Query gi|254780785|ref|YP_003065198.1| 30S ribosomal protein S15 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 89 No_of_seqs 106 out of 1519 Neff 5.0 Searched_HMMs 33803 Date Wed Jun 1 13:53:19 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780785.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3i1m_O 30S ribosomal protein 100.0 2E-37 6.1E-42 227.3 10.9 89 1-89 1-89 (89) 2 >2vqe_O 30S ribosomal protein 100.0 3.6E-37 1.1E-41 225.9 10.2 88 1-88 1-88 (89) 3 >3bbn_O Ribosomal protein S15; 100.0 5.8E-35 1.7E-39 213.7 2.1 85 5-89 2-86 (90) 4 >1a32_A Ribosomal protein S15; 100.0 2.1E-30 6.2E-35 188.5 9.5 69 21-89 1-69 (69) 5 >3jyv_O 40S ribosomal protein 99.9 3.2E-25 9.4E-30 159.9 5.1 77 9-85 3-83 (84) 6 >2oap_1 GSPE-2, type II secret 42.1 19 0.00057 17.5 2.5 56 28-83 18-74 (94) 7 >1z7m_A ATP phosphoribosyltran 20.7 67 0.002 14.5 2.8 35 54-88 4-39 (87) 8 >2nr5_A Hypothetical protein S 17.1 81 0.0024 14.0 4.9 36 8-43 24-60 (67) 9 >1zbp_A Hypothetical protein V 15.1 91 0.0027 13.8 3.6 30 32-61 13-42 (62) 10 >3dss_A Geranylgeranyl transfe 14.6 94 0.0028 13.7 1.9 46 8-53 26-71 (84) No 1 >>3i1m_O 30S ribosomal protein S15; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O 2qbf_O 2qbh_O* 2qbj_O* 2qou_O* 2qow_O* 2qoy_O* 2qp0_O* 2vaz_F 2z4k_O* 2z4m_O* 2qal_O 3i1o_O 3i1q_O 3i1s_O 3i1z_O 3i21_O ... (O:) Probab=100.00 E-value=2e-37 Score=227.29 Aligned_cols=89 Identities=47% Similarity=0.724 Sum_probs=88.5 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 98888999999999545888788899999997799999999999778413527789999997899999998409999999 Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKR 80 (89) Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~ 80 (89) ||+++++|+++|++|++||+||||||||||+||+||.+|++||+.||||++|+|||.++|++|++||+||+++|+++|.+ T Consensus 1 M~i~~~~k~~~i~~~~~~~~DtGS~evQIA~LT~rI~~L~~Hl~~~kkD~~s~rgL~~lv~kRrklL~YLr~~d~~~Y~~ 80 (89) T 3i1m_O 1 MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQ 80 (89) T ss_dssp -CCCHHHHHHHHHHHSSSTTCTTCHHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHH T ss_conf 99878999999999768999878889999988999999999998774440009999999999999999998669999999 Q ss_pred HHHHHCCCC Q ss_conf 999836899 Q gi|254780785|r 81 LVQSLKLRR 89 (89) Q Consensus 81 ~i~~LglRk 89 (89) +|++||||| T Consensus 81 ~i~~Lglrk 89 (89) T 3i1m_O 81 LIERLGLRR 89 (89) T ss_dssp HHHHHTCCC T ss_pred HHHHHCCCC T ss_conf 999958999 No 2 >>2vqe_O 30S ribosomal protein S15; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (O:) Probab=100.00 E-value=3.6e-37 Score=225.94 Aligned_cols=88 Identities=50% Similarity=0.753 Sum_probs=87.6 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 98888999999999545888788899999997799999999999778413527789999997899999998409999999 Q gi|254780785|r 1 MSITLERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKR 80 (89) Q Consensus 1 m~~~~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~ 80 (89) |++++++|+++|++||+||+||||+|||||+||++|.+|++|++.||||++|+|||.++|++|++||+||+++|+++|.+ T Consensus 1 m~l~~~~k~~~i~~~~~~~~DtGS~evQIA~LT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRrklL~YLr~~d~~~Y~~ 80 (89) T 2vqe_O 1 MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRA 80 (89) T ss_dssp -CCCHHHHHHHHHTTCSSTTCCSSHHHHHHHHHHHHHHHHHHTTSSTTCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHH T ss_conf 99889999999999768987789877999998999999999998777742149999999999999999998669999999 Q ss_pred HHHHHCCC Q ss_conf 99983689 Q gi|254780785|r 81 LVQSLKLR 88 (89) Q Consensus 81 ~i~~LglR 88 (89) +|++|||| T Consensus 81 ~i~~Lglr 88 (89) T 2vqe_O 81 LIEKLGIR 88 (89) T ss_dssp HHHHHTCC T ss_pred HHHHHCCC T ss_conf 99993899 No 3 >>3bbn_O Ribosomal protein S15; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (O:) Probab=100.00 E-value=5.8e-35 Score=213.74 Aligned_cols=85 Identities=32% Similarity=0.396 Sum_probs=82.7 Q ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf 89999999995458887888999999977999999999997784135277899999978999999984099999999998 Q gi|254780785|r 5 LERKRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQS 84 (89) Q Consensus 5 ~~~k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~ 84 (89) +++++++|.+|++||+||||||||||+||+||++|++||+.||||++|+|||.+||++|++||+||+++|+++|.++|+. T Consensus 2 ~~~k~~~i~~~~~~~~DtGS~eVQiA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~~RkklL~YL~~~d~~~Y~~li~~ 81 (90) T 3bbn_O 2 KKNSFISVISDEKKEENKGSVEFQVFCFTNKIRRLTLHLELHKKDYSSQRGLRKTLGKRQRLLAYLLKINGVRYKELISK 81 (90) T ss_dssp CHHHHHHHHHHSCCSSSSCSTTHHHHHHHHHHTTTTTTTTTCTTCSTTSHHHHHHHHHHHHHHTTHHHHCSHHHHTTTTT T ss_pred CHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 42789999987159988688999999999999999999998766201588799999999999999986699999999999 Q ss_pred HCCCC Q ss_conf 36899 Q gi|254780785|r 85 LKLRR 89 (89) Q Consensus 85 LglRk 89 (89) ||||+ T Consensus 82 Lglr~ 86 (90) T 3bbn_O 82 LNIRE 86 (90) T ss_dssp TTCCC T ss_pred HCCCC T ss_conf 48997 No 4 >>1a32_A Ribosomal protein S15; multiwavelength anomalous diffraction, protein-RNA, ribosomal protein interactions, ribosome, RNA-binding; 2.10A {Bacillus stearothermophilus} (A:20-88) Probab=99.97 E-value=2.1e-30 Score=188.54 Aligned_cols=69 Identities=54% Similarity=0.840 Sum_probs=68.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCC Q ss_conf 788899999997799999999999778413527789999997899999998409999999999836899 Q gi|254780785|r 21 DTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQSLKLRR 89 (89) Q Consensus 21 DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~~LglRk 89 (89) ||||+|||||+||+||.+|++||+.||||++|+|||.++|++|++||+||+++|+++|.++|++||||| T Consensus 1 DTGS~eVQiA~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kRkkLL~YL~~~d~~~Y~~~i~~Lglrk 69 (69) T 1a32_A 1 DTGSPEVQIAILTEQINNLNEHLRVHKKDHHSRRGLLKMVGKRRRLLAYLRNKDVARYREIVEKLGLRR 69 (69) T ss_dssp CCCSHHHHHHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTC-- T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCC T ss_conf 868879999987999999999998777742149999999999999999998569999999999958999 No 5 >>3jyv_O 40S ribosomal protein S13; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1ysh_E 1s1h_O (O:) Probab=99.91 E-value=3.2e-25 Score=159.94 Aligned_cols=77 Identities=16% Similarity=0.162 Sum_probs=69.6 Q ss_pred HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC--HH--HHHHHHHH Q ss_conf 999999545888788899999997799999999999778413527789999997899999998409--99--99999998 Q gi|254780785|r 9 RELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSKIGLGRLISLRSSLLKYLERKD--VE--RYKRLVQS 84 (89) Q Consensus 9 ~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~kRkklL~YLk~~d--~~--~Y~~~i~~ 84 (89) .+.|.+|+.+++||||+|||||+||+||.+|++||+.||||+||+|||..+|++|++||+||+++| ++ .|...++. T Consensus 3 ~k~i~~~~~~~~dtGs~evqia~Lt~rI~~L~~Hl~~nkkD~~skRgL~~lv~kRkrLl~Ylkr~~~lp~~w~y~~~~a~ 82 (84) T 3jyv_O 3 GNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATAS 82 (84) T ss_dssp HHHHHHHCSSSSCSSSTHHHHHHHHHHHHHHTTSSSSCSCCSHHHHHHHHHHHHHHHHHHHHHHHCCSSCSHHHHHHHHT T ss_pred CHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECHHHHH T ss_conf 11899999987999999389999999999999999878761667899999999999999998705859999726778674 Q ss_pred H Q ss_conf 3 Q gi|254780785|r 85 L 85 (89) Q Consensus 85 L 85 (89) | T Consensus 83 l 83 (84) T 3jyv_O 83 A 83 (84) T ss_dssp C T ss_pred H T ss_conf 0 No 6 >>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus dsm 4304} PDB: 2oaq_1 (1:232-260,1:447-511) Probab=42.12 E-value=19 Score=17.49 Aligned_cols=56 Identities=13% Similarity=0.047 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH Q ss_conf 99997799999999999778-413527789999997899999998409999999999 Q gi|254780785|r 28 QVAVCTERIANLTEHFKSAK-KDVNSKIGLGRLISLRSSLLKYLERKDVERYKRLVQ 83 (89) Q Consensus 28 QIA~lT~rI~~L~~Hl~~~k-KD~~s~rgL~~lv~kRkklL~YLk~~d~~~Y~~~i~ 83 (89) -.|.|---|.+-+.+|+.=. .---+..-|..=+.+|++.|.||..++...|..|-. T Consensus 18 ~~~~~~~~~~~~S~iLeeIa~~rGws~~eL~eEle~Rk~VLeyM~ekgIrDY~~Vs~ 74 (94) T 2oap_1 18 VLAYLWLAIEHKPKKLEKXADFLGVSVQEVYDEXLSRKRYLELXLKRGIRNYKEVTR 74 (94) T ss_dssp HHHHHHHHHHTTCTHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHH T ss_pred HHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 999999997269689999998759998999999999999999999869999999999 No 7 >>1z7m_A ATP phosphoribosyltransferase regulatory subunit; ATP-PRT, histidine biosynthesis, hiszg, allosteric, evolution; 2.90A {Lactococcus lactis} (A:183-269) Probab=20.67 E-value=67 Score=14.52 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=24.2 Q ss_pred HHHHHHHH-HHHHHHHHHHHCCHHHHHHHHHHHCCC Q ss_conf 78999999-789999999840999999999983689 Q gi|254780785|r 54 IGLGRLIS-LRSSLLKYLERKDVERYKRLVQSLKLR 88 (89) Q Consensus 54 rgL~~lv~-kRkklL~YLk~~d~~~Y~~~i~~LglR 88 (89) +||....+ ....+..++.+||+..+...++.+++. T Consensus 4 ~~Ll~~~~~~ee~l~~~i~~Kn~~~l~~~l~~~~~~ 39 (87) T 1z7m_A 4 QRLCQLADGSTELLTELLLKKDLSGLNAFIEKNNFS 39 (87) T ss_dssp HHHHHHTTTCHHHHHHHHHTTCHHHHHHHHTTSCCC T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 766664200112246676542021057787652478 No 8 >>2nr5_A Hypothetical protein SO2669; PSI-2, MCSG, MAD, structural genomics, protein structure initiative; 1.90A {Shewanella oneidensis mr-1} (A:) Probab=17.05 E-value=81 Score=14.05 Aligned_cols=36 Identities=22% Similarity=0.388 Sum_probs=23.7 Q ss_pred HHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHH Q ss_conf 999999954588878889999-999779999999999 Q gi|254780785|r 8 KRELMKEYAVSPGDTGSPEVQ-VAVCTERIANLTEHF 43 (89) Q Consensus 8 k~~~i~~f~~~~~DtGS~evQ-IA~lT~rI~~L~~Hl 43 (89) |-..|......+....|+..| +.+.|.||..|.+-+ T Consensus 24 klkairqlcgaedssdssd~qeveiwtnrikeledwl 60 (67) T 2nr5_A 24 KLKAIRQLCGAEDSSDSSDXQEVEIWTNRIKELEDWL 60 (67) T ss_dssp HHHHHHHTTTTTCC----HHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999957766775103489999998899999986 No 9 >>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.40A {Vibrio parahaemolyticus rimd 2210633} (A:1-62) Probab=15.11 E-value=91 Score=13.76 Aligned_cols=30 Identities=20% Similarity=0.272 Sum_probs=24.1 Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 779999999999977841352778999999 Q gi|254780785|r 32 CTERIANLTEHFKSAKKDVNSKIGLGRLIS 61 (89) Q Consensus 32 lT~rI~~L~~Hl~~~kKD~~s~rgL~~lv~ 61 (89) +.+-|..+.++++.+|.|...|-.|..+++ T Consensus 13 l~~al~~~~~~ir~~P~da~~R~~lfqLLC 42 (62) T 1zbp_A 13 LQQALELLIEAIKASPKDASLRSSFIELLC 42 (62) T ss_dssp HHHHHHHHHHHHHTCTTCHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 999999999999868999999999999999 No 10 >>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3c72_A* (A:160-243) Probab=14.64 E-value=94 Score=13.69 Aligned_cols=46 Identities=11% Similarity=0.144 Sum_probs=27.7 Q ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH Q ss_conf 9999999545888788899999997799999999999778413527 Q gi|254780785|r 8 KRELMKEYAVSPGDTGSPEVQVAVCTERIANLTEHFKSAKKDVNSK 53 (89) Q Consensus 8 k~~~i~~f~~~~~DtGS~evQIA~lT~rI~~L~~Hl~~~kKD~~s~ 53 (89) +.-++......+.....+..--.++-..+.....-+..+|+|+++= T Consensus 26 R~~vl~~~~~~~~~~~~~~~~~~~l~~El~~~~~~i~~~p~N~saW 71 (84) T 3dss_A 26 RSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAW 71 (84) T ss_dssp HHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHH T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 9999998046577888898889987888999999998387405799 Done!