Query gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 83 No_of_seqs 108 out of 995 Neff 5.3 Searched_HMMs 23785 Date Mon May 30 08:23:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780330.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3i1m_R 30S ribosomal protein S 100.0 4.5E-29 1.9E-33 182.7 5.1 71 13-83 3-73 (75) 2 2vqe_R 30S ribosomal protein S 99.9 2.4E-27 9.9E-32 173.1 6.0 82 1-82 1-83 (88) 3 3bbn_R Ribosomal protein S18; 99.9 4.7E-27 2E-31 171.4 0.3 79 3-83 2-80 (103) 4 3ofo_R 30S ribosomal protein S 99.9 5.4E-24 2.3E-28 154.3 5.1 53 30-82 1-53 (55) 5 2waq_C DNA-directed RNA polyme 28.0 12 0.00052 18.2 0.5 32 29-60 306-337 (395) 6 2aam_A Hypothetical protein TM 17.0 41 0.0017 15.3 1.3 22 61-82 258-279 (309) 7 2rpa_A Katanin P60 ATPase-cont 14.6 43 0.0018 15.2 0.9 16 64-79 11-26 (78) 8 3h0g_A DNA-directed RNA polyme 13.1 61 0.0026 14.3 1.3 29 30-58 1368-1396(1752) 9 2elu_A Zinc finger protein 406 12.1 47 0.002 15.0 0.5 24 18-46 9-32 (37) 10 1su3_A Interstitial collagenas 11.9 45 0.0019 15.1 0.3 49 33-81 9-57 (450) No 1 >3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 3kc4_R 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R 2i2u_R 2i2p_R* 2qan_R* 2qb9_R* 2qbb_R* 2qbd_R 2qbf_R ... Probab=99.95 E-value=4.5e-29 Score=182.74 Aligned_cols=71 Identities=49% Similarity=0.828 Sum_probs=67.0 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 77778888543503885114468899999628998485503317489999999999999997046586769 Q gi|254780330|r 13 NVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVNL 83 (83) Q Consensus 13 ~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~~ 83 (83) ++++++|+|+||.+++++|||||+++|++||||+|+|+||++||+|++|||+|++|||+||+|||||||+- T Consensus 3 r~~~rkk~C~~c~~~~~~idYKd~~lL~~Fis~~GkI~prr~TG~~~k~Qr~l~~aIkrAR~~gLlP~~~~ 73 (75) T 3i1m_R 3 RYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDR 73 (75) T ss_dssp -----------------CCSTTCHHHHGGGBCTTCCBCCHHHHCCCHHHHHHHHHHHHHHHTTTSSCSSSC T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 75678988988768998478659899998568887584774478699999999999999998536773547 No 2 >2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R 1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R* 1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U* 1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ... Probab=99.94 E-value=2.4e-27 Score=173.14 Aligned_cols=82 Identities=37% Similarity=0.556 Sum_probs=70.8 Q ss_pred CCCCCCCCHHHCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCC Q ss_conf 98766671322777-77888854350388511446889999962899848550331748999999999999999704658 Q gi|254780330|r 1 MAEVAPTPLLRRNV-SHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIA 79 (83) Q Consensus 1 ms~~~p~p~~~~~~-~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlP 79 (83) ||+.+..|...... ..+++.|.++..+++.+||||+++|++||||+|+|+||++||+|+++||+|++|||+||+||||| T Consensus 1 ms~k~~~~kk~~~rr~~~k~~~~~~~~~~~~iDyKdv~lL~~Fis~~GkI~prr~TGl~~k~Qr~l~~aIKrAR~~gLlp 80 (88) T 2vqe_R 1 MSTKNAKPKKEAQRRPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLP 80 (88) T ss_dssp ---------------CCCSCCTTTSCCCEETTCTTCHHHHGGGBCSSSCBCCHHHHCCCHHHHHHHHHHHHHHHHTTSSC T ss_pred CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf 99876564510111887777663344667856755889999866998748287427879999999999999999975465 Q ss_pred CCC Q ss_conf 676 Q gi|254780330|r 80 YVN 82 (83) Q Consensus 80 y~~ 82 (83) ||+ T Consensus 81 ~~~ 83 (88) T 2vqe_R 81 FTE 83 (88) T ss_dssp SCC T ss_pred CCH T ss_conf 228 No 3 >3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Probab=99.92 E-value=4.7e-27 Score=171.45 Aligned_cols=79 Identities=35% Similarity=0.694 Sum_probs=70.4 Q ss_pred CCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 76667132277777888854350388511446889999962899848550331748999999999999999704658676 Q gi|254780330|r 3 EVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN 82 (83) Q Consensus 3 ~~~p~p~~~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~ 82 (83) |.++.|..+++...+++.|+++.. +.|||||+++|++|||++|+|+||++||+|++|||+|++|||+||+|||||||+ T Consensus 2 ~~~kr~f~k~~~~~rrr~~~~~~~--~~IDYKnv~lL~~Fis~~GkI~prr~TGl~~k~Qrkl~~aIKrAR~~gLLPyv~ 79 (103) T 3bbn_R 2 DKSKRPFIKSKRSFRRRLPPIQSG--DRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITSAIKQARILSLLPFLN 79 (103) T ss_dssp -----------------------C--CSSCCSCHHHHTTTSCSSSSCCCSSSTTCCTTTTTTTHHHHHHHTTTTSSCTTC T ss_pred CCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 866676332467888789988878--866764889999866998728387338869999999999999999960677464 Q ss_pred C Q ss_conf 9 Q gi|254780330|r 83 L 83 (83) Q Consensus 83 ~ 83 (83) . T Consensus 80 ~ 80 (103) T 3bbn_R 80 N 80 (103) T ss_dssp C T ss_pred C T ss_conf 6 No 4 >3ofo_R 30S ribosomal protein S18; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_R* 3iy8_R 2wwl_R 3ofp_R Probab=99.89 E-value=5.4e-24 Score=154.34 Aligned_cols=53 Identities=57% Similarity=0.940 Sum_probs=51.6 Q ss_pred CCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 11446889999962899848550331748999999999999999704658676 Q gi|254780330|r 30 RIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN 82 (83) Q Consensus 30 ~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~ 82 (83) .|||||+++|++||||+|+|+|||+||+|+++||+|++|||+||+||||||++ T Consensus 1 didyKn~~~L~~Fis~~GkIlprr~Tg~~~k~Qr~l~~aIkrAR~~gLlP~~~ 53 (55) T 3ofo_R 1 EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTD 53 (55) T ss_dssp CCCTTCHHHHGGGBCTTCCBCCHHHHCCCHHHHHHHHHHHHHHHTTTSSCSST T ss_pred CCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 96833789999876998868287527878999999999999999840678455 No 5 >2waq_C DNA-directed RNA polymerase RPO1C subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_C 3hkz_C 2pmz_C Probab=28.03 E-value=12 Score=18.21 Aligned_cols=32 Identities=16% Similarity=0.276 Sum_probs=28.2 Q ss_pred CCCCCCCHHHHHHHCCCCCEECCCHHHCCCHH Q ss_conf 51144688999996289984855033174899 Q gi|254780330|r 29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVSHK 60 (83) Q Consensus 29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k 60 (83) ..||+++..++...++..|++.+--+||++.. T Consensus 306 v~In~rHi~liad~Mt~~G~~~~~~r~g~~~~ 337 (395) T 2waq_C 306 LDVDMRHILLVADVMTRTGVVRQIGRHGVTGE 337 (395) T ss_dssp SCCCHHHHHHHHHHHHSSSSCCCTTTTSSTTS T ss_pred CCCCHHHHHHHHHHHCCCCEEECCCCCCCCCC T ss_conf 50351575345433112352651576366579 No 6 >2aam_A Hypothetical protein TM1410; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; HET: MSE UNL; 2.20A {Thermotoga maritima} SCOP: c.1.8.15 Probab=17.01 E-value=41 Score=15.33 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=16.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 9999999999999704658676 Q gi|254780330|r 61 KQRELAKAIKRARYLGLIAYVN 82 (83) Q Consensus 61 ~Qr~i~~aIKrAR~~gLlPy~~ 82 (83) .-.++....+++|..|++|||+ T Consensus 258 ~~~~~~~~~~~~~~~GF~pYVa 279 (309) T 2aam_A 258 NISRILDYYEKAKRNGCIPYAA 279 (309) T ss_dssp HHHHHHHHHHHHHHTTEEEEEE T ss_pred HHHHHHHHHHHHHHCCCEEEEC T ss_conf 4999999999999779988844 No 7 >2rpa_A Katanin P60 ATPase-containing subunit A1; AAA ATPase, ATP-binding, cell cycle, cell division, cytoplas hydrolase, microtubule; NMR {Mus musculus} Probab=14.64 E-value=43 Score=15.17 Aligned_cols=16 Identities=25% Similarity=0.378 Sum_probs=12.0 Q ss_pred HHHHHHHHHHHCCCCC Q ss_conf 9999999999704658 Q gi|254780330|r 64 ELAKAIKRARYLGLIA 79 (83) Q Consensus 64 ~i~~aIKrAR~~gLlP 79 (83) .|...+|.||.+||+. T Consensus 11 ~i~e~vklARe~Al~G 26 (78) T 2rpa_A 11 MIVENVKLAREYALLG 26 (78) T ss_dssp HHHHHHHHHHHHHHHT T ss_pred HHHHHHHHHHHHHHHC T ss_conf 9999999999999975 No 8 >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Probab=13.14 E-value=61 Score=14.33 Aligned_cols=29 Identities=17% Similarity=0.501 Sum_probs=22.2 Q ss_pred CCCCCCHHHHHHHCCCCCEECCCHHHCCC Q ss_conf 11446889999962899848550331748 Q gi|254780330|r 30 RIDYKDIRLLNRFLSQRGKIVPSRISSVS 58 (83) Q Consensus 30 ~iDYKn~~lL~~Fis~~GkI~prr~TG~~ 58 (83) .||||+.++|-.+++..|.+++=-..|+. T Consensus 1368 ~Vn~RHL~LIaD~MT~~G~l~~ItR~Gi~ 1396 (1752) T 3h0g_A 1368 YVNYRHLALLCDVMTSRGHLMAITRHGIN 1396 (1752) T ss_dssp CCCHHHHHHHHHHHTSSSSCCCCCTTSCS T ss_pred EECHHHHHHHHHHHCCCCEEEEECHHHCC T ss_conf 75399999999998359747544677667 No 9 >2elu_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2elw_A Probab=12.12 E-value=47 Score=14.96 Aligned_cols=24 Identities=21% Similarity=0.575 Sum_probs=15.7 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHCCCC Q ss_conf 88854350388511446889999962899 Q gi|254780330|r 18 RKSCPLSGKGAPRIDYKDIRLLNRFLSQR 46 (83) Q Consensus 18 ~k~c~~~~~~~~~iDYKn~~lL~~Fis~~ 46 (83) +.-|+||.. .|-|+.-|-+.|.|. T Consensus 9 kqhcrfckk-----kysdvknlikhire~ 32 (37) T 2elu_A 9 KQHCRFCKK-----KYSDVKNLIKHIRDA 32 (37) T ss_dssp CCEETTTTE-----ECSSHHHHHHHHHHT T ss_pred HHHHHHHHH-----HHHHHHHHHHHHHHH T ss_conf 999999998-----878899999999872 No 10 >1su3_A Interstitial collagenase; prodomain, hemopexin domain, exocite, structural proteomics in europe, spine, structural genomics, hydrolase; HET: EPE; 2.20A {Homo sapiens} SCOP: a.20.1.2 b.66.1.1 d.92.1.11 PDB: 2clt_A 1fbl_A* Probab=11.95 E-value=45 Score=15.08 Aligned_cols=49 Identities=8% Similarity=0.143 Sum_probs=32.5 Q ss_pred CCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 4688999996289984855033174899999999999999970465867 Q gi|254780330|r 33 YKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYV 81 (83) Q Consensus 33 YKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~ 81 (83) =.|+++.++|+...|-+.+.............++.||+.=+.++=||-| T Consensus 9 ~~d~~~~~~yL~~~gy~~~~~~~~~~~~~~~~~~~ai~~~Q~~~~l~~T 57 (450) T 1su3_A 9 EQDVDLVQKYLEKYYNLKNDGRQVEKRRNSGPVVEKLKQMQEFFGLKVT 57 (450) T ss_dssp ----CHHHHHHHHHSCCC------------CHHHHHHHHHHHHTTCCCC T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCC T ss_conf 2419999999997189998864323445678999999999997599977 Done!