Query gi|254780248|ref|YP_003064661.1| 30S ribosomal protein S14 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 101 No_of_seqs 107 out of 1176 Neff 5.4 Searched_HMMs 23785 Date Tue May 24 05:31:09 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780248.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3ofo_N 30S ribosomal protein S 100.0 4E-42 0 275.8 1.2 100 2-101 1-100 (100) 2 3bbn_N Ribosomal protein S14; 100.0 1.1E-41 0 273.2 -6.0 100 1-101 1-100 (100) 3 2vqe_N 30S ribosomal protein S 99.9 9.4E-24 3.9E-28 164.0 1.8 54 46-101 8-61 (61) 4 2zkq_n 40S ribosomal protein S 91.8 0.036 1.5E-06 32.7 0.8 30 61-90 18-49 (56) 5 3jyv_N 40S ribosomal protein S 91.5 0.042 1.8E-06 32.3 0.9 29 62-90 15-45 (50) 6 1y6u_A XIS, excisionase from t 38.9 12 0.00052 17.3 1.9 23 74-96 23-45 (70) 7 1z4h_A TORI, TOR inhibition pr 20.5 22 0.00092 15.8 0.5 26 70-95 13-38 (66) 8 1l8d_A DNA double-strand break 11.8 48 0.002 13.8 0.4 25 38-71 33-57 (112) 9 2ko6_A Uncharacterized protein 10.8 77 0.0033 12.5 1.5 22 78-99 50-71 (89) 10 2zqe_A MUTS2 protein; alpha/be 10.1 82 0.0035 12.3 1.3 35 42-76 15-49 (83) No 1 >3ofo_N 30S ribosomal protein S14; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_N 1p87_N 2aw7_N 2avy_N 2i2u_N 2i2p_N* 2qan_N* 2qb9_N* 2qbb_N* 2qbd_N 2qbf_N 2qbh_N* 2qbj_N* 2qou_N* 2qow_N* 2qoy_N* 2qp0_N* 2vho_N 2vhp_N 2z4k_N* ... Probab=100.00 E-value=4e-42 Score=275.78 Aligned_cols=100 Identities=44% Similarity=0.714 Sum_probs=99.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHH Q ss_conf 12689999999999999999999999998348798989999999997208604432444022143566411440425629 Q gi|254780248|r 2 AKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSR 81 (101) Q Consensus 2 akks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSR 81 (101) ||+|+|+||.+|++++++|+.+|.+||+++.|+++|++++++|+.+|++||+|||||||+|||++||||||||++||||| T Consensus 1 AK~s~i~R~~kR~~l~~k~~~kR~~Lk~i~~~~~l~~~~r~~a~~kL~~LPrnSs~~RirNRC~~TGR~Rgv~r~f~lsR 80 (100) T 3ofo_N 1 AKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSR 80 (100) T ss_dssp CCHHHHHHHHHHHHHHHHSTTTGGGTTTTTTSSCC----CCTHHHHSCCCCSSCSGGGCCCCCTTTCCCSSEETTTTEEH T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHCCCHHCCCCCCCCCCCCCCHH T ss_conf 90489999999999999999999999999847799999999999999847834200154046023796652213425439 Q ss_pred HHHHHHHHCCCCCCCCCCCC Q ss_conf 99999996589998321469 Q gi|254780248|r 82 LALRELGGVGKIPGIIKSSW 101 (101) Q Consensus 82 i~fRela~~G~ipGv~KaSW 101 (101) |+|||||+.|+||||+|||| T Consensus 81 i~fRela~~G~ipGv~KaSW 100 (100) T 3ofo_N 81 IKVREAAMRGEIPGLKKASW 100 (100) T ss_dssp HHHHHHHTTSCSTTEEECCC T ss_pred HHHHHHHHCCCCCCEECCCC T ss_conf 99999997697888431679 No 2 >3bbn_N Ribosomal protein S14; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=100.00 E-value=1.1e-41 Score=273.24 Aligned_cols=100 Identities=33% Similarity=0.525 Sum_probs=97.3 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHH Q ss_conf 91268999999999999999999999999834879898999999999720860443244402214356641144042562 Q gi|254780248|r 1 MAKVSAVERNKRRLRVVAKQASKRLALKKIVMDKSVTLEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLS 80 (101) Q Consensus 1 Makks~i~rd~kRr~l~~k~~~kR~~lk~~~~~~~l~~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lS 80 (101) |||||+|+||.+|++++++||.+|.+|+++++|. ++++++++|+.+|++||+||||||++|||++||||||||++|||| T Consensus 1 Makks~I~rd~kRr~l~~k~~~~R~~lk~~i~~~-~~~~~r~~~~~kL~~lprnss~~Ri~NRC~~TGR~Rg~~r~f~lS 79 (100) T 3bbn_N 1 MARKSLIQREKKRRNLEQKYHLIRRSSKQEIRKV-TSLSDKWEIHGKLQSPPRNSAPARLHRRCFLTGRPRANIRDFGLS 79 (100) T ss_dssp -CCTTHHHHHHTTTSSTTTTSSSTTTTTTTTSSC-CSSSCCCSHHHHSCCSCSSCCGGGCCCCCSSSCCSSSBCTTTCSB T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCCCCCH T ss_conf 9568999999999999999999999999988056-887799999999874775446589966355689976224554645 Q ss_pred HHHHHHHHHCCCCCCCCCCCC Q ss_conf 999999996589998321469 Q gi|254780248|r 81 RLALRELGGVGKIPGIIKSSW 101 (101) Q Consensus 81 Ri~fRela~~G~ipGv~KaSW 101 (101) ||+|||||+.|+||||+|||| T Consensus 80 Ri~fR~lA~~G~ipGv~KaSW 100 (100) T 3bbn_N 80 GHILREMVHTCLLPGATRSSW 100 (100) T ss_dssp TTHHHHHHTTTCSSSCEECCC T ss_pred HHHHHHHHHCCCCCCEECCCC T ss_conf 999999998698888522779 No 3 >2vqe_N 30S ribosomal protein S14 type Z; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: g.39.1.7 PDB: 1gix_Q* 1hnw_N* 1hnx_N* 1hnz_N* 1hr0_N 1ibk_N* 1ibl_N* 1ibm_N 1jgo_Q* 1jgp_Q* 1jgq_Q* 1ml5_Q* 1xmo_N* 1xmq_N* 1xnq_N* 1xnr_N* 1yl4_Q 2b64_N* 2b9m_N* 2b9o_N* ... Probab=99.87 E-value=9.4e-24 Score=164.05 Aligned_cols=54 Identities=44% Similarity=0.799 Sum_probs=50.1 Q ss_pred HHHHHCCHHHHHHHHCCCCCCCCCCCHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 99720860443244402214356641144042562999999996589998321469 Q gi|254780248|r 46 LQLGSLPRDGSRVRVRNRCEISGRSRGVYRDFRLSRLALRELGGVGKIPGIIKSSW 101 (101) Q Consensus 46 ~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~f~lSRi~fRela~~G~ipGv~KaSW 101 (101) .+++++|++ +||++|||++||||||||++||||||+|||+|+.|+||||+|||| T Consensus 8 ~k~~~~pk~--~tR~~nRC~~tGR~Rg~~r~f~lsRi~fR~la~~G~iPGv~KaSW 61 (61) T 2vqe_N 8 EKAKRTPKF--KVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW 61 (61) T ss_dssp GGCCSCCSS--GGGCCCCCTTTCCCTTCCTTTSSCHHHHHHHHHHTCSSSCEECCC T ss_pred HHHHCCCCC--CCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEECCC T ss_conf 997718998--763302125789976202452617999999997598888360679 No 4 >2zkq_n 40S ribosomal protein S29E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_N Probab=91.81 E-value=0.036 Score=32.73 Aligned_cols=30 Identities=17% Similarity=0.495 Sum_probs=26.4 Q ss_pred CCCCCCCCCCCHHHHHHC--HHHHHHHHHHHC Q ss_conf 022143566411440425--629999999965 Q gi|254780248|r 61 RNRCEISGRSRGVYRDFR--LSRLALRELGGV 90 (101) Q Consensus 61 ~NRC~~TGR~Rgv~r~f~--lSRi~fRela~~ 90 (101) -+.|.++|+..|++++|| |||-+|||.|.. T Consensus 18 sr~Cr~Cg~~~glIrKYgL~~CRqCFre~A~d 49 (56) T 2zkq_n 18 SRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKD 49 (56) T ss_dssp CCCCSSSCCSTTCCTTTCCCSCHHHHHHTTTT T ss_pred CCEEEECCCCCCEEEEECCCHHHHHHHHHHHH T ss_conf 76236779974311001732288899988785 No 5 >3jyv_N 40S ribosomal protein S29(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} Probab=91.54 E-value=0.042 Score=32.31 Aligned_cols=29 Identities=21% Similarity=0.537 Sum_probs=26.2 Q ss_pred CCCCCCCCCCHHHHHHC--HHHHHHHHHHHC Q ss_conf 22143566411440425--629999999965 Q gi|254780248|r 62 NRCEISGRSRGVYRDFR--LSRLALRELGGV 90 (101) Q Consensus 62 NRC~~TGR~Rgv~r~f~--lSRi~fRela~~ 90 (101) +.|.++|+..|++++|| +||-+|||.|.. T Consensus 15 r~CrvCg~~~glIrKYgL~~CRqCFre~A~d 45 (50) T 3jyv_N 15 RQCRVCSSHTGLVRKYDLNICRQCFREKAND 45 (50) T ss_dssp CCCSSSCCCSSCCSSCSCSSSSHHHHHHHHH T ss_pred CEEEECCCCCCEEEECCCCHHHHHHHHHHHH T ss_conf 7027779984553122763067799998986 No 6 >1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis} Probab=38.89 E-value=12 Score=17.32 Aligned_cols=23 Identities=26% Similarity=0.299 Sum_probs=19.2 Q ss_pred HHHHCHHHHHHHHHHHCCCCCCC Q ss_conf 40425629999999965899983 Q gi|254780248|r 74 YRDFRLSRLALRELGGVGKIPGI 96 (101) Q Consensus 74 ~r~f~lSRi~fRela~~G~ipGv 96 (101) -..||+++-.+|+|++.+..|+. T Consensus 23 a~Y~gIg~~klr~L~~e~~~~~f 45 (70) T 1y6u_A 23 SKYFRIGENKLRRLAEENKNANW 45 (70) T ss_dssp HHHTCSCHHHHHHHHHHCTTCSS T ss_pred HHHHCCCHHHHHHHHHHCCCCCC T ss_conf 99969279999999984889997 No 7 >1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli} Probab=20.48 E-value=22 Score=15.80 Aligned_cols=26 Identities=12% Similarity=0.156 Sum_probs=20.9 Q ss_pred CCHHHHHHCHHHHHHHHHHHCCCCCC Q ss_conf 41144042562999999996589998 Q gi|254780248|r 70 SRGVYRDFRLSRLALRELGGVGKIPG 95 (101) Q Consensus 70 ~Rgv~r~f~lSRi~fRela~~G~ipG 95 (101) -.-|....|+||-.+..++..|.+|= T Consensus 13 ~keV~~~~glsrstiy~~i~~G~FP~ 38 (66) T 1z4h_A 13 LKFIMADTGFGKTFIYDRIKSGDLPK 38 (66) T ss_dssp HHHHHHHHSSCHHHHHHHHHHHHCCC T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCC T ss_conf 99999998979999999998799999 No 8 >1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1 Probab=11.76 E-value=48 Score=13.75 Aligned_cols=25 Identities=20% Similarity=0.473 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCC Q ss_conf 8999999999720860443244402214356641 Q gi|254780248|r 38 LEERFDAMLQLGSLPRDGSRVRVRNRCEISGRSR 71 (101) Q Consensus 38 ~~~r~~a~~kL~~Lprnss~tRi~NRC~~TGR~R 71 (101) ..+.-.|...|.+ ..-+|-+||||= T Consensus 33 i~elkKal~ELk~---------a~GkCPvCgreL 57 (112) T 1l8d_A 33 IGDLKTAIEELKK---------AKGKCPVCGREL 57 (112) T ss_dssp HHHHHHHHHHHTT---------CSEECTTTCCEE T ss_pred HHHHHHHHHHHHH---------HCCCCCCCCCCC T ss_conf 9999999999997---------478799889937 No 9 >2ko6_A Uncharacterized protein YIHD; alpha protein, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Probab=10.79 E-value=77 Score=12.46 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=15.9 Q ss_pred CHHHHHHHHHHHCCCCCCCCCC Q ss_conf 5629999999965899983214 Q gi|254780248|r 78 RLSRLALRELGGVGKIPGIIKS 99 (101) Q Consensus 78 ~lSRi~fRela~~G~ipGv~Ka 99 (101) =+-....|.-...-.|||++|- T Consensus 50 lIYhLKMr~s~k~e~IPGlkKD 71 (89) T 2ko6_A 50 LIYHLKMRDSAKDAVIPGLQKD 71 (89) T ss_dssp HHHHHHHHHHTTSSSCSSCCCC T ss_pred EEEEHEECCCCCCCCCCCCCHH T ss_conf 0000000488766758861022 No 10 >2zqe_A MUTS2 protein; alpha/beta, ATP-binding, DNA-binding, nucleotide-binding, DNA binding protein; 1.70A {Thermus thermophilus HB8} Probab=10.05 E-value=82 Score=12.30 Aligned_cols=35 Identities=14% Similarity=0.314 Sum_probs=21.9 Q ss_pred HHHHHHHHHCCHHHHHHHHCCCCCCCCCCCHHHHH Q ss_conf 99999972086044324440221435664114404 Q gi|254780248|r 42 FDAMLQLGSLPRDGSRVRVRNRCEISGRSRGVYRD 76 (101) Q Consensus 42 ~~a~~kL~~Lprnss~tRi~NRC~~TGR~Rgv~r~ 76 (101) .+|...|.+.=-++-...++.-+++||...|+.+. T Consensus 15 ~eA~~~l~~~i~~a~~~~~~~v~IIHGkG~gvLk~ 49 (83) T 2zqe_A 15 AEALLEVDQALEEARALGLSTLRLLHGKGTGALRQ 49 (83) T ss_dssp HHHHHHHHHHHHHHHHTTCSEEEEECCSTTSHHHH T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHH T ss_conf 99999999999999985993899994478823899 Done!