Query gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 116 No_of_seqs 112 out of 1084 Neff 5.9 Searched_HMMs 23785 Date Tue May 31 17:26:49 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780712.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3bn0_A 30S ribosomal protein S 100.0 1E-40 4.2E-45 268.3 -0.5 108 1-112 1-109 (112) 2 3mr8_P 30S ribosomal protein S 100.0 1.2E-36 5.1E-41 243.5 7.9 82 2-85 1-82 (83) 3 3ofo_P 30S ribosomal protein S 100.0 1.7E-35 7.1E-40 236.5 5.3 79 2-81 1-79 (82) 4 3bbn_P Ribosomal protein S16; 100.0 3.2E-36 1.3E-40 240.9 -5.5 85 2-91 1-85 (88) 5 1vbv_A Hypothetical protein B0 46.5 9.3 0.00039 18.8 2.3 17 9-26 44-60 (105) 6 1dw0_A Cytochrome C; asparagin 28.1 26 0.0011 16.1 2.1 31 29-66 58-88 (112) 7 3f62_A Interleukin 18 binding 20.7 30 0.0013 15.7 1.3 20 20-39 37-56 (109) 8 1e8e_A Cytochrome C''; oxidore 16.5 37 0.0015 15.2 0.9 32 28-66 64-95 (124) 9 1wkv_A Cysteine synthase; homo 14.7 20 0.00085 16.8 -0.8 28 7-43 50-77 (389) 10 2dlx_A UBX domain-containing p 13.0 73 0.0031 13.4 2.6 29 9-42 96-124 (153) No 1 >3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} SCOP: d.27.1.1 Probab=100.00 E-value=1e-40 Score=268.28 Aligned_cols=108 Identities=33% Similarity=0.557 Sum_probs=88.0 Q ss_pred CCCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHC Q ss_conf 93014123066878882799992067877684102221215678788864479739999999841983568999999972 Q gi|254780712|r 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKA 80 (116) Q Consensus 1 M~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~ 80 (116) |+|+|||+|+||||+|||||||+|||+||||+|||+||||||+ ++++|.||.|||+|||++||||||+|.+||+.+ T Consensus 1 MavkIRL~r~G~k~~p~yriVv~d~r~~rdgk~iE~lG~YnP~----~~~~i~l~~eri~~Wl~~GAqps~~V~~lL~~~ 76 (112) T 3bn0_A 1 MAVRIRLAKFGRKHHPIYRIVVMDAKSPREGKYIDILGTYDPK----RKVLINVYPEKVKEWVLKGVELSHRAKAILWNH 76 (112) T ss_dssp -CEEEEEEEEEETTEEEEEEEEEECC------CSEEEEEEETT----TTEEEEECHHHHHHHHHTTCEEEHHHHHHHHHT T ss_pred CCEEEEHHCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEECCC----CCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHC T ss_conf 9788703108888898578998436878899650232377587----642124689999999987897479999999985 Q ss_pred CCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 986668-00051122542889889999874303 Q gi|254780712|r 81 GLIKRS-PQNNPKKSQPKKKALERLASKKNADE 112 (116) Q Consensus 81 Gl~~~~-~~~~~~~~~~~kk~~e~~~~kk~~~e 112 (116) |+++.. +.....+.....+..++.++++.+.+ T Consensus 77 Gll~~~~~~~~~~k~~~~~~~~ek~~~~~~~~~ 109 (112) T 3bn0_A 77 GILKEVVPEGYEMKRVGDYYVFEKRESKKSKGG 109 (112) T ss_dssp THHHHHCCTTEEEEEETTEEEEEECC------- T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 986444544333243442100467999875341 No 2 >3mr8_P 30S ribosomal protein S16; ribosome, termination, RF1, amber, STOP UAG; 3.62A {Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P 3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* 1i95_P* 1i96_P* 1i97_P* 1ibk_P* ... Probab=100.00 E-value=1.2e-36 Score=243.45 Aligned_cols=82 Identities=46% Similarity=0.774 Sum_probs=78.4 Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC Q ss_conf 30141230668788827999920678776841022212156787888644797399999998419835689999999729 Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG 81 (116) Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G 81 (116) ||+|||+|+||||+|||||||+|+|++|||+|||+||||||+. .+++.+.||.||++|||++|||||++|.+||+++| T Consensus 1 MvkIRL~R~G~k~~P~YrIVv~d~r~~rdgk~iE~lG~YnP~~--~~~~~i~i~~eRi~~WL~~GAqpS~~V~~Ll~~~g 78 (83) T 3mr8_P 1 MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRK--TTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAG 78 (83) T ss_dssp CEEEEECCCSSTTCCCCCEEEEETTSCTTSCCSEECEEECTTC--CSTTSEEECHHHHHHHHHTCCCCCHHHHHHHHHHT T ss_pred CEEEECCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCC--CCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC T ss_conf 9288212489989986899997668788996467888889998--88501564699999999878906789999999838 Q ss_pred CCCC Q ss_conf 8666 Q gi|254780712|r 82 LIKR 85 (116) Q Consensus 82 l~~~ 85 (116) +++. T Consensus 79 i~~~ 82 (83) T 3mr8_P 79 VFRQ 82 (83) T ss_dssp SSCC T ss_pred CCCC T ss_conf 8567 No 3 >3ofo_P 30S ribosomal protein S16; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_P 1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ... Probab=100.00 E-value=1.7e-35 Score=236.49 Aligned_cols=79 Identities=38% Similarity=0.743 Sum_probs=74.6 Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC Q ss_conf 30141230668788827999920678776841022212156787888644797399999998419835689999999729 Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG 81 (116) Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G 81 (116) ||+|||+|+||||+|||||||+|+|++|||+|||+||||||+++ .+++.+.||.|||+|||++|||||++|++||+++. T Consensus 1 MVkIRL~R~G~k~rP~YrIVv~d~r~~RdGk~iE~lG~YnP~~~-~~~~~i~l~~eri~~Wl~~GAqps~~V~~llk~~~ 79 (82) T 3ofo_P 1 MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIAS-EKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVN 79 (82) T ss_dssp CEEEEECCCCCTTSCCBCEEEEETTSCTTSCCSEECBCBCSCCC-SSSCCCCBCHHHHHHHHHHTCEECHHHHHHHTTSC T ss_pred CEEECCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCC-CCCCCEEECHHHHHHHHHCCCEECHHHHHHHHHHH T ss_conf 93792336999999858999965788999983378615769268-98654564499999999880970899999999876 No 4 >3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Probab=100.00 E-value=3.2e-36 Score=240.90 Aligned_cols=85 Identities=34% Similarity=0.554 Sum_probs=78.1 Q ss_pred CCHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCCCCCCHHHHHHHHHCC Q ss_conf 30141230668788827999920678776841022212156787888644797399999998419835689999999729 Q gi|254780712|r 2 TLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAG 81 (116) Q Consensus 2 ~vkIRL~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~GAqpS~~V~~LL~~~G 81 (116) ||+|||+|+||||+|||||||+|||++|||+|||+||||||+++ .+.||.||++|||++||||||+|++||+++| T Consensus 1 MvkIRL~R~G~k~~P~YrIVvadsr~~RdGk~iE~lG~ynP~~~-----~~~l~~eri~~Wl~~GAqpS~~V~~LL~~~g 75 (88) T 3bbn_P 1 MVKLRLKRCGRKQRAVYRIVAIDVRSRREGRDLQKVGFYDPIKS-----QTYLNVPAILDFLEKGAQPTETVYDILKRAE 75 (88) T ss_dssp CEEECCCCCSCTTCCCCCCCCEETTSCSSSCCSSCCCCBCTTSS-----CBCCCTTTSSSSTTSSCEECTTTSSSSTTTT T ss_pred CEEEECCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCC-----CCCCCHHHHHHHHHCCCCCCHHHHHHHHHCC T ss_conf 92883134899899858999855688899970667500669998-----5414789999999969955899999999808 Q ss_pred CCCCCCCCCC Q ss_conf 8666800051 Q gi|254780712|r 82 LIKRSPQNNP 91 (116) Q Consensus 82 l~~~~~~~~~ 91 (116) +++....+.. T Consensus 76 ~~~~~~~n~~ 85 (88) T 3bbn_P 76 VFKEFRLNQT 85 (88) T ss_dssp SSSCC----- T ss_pred CHHHHHCCCC T ss_conf 3366624665 No 5 >1vbv_A Hypothetical protein B0966; protein degradation, structural genomics, unknown function; 2.70A {Escherichia coli} SCOP: b.34.17.1 Probab=46.52 E-value=9.3 Score=18.82 Aligned_cols=17 Identities=12% Similarity=0.245 Sum_probs=12.5 Q ss_pred HCCCCCCCEEEEEEEECC Q ss_conf 066878882799992067 Q gi|254780712|r 9 CGGSKSRHHYRIVVANSR 26 (116) Q Consensus 9 r~G~k~rp~yrIVvadsr 26 (116) +.+ |+.|||+|.|.|+. T Consensus 44 ~~~-k~QPfYhvLv~~~~ 60 (105) T 1vbv_A 44 DEL-RAAPWYHVVMEDDN 60 (105) T ss_dssp -----CCCEEEEEEECSS T ss_pred CCC-CCCCCEEEEEECCC T ss_conf 766-68986489996489 No 6 >1dw0_A Cytochrome C; asparagine ligation, oxygen binding, disulfide bridge, oxygen storage/transport complex; HET: HEM; 1.82A {Rhodobacter sphaeroides} SCOP: a.3.1.1 PDB: 1dw1_A* 1dw2_A* 1dw3_A* Probab=28.12 E-value=26 Score=16.11 Aligned_cols=31 Identities=39% Similarity=0.814 Sum_probs=24.8 Q ss_pred CCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCC Q ss_conf 76841022212156787888644797399999998419 Q gi|254780712|r 29 RDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKG 66 (116) Q Consensus 29 Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~G 66 (116) +.||.|| ||.|.-||+++. |..+|..|+... T Consensus 58 ~TgK~I~------PlAps~Np~Rft-D~akvEKWF~RN 88 (112) T 1dw0_A 58 RTGKEIA------PLAPSATPDRFT-DSARVEKWLGRN 88 (112) T ss_dssp TTSCEEC------CSSTTTSTTTTC-CHHHHHHHHHHH T ss_pred CCCCCCC------CCCCCCCHHHCC-CHHHHHHHHHCC T ss_conf 7888856------778766856407-889999999720 No 7 >3f62_A Interleukin 18 binding protein; immunoglobulin, IL-18, beta trefoil, cytokine, secreted; 2.00A {Ectromelia virus} Probab=20.73 E-value=30 Score=15.73 Aligned_cols=20 Identities=40% Similarity=0.629 Sum_probs=17.2 Q ss_pred EEEEECCCCCCCCCEEEEEE Q ss_conf 99920678776841022212 Q gi|254780712|r 20 IVVANSRSPRDGKFIEKLGT 39 (116) Q Consensus 20 IVvadsr~~Rdgk~iE~lG~ 39 (116) -.+-|-++--|-+|||.||- T Consensus 37 wlakdmksdedtkfiehlgd 56 (109) T 3f62_A 37 WLAKDMKSDEDTKFIEHLGD 56 (109) T ss_dssp EEEEETTSCCCCEEGGGSCT T ss_pred HHHHHHCCCCHHHHHHHHCC T ss_conf 66644145421458998646 No 8 >1e8e_A Cytochrome C''; oxidoreductase(cytochrome), ligand detachment, redox-BOHR effect, paramagnetic; HET: HEC; NMR {Methylophilus methylotrophus} SCOP: a.3.1.1 PDB: 1gu2_A* 1oae_A* Probab=16.46 E-value=37 Score=15.20 Aligned_cols=32 Identities=31% Similarity=0.508 Sum_probs=24.2 Q ss_pred CCCCCCEEEEEEECCCCCCCCCCEEEECHHHHHHHHHCC Q ss_conf 776841022212156787888644797399999998419 Q gi|254780712|r 28 PRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKG 66 (116) Q Consensus 28 ~Rdgk~iE~lG~YnP~~~k~~~~~i~l~~eRi~yWL~~G 66 (116) .+.||.|| ||.|.-||+++. |...|..|+... T Consensus 64 ~~TgK~I~------PmAps~np~Rft-D~~kvEKwf~Rn 95 (124) T 1e8e_A 64 IVTGKEIP------PLAPRVNTKRFT-DIDKVEDEFTKH 95 (124) T ss_dssp TTTCCCBC------CCCTTTSTTSSC-CSTTHHHHHHHH T ss_pred CCCCCCCC------CCCCCCCHHHCC-CHHHHHHHHHCC T ss_conf 66788656------768766856407-889999999720 No 9 >1wkv_A Cysteine synthase; homodimer, open alpha/beta folding, transferase; HET: PLP; 2.00A {Aeropyrum pernix K1} SCOP: c.79.1.1 Probab=14.74 E-value=20 Score=16.79 Aligned_cols=28 Identities=32% Similarity=0.455 Sum_probs=14.0 Q ss_pred HHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECCC Q ss_conf 2306687888279999206787768410222121567 Q gi|254780712|r 7 LACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPT 43 (116) Q Consensus 7 L~r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP~ 43 (116) |.-.|++ ||-+-+.++. -||+|||||-. T Consensus 50 ~~~~~~~-----~~~~~~~~~~----~~~~~~~~~~~ 77 (389) T 1wkv_A 50 LYVIGAS-----RIPVGDGCSH----TLEELGVFDIS 77 (389) T ss_dssp HHHHTCS-----EEEBSSSCEE----ETTTTTTTCCC T ss_pred HHHHCCC-----CCCCCCCCCC----CHHHCCCCCCC T ss_conf 9984455-----4556766420----16761731048 No 10 >2dlx_A UBX domain-containing protein 7; UAS domain, protein KIAA0794, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: c.47.1.24 Probab=13.01 E-value=73 Score=13.37 Aligned_cols=29 Identities=14% Similarity=0.079 Sum_probs=19.2 Q ss_pred HCCCCCCCEEEEEEEECCCCCCCCCEEEEEEECC Q ss_conf 0668788827999920678776841022212156 Q gi|254780712|r 9 CGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNP 42 (116) Q Consensus 9 r~G~k~rp~yrIVvadsr~~Rdgk~iE~lG~YnP 42 (116) +.+...-|++-|+ .|++|..|..+|.++| T Consensus 96 ~y~v~~~P~i~~i-----dP~tGe~i~~~~~~~~ 124 (153) T 2dlx_A 96 FYKLGDFPYVSIL-----DPRTGQKLVEWHQLDV 124 (153) T ss_dssp HHTCCSSSEEEEE-----CTTTCCCCEEESSCCH T ss_pred HCCCCCCCEEEEE-----ECCCCCEEEEECCCCH T ss_conf 3676899879999-----4899948777567899 Done!