.95  E-value=0.13  Score=27.85  Aligned_cols=22  Identities=18%  Similarity=0.161  Sum_probs=17.4

Q ss_pred             EEEEECCCCCCCEEEEEEEEEC
Q ss_conf             6994131744634466886509
Q gi|254780475|r   34 MVKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus        34 lel~Ky~p~~~kHvl~~E~KiK   55 (55)
                      =+.+-|||.|++|++|+-+..|
T Consensus         6 K~~ktyC~kCkkHt~HkV~qyK   27 (106)
T 2zkr_4            6 KTRRTFCKKCGKHQPHKVTQYK   27 (106)
T ss_dssp             SEEEEEETTTTEEEEEEEEECC
T ss_pred             CCEEECCCCCCCCCCCEEEEEE
T ss_conf             5210007065787771799961


No 9  
>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718}
Probab=22.98  E-value=23  Score=16.07  Aligned_cols=13  Identities=15%  Similarity=0.174  Sum_probs=5.5

Q ss_pred             EEEEECCCCCCEE
Q ss_conf             9999517788759
Q gi|254780475|r    9 IKLISSAGTGSFY   21 (55)
Q Consensus         9 I~L~st~~tg~~Y   21 (55)
                      ..+.|.+|....|
T Consensus        24 ~~~~C~~C~~~~y   36 (189)
T 3cng_A           24 PRYICPKCHTIHY   36 (189)
T ss_dssp             CEEEETTTTEEEC
T ss_pred             EEEECCCCCCCCC
T ss_conf             4753799997608


No 10 
>3kde_C Transposable element P transposase; THAP domain, DNA-binding domain, zinc-finger, beta-alpha- beta, P-element transposase; HET: BRU; 1.74A {Drosophila melanogaster}
Probab=21.95  E-value=19  Score=16.55  Aligned_cols=12  Identities=33%  Similarity=0.210  Sum_probs=7.8

Q ss_pred             EECCCCCCCEEE
Q ss_conf             413174463446
Q gi|254780475|r   37 NKYDPVIRKHVE   48 (55)
Q Consensus        37 ~Ky~p~~~kHvl   48 (55)
                      ++||.+|++||-
T Consensus         1 M~~C~fc~k~v~   12 (77)
T 3kde_C            1 MKYCKFCCKAVT   12 (77)
T ss_dssp             CCEETTTTEECC
T ss_pred             CCHHHHHHCCCC
T ss_conf             956665131167


No 11 
>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1
Probab=21.61  E-value=23  Score=16.14  Aligned_cols=32  Identities=9%  Similarity=-0.111  Sum_probs=21.8

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEE
Q ss_conf             99999517788759835488998333699413174463446688
Q gi|254780475|r    8 KIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKE   51 (55)
Q Consensus         8 ~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E   51 (55)
                      .-.|.|.||-    .++++-        -+.|||.|.-.+|-+-
T Consensus        13 ~~vLrC~aCf----~~t~d~--------~k~FCpkCGn~TL~Rv   44 (79)
T 2con_A           13 SYILRCHGCF----KTTSDM--------NRVFCGHCGNKTLKKV   44 (79)
T ss_dssp             CEEEECSSSC----CEESCS--------SCCSCSSSCCSCCEEE
T ss_pred             HHHEEEEECC----CCCCCC--------CCCCCCCCCCCCCEEE
T ss_conf             4222642446----696896--------6632754798801589


Done!