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!