Query gi|254780786|ref|YP_003065199.1| ribosome-binding factor A [Candidatus Liberibacter asiaticus str. psy62] Match_columns 128 No_of_seqs 102 out of 1288 Neff 6.6 Searched_HMMs 13730 Date Wed Jun 1 06:13:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780786.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 d1kkga_ d.52.7.1 (A:) Ribosome 100.0 4.8E-30 3.5E-34 187.4 7.1 105 5-112 1-108 (108) 2 d2e7ga1 d.52.7.1 (A:86-201) Ri 100.0 3.3E-30 2.4E-34 188.3 1.3 113 6-120 2-115 (116) 3 d1josa_ d.52.7.1 (A:) Ribosome 99.9 1.8E-27 1.3E-31 172.9 11.5 96 11-110 1-99 (100) 4 d1pa4a_ d.52.7.1 (A:) Ribosome 99.9 1.1E-27 8.3E-32 174.0 1.5 95 12-110 1-95 (96) 5 d2dyja1 d.52.7.1 (A:4-94) Ribo 99.9 1.4E-23 9.9E-28 151.0 11.6 89 12-107 2-90 (91) 6 d2uubb1 c.23.15.1 (B:7-240) Ri 19.5 26 0.0019 13.9 2.3 33 77-110 134-166 (234) 7 d1aoya_ a.4.5.3 (A:) Arginine 17.4 6.6 0.00048 17.3 -1.5 46 1-56 1-53 (78) 8 d2dita1 d.58.7.1 (A:8-106) HIV 13.9 30 0.0022 13.5 1.1 34 43-76 45-78 (99) 9 d1fxla2 d.58.7.1 (A:119-203) H 11.6 43 0.0031 12.7 2.7 33 44-76 33-69 (85) 10 d1b4aa1 a.4.5.3 (A:4-78) Argin 10.8 45 0.0033 12.5 1.4 58 10-77 2-75 (75) No 1 >d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]} Probab=99.96 E-value=4.8e-30 Score=187.42 Aligned_cols=105 Identities=33% Similarity=0.473 Sum_probs=94.4 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH Q ss_conf 8777738999999999999999951413420126516898888985875655999982798647---7899999985689 Q gi|254780786|r 5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF 81 (128) Q Consensus 5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~ 81 (128) |++++.|+.||+++|+++||++|.+ ++.||++++ +||||+|++|+||++|+||||++++.++ ++++++||+++|+ T Consensus 1 M~~~~~R~~rv~~~i~r~is~il~~-~~~dp~l~~-~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~~~L~~~~~~ 78 (108) T d1kkga_ 1 MAKEFGRPQRVAQEMQKEIALILQR-EIKDPRLGM-MTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGF 78 (108) T ss_dssp CCCCSSSHHHHHHHHHHHHHHHTTS-SSSSGGGTS-CCBCSCEEEETTTTEEEEEEBCSGGGCHHHHHHHHHHHHHTHHH T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCCC-EEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHH T ss_conf 9986727899999999999999997-563865577-06994899768813189999954772067799999999997899 Q ss_pred HHHHHHHHHHHCCCCCEEEEEECCCHHHHHH Q ss_conf 9999999875214578589997386888999 Q gi|254780786|r 82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWK 112 (128) Q Consensus 82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~ 112 (128) ||++||++| ++||||+|+|++|+++|++.+ T Consensus 79 ir~~l~~~l-~lr~~P~L~F~~D~s~e~a~R 108 (108) T d1kkga_ 79 IRSLLGKAM-RLRIVPELTFFYDNSLVEGMR 108 (108) T ss_dssp HHHHHHHHT-TCSCCCEEEEEECCTTSSSCC T ss_pred HHHHHHHHC-CCEECCEEEEEECCCHHHHCC T ss_conf 999998447-980898889996595530057 No 2 >d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]} Probab=99.95 E-value=3.3e-30 Score=188.29 Aligned_cols=113 Identities=17% Similarity=0.232 Sum_probs=101.1 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCC-HHHHHHHHHHHHHHHHH Q ss_conf 77773899999999999999995141342012651689888898587565599998279864-77899999985689999 Q gi|254780786|r 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS-PDRVISALNCNIKFIRG 84 (128) Q Consensus 6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~-~~~~~~~L~~~~~~ir~ 84 (128) +++|.|+.|++++|+++|+++|.++.+.++ +.+..||||+|+||+||++|+||||++|+.+ .+.+.++|++++|+||+ T Consensus 2 k~~s~R~~kv~~li~k~is~il~~~~~~~~-l~~~~ItIt~V~vS~Dl~~AkVy~s~~~~~~~~~~~~~~L~~~~~~ir~ 80 (116) T d2e7ga1 2 KEDHARLRALNGLLYKALTDLLCTPEVSQE-LYDLNVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAVLQRSAAHMRH 80 (116) T ss_dssp SHHHHHHHHHHHHHHHHHHHHTTCTTTCHH-HHHHTCCEEEEEECTTSCCEEEEECCCSCHHHHHHHHHHHHHTHHHHHH T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCEEEEEEEEECCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHH T ss_conf 841478999999999999999985475766-5685699999997588767899998479656677779999999999999 Q ss_pred HHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCH Q ss_conf 999987521457858999738688899999985576 Q gi|254780786|r 85 RIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLP 120 (128) Q Consensus 85 ~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~ 120 (128) .|++++ .+||+|+|+|++|++++++.+|++||+.. T Consensus 81 ~l~~~l-~lr~~P~L~F~~D~s~~~~~~i~~ll~~~ 115 (116) T d2e7ga1 81 LLMSQQ-TLRNVPPIVFVQDKGNAALAELDQLLAVA 115 (116) T ss_dssp HHHTCT-TCSCCCCEEEEETTCCCCCCCCCCCSCCC T ss_pred HHHHHH-CCCCCCEEEEEECCCHHHHHHHHHHHHHC T ss_conf 999771-86233607999579888999999998723 No 3 >d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]} Probab=99.95 E-value=1.8e-27 Score=172.89 Aligned_cols=96 Identities=30% Similarity=0.549 Sum_probs=87.5 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCC---HHHHHHHHHHHHHHHHHHHH Q ss_conf 899999999999999995141342012651689888898587565599998279864---77899999985689999999 Q gi|254780786|r 11 RALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS---PDRVISALNCNIKFIRGRIG 87 (128) Q Consensus 11 R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~---~~~~~~~L~~~~~~ir~~l~ 87 (128) |+.||+++|+++||++|.+ ++.||+++ +||||+|++|+|+++|+||||++++.+ .++++++||+++|+||+++| T Consensus 1 R~~rv~~~i~~~is~il~~-~i~d~~l~--~vtIt~V~~S~Dl~~A~Vy~s~~~~~~~~~~~~~~~~L~~~~~~ir~~la 77 (100) T d1josa_ 1 RSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPYIRSLLG 77 (100) T ss_dssp CHHHHHHHHHHHHHHHHHH-HCCCTTTC--CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHHHTHHHHHHHHH T ss_pred CCHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9189999999999999997-56586668--05898999769834279999965761245599999999998999999999 Q ss_pred HHHHHCCCCCEEEEEECCCHHHH Q ss_conf 98752145785899973868889 Q gi|254780786|r 88 RSLRNLRYVPELRFRYDTSLQSY 110 (128) Q Consensus 88 ~~l~~lr~~P~L~F~~D~s~e~~ 110 (128) +++ ++||+|+|+|++|+++|++ T Consensus 78 ~~l-~~r~~P~L~F~~D~s~e~g 99 (100) T d1josa_ 78 KAM-RLRIVPEIRFIYDQSLVEG 99 (100) T ss_dssp HHH-CCSSCCEEEEEECCCCCCC T ss_pred HHC-CCCCCCEEEEEECCCHHCC T ss_conf 766-8816986899956862135 No 4 >d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]} Probab=99.93 E-value=1.1e-27 Score=173.99 Aligned_cols=95 Identities=19% Similarity=0.250 Sum_probs=88.4 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999995141342012651689888898587565599998279864778999999856899999999875 Q gi|254780786|r 12 ALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLR 91 (128) Q Consensus 12 ~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~~l~ 91 (128) ++|++++|+++||++|.+ +++||+++ +||||+|++|+||++|+||||++++.+.++++++||+++|+||++||+++. T Consensus 1 ~eR~~~~i~r~is~~l~~-ei~d~~l~--~vtIt~V~vS~Dl~~AkVy~s~~~~~~~~~~~~~L~~~~g~ir~~l~~~l~ 77 (96) T d1pa4a_ 1 KERLENDIIRLINRTVIH-EIYNETVK--TGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVLAHNLY 77 (96) T ss_dssp CCHHHHHHHHHHHHHHTT-CSSSSCHH--HHCCSCCEEETTTTEEEECCCCSSSSSHHHHHHHHHHTHHHHHHHHHTTCC T ss_pred CHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 957999999999999998-67796668--158979997799767999998278410689999999989999999997668 Q ss_pred HCCCCCEEEEEECCCHHHH Q ss_conf 2145785899973868889 Q gi|254780786|r 92 NLRYVPELRFRYDTSLQSY 110 (128) Q Consensus 92 ~lr~~P~L~F~~D~s~e~~ 110 (128) ||++|+|+|++|+++|++ T Consensus 78 -lr~~P~L~F~~D~s~e~~ 95 (96) T d1pa4a_ 78 -LAKAVQIHFVKDKAIDNA 95 (96) T ss_dssp -CGGGCCCEECSSSTTSSC T ss_pred -CCCCCEEEEEECCCHHCC T ss_conf -703886899967864405 No 5 >d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]} Probab=99.90 E-value=1.4e-23 Score=150.98 Aligned_cols=89 Identities=19% Similarity=0.272 Sum_probs=80.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999995141342012651689888898587565599998279864778999999856899999999875 Q gi|254780786|r 12 ALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLR 91 (128) Q Consensus 12 ~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~~l~ 91 (128) ..|++++|+++||++|. ++.||+++ +||||+|++|+|+++|+||||++++ .++++++||+++|+||+++++.+ T Consensus 2 k~rle~~i~r~is~il~--~~~d~~~~--~vtIt~V~~S~Dl~~akVyvs~~~~--~~~~~~~L~~~~~~ir~~l~~~l- 74 (91) T d2dyja1 2 KAHLEAQLKRALAEEIQ--ALEDPRLF--LLTVEAVRLSKDGSVLSVYVEAFRE--EEGALRALSRAERRLVAALARRV- 74 (91) T ss_dssp HHHHHHHHHHHHHHHHH--TCCCGGGT--TCEEEEEEECTTSSEEEEEEECSSC--HHHHHHHHHHTHHHHHHHHHTTS- T ss_pred HHHHHHHHHHHHHHHHH--HCCCCCCC--CEEEEEEEECCCCCCEEEEEEECCC--HHHHHHHHHHHHHHHHHHHHHHC- T ss_conf 37899999999999999--80686659--4599799988980037999996243--47899999998999999998567- Q ss_pred HCCCCCEEEEEECCCH Q ss_conf 2145785899973868 Q gi|254780786|r 92 NLRYVPELRFRYDTSL 107 (128) Q Consensus 92 ~lr~~P~L~F~~D~s~ 107 (128) ++|++|+|+|++|++. T Consensus 75 ~~r~~P~L~F~~D~s~ 90 (91) T d2dyja1 75 RMRRLPRLEFLPWRAS 90 (91) T ss_dssp CCSSCCEEEEEEGGGC T ss_pred CCCCCCEEEEEECCCC T ss_conf 9816987999968999 No 6 >d2uubb1 c.23.15.1 (B:7-240) Ribosomal protein S2 {Thermus thermophilus [TaxId: 274]} Probab=19.52 E-value=26 Score=13.90 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=22.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHH Q ss_conf 8568999999998752145785899973868889 Q gi|254780786|r 77 CNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSY 110 (128) Q Consensus 77 ~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~ 110 (128) +....+.+.++. ++.|+..|++.|..|...+.. T Consensus 134 ~~~~kl~k~~~G-i~~m~~~Pd~viv~d~~~~~~ 166 (234) T d2uubb1 134 HELERLQKYLSG-FRLLKRLPDAIFVVDPTKEAI 166 (234) T ss_dssp HHHHHHHHHSTT-GGGCSSCCSEEEESCTTTTHH T ss_pred HHHHHHHHHHCC-CHHHHHCCEEEEEECCCCCHH T ss_conf 999999986222-000110331688705774288 No 7 >d1aoya_ a.4.5.3 (A:) Arginine repressor (ArgR), N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]} Probab=17.41 E-value=6.6 Score=17.27 Aligned_cols=46 Identities=9% Similarity=0.056 Sum_probs=25.2 Q ss_pred CCCCCCCCCHHHHHHHHHH-------HHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEE Q ss_conf 9988877773899999999-------9999999951413420126516898888985875655 Q gi|254780786|r 1 MKNKNPKNSRRALRVGEEV-------RSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVA 56 (128) Q Consensus 1 mk~~~~~~s~R~~rv~~~i-------~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~A 56 (128) |++..++. .|..-+..+| |++|.+.|... ++.+||..-+|+||+-- T Consensus 1 M~k~~kq~-~~l~~I~~li~~~~i~tQ~eL~~~L~~~---------G~~~vTQaTiSRDL~eL 53 (78) T d1aoya_ 1 MRSSAKQE-ELVKAFKALLKEEKFSSQGEIVAALQEQ---------GFDNINQSKVSRMLTKF 53 (78) T ss_dssp CCCCCCST-THHHHHHHHHHTCCCCSHHHHHHHHHHH---------TCSSCCHHHHHHHHHHH T ss_pred CCCHHHHH-HHHHHHHHHHHHCCCCCHHHHHHHHHHC---------CCCCHHHHHHHHHHHHH T ss_conf 97157899-9999999999848867899999999983---------98501098899999992 No 8 >d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Probab=13.87 E-value=30 Score=13.53 Aligned_cols=34 Identities=15% Similarity=0.095 Sum_probs=21.4 Q ss_pred EEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHH Q ss_conf 9888898587565599998279864778999999 Q gi|254780786|r 43 SISEVCMSVDLRVATVYISLPLDVSPDRVISALN 76 (128) Q Consensus 43 tIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~ 76 (128) .|+.|.+..+-....+||.+....+...++..|| T Consensus 45 ~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~ln 78 (99) T d2dita1 45 QIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLD 78 (99) T ss_dssp CCSEEEEETTCTTCEEEEECSCHHHHHHHHHHST T ss_pred CEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHC T ss_conf 0799963477886479999898999999999868 No 9 >d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Probab=11.62 E-value=43 Score=12.69 Aligned_cols=33 Identities=21% Similarity=0.282 Sum_probs=14.1 Q ss_pred EEEEEECCCC----CEEEEEEEECCCCCHHHHHHHHH Q ss_conf 8888985875----65599998279864778999999 Q gi|254780786|r 44 ISEVCMSVDL----RVATVYISLPLDVSPDRVISALN 76 (128) Q Consensus 44 It~V~vS~Dl----~~AkVyvs~~~~~~~~~~~~~L~ 76 (128) |.+|++-.|- .....|+.+....+.+.+++.|| T Consensus 33 v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~ln 69 (85) T d1fxla2 33 IITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 69 (85) T ss_dssp EEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT T ss_pred CCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHC T ss_conf 6310301245443578716999858999999999838 No 10 >d1b4aa1 a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]} Probab=10.78 E-value=45 Score=12.53 Aligned_cols=58 Identities=12% Similarity=0.190 Sum_probs=0.0 Q ss_pred HHHHHHHHHH-------HHHHHHHHHHCCCCCCCCCCCEEEEEEEEECC---CCCEEEE------EEEECCCCCHHHHHH Q ss_conf 3899999999-------99999999514134201265168988889858---7565599------998279864778999 Q gi|254780786|r 10 RRALRVGEEV-------RSALMWVILNNEFQDRLISRDVISISEVCMSV---DLRVATV------YISLPLDVSPDRVIS 73 (128) Q Consensus 10 ~R~~rv~~~i-------~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~---Dl~~AkV------yvs~~~~~~~~~~~~ 73 (128) +|+..+.++| |++|.+.|... | ++||..-+|+ +|...|| |+..+++.......+ T Consensus 2 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~--------G--i~vTQaTlSRDL~eLg~vKv~~~~g~~~Y~lp~~~~~~~~~ 71 (75) T d1b4aa1 2 QRHIKIREIIMSNDIETQDELVDRLREA--------G--FNVTQATVSRDIKEMQLVKVPMANGRYKYSLPSDQRFNPLQ 71 (75) T ss_dssp HHHHHHHHHHHHSCCCSHHHHHHHHHHT--------T--CCCCHHHHHHHHHHTTCEEEECSSSCEEEECTTCSSSCHHH T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHC--------C--CCEEHHHHHHHHHHHCCEEEECCCCCEEEECCCCCCCCHHH T ss_conf 2799999999868977899999999985--------9--86308999979999298881479986898628756669887 Q ss_pred HHHH Q ss_conf 9998 Q gi|254780786|r 74 ALNC 77 (128) Q Consensus 74 ~L~~ 77 (128) .|.+ T Consensus 72 ~L~r 75 (75) T d1b4aa1 72 KLKR 75 (75) T ss_dssp HHHH T ss_pred HHCC T ss_conf 7349 Done!