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!