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 33803
Date          Wed Jun  1 13:07:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780475.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3i1n_1 50S ribosomal protein   99.9 1.7E-25   5E-30  153.5   2.7   55    1-55      1-55  (55)
  2 >2zjr_1 50S ribosomal protein   99.9   3E-24 8.9E-29  147.0   6.6   54    1-54      1-55  (55)
  3 >1nkw_1 50S ribosomal protein   99.9 1.4E-23 4.1E-28  143.5   6.2   54    1-54     27-82  (82)
  4 >2j01_6 50S ribosomal protein   99.9 1.2E-24 3.4E-29  149.2  -1.7   54    1-54      1-54  (54)
  5 >2ftc_P Mitochondrial ribosoma  99.8 2.3E-21 6.9E-26  131.9   5.8   50    2-53      3-52  (52)
  6 >3bbo_3 Ribosomal protein L33;  99.8 2.8E-22 8.2E-27  136.7  -0.7   53    1-53      1-65  (66)
  7 >2zkr_4 60S ribosomal protein   91.9    0.13 3.7E-06   28.7   2.9   21   35-55      7-27  (106)
  8 >1vq8_3 50S ribosomal protein   91.4    0.16 4.7E-06   28.2   2.9   21   35-55      6-26  (92)
  9 >2z3z_A Dipeptidyl aminopeptid  24.7      55  0.0016   14.9   6.3   44    8-53      6-51  (56)
 10 >2con_A RUH-035 protein, NIN o  24.4      26 0.00077   16.6   0.8   31    9-51     14-44  (79)
 11 >3cng_A Nudix hydrolase; struc  21.5      40  0.0012   15.6   1.3   15   36-50      2-16  (37)

No 1  
>>3i1n_1 50S ribosomal protein L33; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_1 1vs6_1 3i1p_1 3i1r_1 3i1t_1 3i20_1 3i22_1 2qam_1* 1p85_1 1p86_1 2awb_1 2aw4_1 2i2v_1 2j28_1 2i2t_1* 2qao_1* 2qba_1* 2qbc_1* 2qbe_1 2qbg_1 ... (1:)
Probab=99.91  E-value=1.7e-25  Score=153.54  Aligned_cols=55  Identities=60%  Similarity=0.860  Sum_probs=54.4

Q ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEEC
Q ss_conf             9877626999995177887598354889983336994131744634466886509
Q gi|254780475|r    1 MAKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus         1 MaK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~KiK   55 (55)
                      |||+.|++|+|+|++|+++||+|+||++++||||||+||||+|++||+|+|+|||
T Consensus         1 Mak~~r~~i~L~ct~c~~~nY~T~KN~~~~~~rLel~Kycp~~~khtlhkE~Kik   55 (55)
T 3i1n_1            1 MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK   55 (55)
T ss_dssp             ---CCCBCCCEEESSSSCCEECCCBCSSSCCSCCCEEEEETTTTEEEEEECCC--
T ss_pred             CCCCCCCEEEEEEECCCCEEEEECCCCCCCCHHEEEECCCCCCCCEEEEEEEECC
T ss_conf             9976551699998288881797647888994144897418787856608876529


No 2  
>>2zjr_1 50S ribosomal protein L33; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (1:)
Probab=99.90  E-value=3e-24  Score=147.00  Aligned_cols=54  Identities=52%  Similarity=0.782  Sum_probs=52.4

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~~r~~i~L~ct~c~~~nY~T~KN~~~~~~rLelkKycp~~~kht~hkE~Ki   55 (55)
T 2zjr_1            1 MAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV   55 (55)
T ss_pred             CCCCCCCEEEEEEEECCCCCEEEECCCCCCCCCCEEEECCCCCCCCEEEEEEECC
T ss_conf             9887781799999828889889872788999520589764878873562886209


No 3  
>>1nkw_1 50S ribosomal protein L33; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} (1:)
Probab=99.89  E-value=1.4e-23  Score=143.54  Aligned_cols=54  Identities=46%  Similarity=0.730  Sum_probs=51.4

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        27 Mak~K~~R~~I~L~ct~c~~~nY~T~KNrk~~pekLeLkKYcP~~rkhtlhkE~Ki   82 (82)
T 1nkw_1           27 IMAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKKV   82 (82)
T ss_pred             HHCCCCCCEEEEEEEECCCCCEEEECCCCCCCCCCEEEECCCCCCCCEEEEEEEEC
T ss_conf             10367882799999847889889764678899302378635876553352775109


No 4  
>>2j01_6 50S ribosomal protein L33; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (6:)
Probab=99.88  E-value=1.2e-24  Score=149.15  Aligned_cols=54  Identities=37%  Similarity=0.442  Sum_probs=53.4

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 Mak~~r~~i~L~ct~c~~~nY~T~KN~~~~~erLelkKycp~c~kHtlhkE~Ki   54 (54)
T 2j01_6            1 MASEVRIKLLLECTECKRRNYATEKNKRNTPNKLELRKYCPWCRKHTVHREVKI   54 (54)
T ss_dssp             --------CCCCCCCTTSCCCCCCCCCTTSSCSSCCCCCCCSSSCCCCCCCC--
T ss_pred             CCCCCEEEEEEEECCCCCCCEEECCCCCCCCCEEEEECCCCCCCCEEEEEEEEC
T ss_conf             987752369998537778873497777889662689762877788442766219


No 5  
>>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 (P:)
Probab=99.84  E-value=2.3e-21  Score=131.89  Aligned_cols=50  Identities=38%  Similarity=0.648  Sum_probs=47.6

Q ss_pred             CCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             8776269999951778875983548899833369941317446344668865
Q gi|254780475|r    2 AKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         2 aK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      +|++|++|+|+|+||+|++|+|++|+  .|+||||+||||+|++||+|+|+|
T Consensus         3 ~K~~r~~V~L~st~~~~~~Y~t~knr--~~~rlel~KydP~~~kHvl~kE~K   52 (52)
T 2ftc_P            3 SKSKNILVRMVSEAGTGFCFNTKRNR--LREKLTLLHYDPVVKQRVLFVEKK   52 (52)
T ss_pred             CCCCEEEEEEEEECCCCEEEEEECCC--CCCCCEEEECCCCCEEEEEEEECC
T ss_conf             77650899999907887089983489--887545885393043568998449


No 6  
>>3bbo_3 Ribosomal protein L33; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (3:)
Probab=99.83  E-value=2.8e-22  Score=136.71  Aligned_cols=53  Identities=28%  Similarity=0.348  Sum_probs=49.0

Q ss_pred             CCC--CCEEEEEEEECCCCCC----------EEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             987--7626999995177887----------5983548899833369941317446344668865
Q gi|254780475|r    1 MAK--AATIKIKLISSAGTGS----------FYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   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~Ctec~~rn~~~~~~~~~~Y~T~KNkrn~p~RLelkKycp~c~khtlhkE~K   65 (66)
T 3bbo_3            1 MAKGKDVRVKVILECTGCVRKSVNKGSRGVSRYITQKNRHNTPSRLELRKFCPYCYKHTIHGEIK   65 (66)
T ss_dssp             CCCSSSSCCCCEECCCCTTCCSSSCCSSSCCCSSCEECCTTSSCCSCCCCCCCSSSSCCCCCCCC
T ss_pred             CCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCCCCEEEEEECC
T ss_conf             98777872689997266543675556788641586776788954067841186667631364114


No 7  
>>2zkr_4 60S ribosomal protein L44E; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (4:)
Probab=91.95  E-value=0.13  Score=28.71  Aligned_cols=21  Identities=19%  Similarity=0.191  Sum_probs=17.3

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         7 ~~~tyCp~CkkHt~HkV~qyK   27 (106)
T 2zkr_4            7 TRRTFCKKCGKHQPHKVTQYK   27 (106)
T ss_dssp             EEEEEETTTTEEEEEEEEECC
T ss_pred             CEEEECCCCCCCCCEEEEEEE
T ss_conf             211208164787640799951


No 8  
>>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} (3:)
Probab=91.40  E-value=0.16  Score=28.21  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=17.1

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~qyK   26 (92)
T 1vq8_3            6 RFNTYCPHCNEHQEHEVEKVR   26 (92)
T ss_dssp             EEEEEETTTTEEEEEEEEECC
T ss_pred             CEECCCCCCCCCCCEEEEEEE
T ss_conf             010008364687427999861


No 9  
>>2z3z_A Dipeptidyl aminopeptidase IV; peptidase family S9, prolyl oligopeptidase family, serine protease, proline-specific peptidase; HET: AIO; 1.95A {Porphyromonas gingivalis W83} PDB: 2z3w_A* 2d5l_A 2eep_A* 2dcm_A* (A:255-310)
Probab=24.67  E-value=55  Score=14.92  Aligned_cols=44  Identities=23%  Similarity=0.254  Sum_probs=33.8

Q ss_pred             EEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCC--EEEEEEEE
Q ss_conf             99999517788759835488998333699413174463--44668865
Q gi|254780475|r    8 KIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRK--HVEFKEGK   53 (55)
Q Consensus         8 ~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~k--Hvl~~E~K   53 (55)
                      +.++.-+...+..|...=||  .+..|.|..+||....  .++|.|+-
T Consensus         6 i~rv~W~~d~~~l~vq~lnR--~Q~~l~l~~~d~~TG~~~~~l~~E~~   51 (56)
T 2z3z_A            6 LTNLSWSPDENILYVAEVNR--AQNECKVNAYDAETGRFVRTLFVETD   51 (56)
T ss_dssp             EEEEEECTTSSEEEEEEECT--TSCEEEEEEEETTTCCEEEEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEEECC--CCCEEEEEEECCCCCCCEEEEEEECC
T ss_conf             89999867986269996033--56421016860223542035678425


No 10 
>>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} (A:)
Probab=24.41  E-value=26  Score=16.60  Aligned_cols=31  Identities=10%  Similarity=-0.037  Sum_probs=21.2

Q ss_pred             EEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEE
Q ss_conf             9999517788759835488998333699413174463446688
Q gi|254780475|r    9 IKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKE   51 (55)
Q Consensus         9 I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E   51 (55)
                      -.|.|.||    |.++++.        -+.|||.|...+|-+-
T Consensus        14 ~iLrC~aC----f~~t~~~--------~k~FCp~CGn~TL~rv   44 (79)
T 2con_A           14 YILRCHGC----FKTTSDM--------NRVFCGHCGNKTLKKV   44 (79)
T ss_dssp             EEEECSSS----CCEESCS--------SCCSCSSSCCSCCEEE
T ss_pred             HHEEEEEC----CCCCCCC--------CCCCCCCCCCCCEEEE
T ss_conf             12264233----5586887--------6662743698810589


No 11 
>>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718} (A:1-37)
Probab=21.50  E-value=40  Score=15.62  Aligned_cols=15  Identities=13%  Similarity=0.162  Sum_probs=9.8

Q ss_pred             EEECCCCCCCEEEEE
Q ss_conf             941317446344668
Q gi|254780475|r   36 KNKYDPVIRKHVEFK   50 (55)
Q Consensus        36 l~Ky~p~~~kHvl~~   50 (55)
                      .+|||+.|..-|.++
T Consensus         2 ~~kfC~~CG~~v~~~   16 (37)
T 3cng_A            2 HXKFCSQCGGEVILR   16 (37)
T ss_dssp             -CCBCTTTCCBCEEE
T ss_pred             CCEECCCCCCCCCCC
T ss_conf             762882337856135


Done!