Query gi|254780381|ref|YP_003064794.1| flagellar basal body rod protein FlgB [Candidatus Liberibacter asiaticus str. psy62] Match_columns 130 No_of_seqs 119 out of 1340 Neff 7.9 Searched_HMMs 23785 Date Mon May 30 09:48:28 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780381.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3a69_A Flagellar HOOK protein 99.1 2.8E-11 1.2E-15 78.1 3.5 38 92-129 363-400 (402) 2 3a69_A Flagellar HOOK protein 98.2 1.8E-06 7.7E-11 52.4 5.1 54 7-61 2-55 (402) 3 1ucu_A Phase 1 flagellin; flag 90.4 0.44 1.8E-05 23.8 5.2 37 93-129 455-491 (494) 4 1ory_B Flagellin; flagellar ch 71.6 1.2 5E-05 21.5 1.3 36 93-128 16-51 (55) 5 2q6f_A Fragment, infectious br 35.6 7.4 0.00031 17.2 0.4 17 27-43 92-108 (309) 6 2zu2_A 3C-like proteinase; pro 35.1 7.7 0.00032 17.2 0.4 17 27-43 91-107 (302) 7 2h2z_A PP1AB, ORF1AB, replicas 32.6 7.8 0.00033 17.1 0.0 17 27-43 92-108 (306) 8 1lvo_A Replicase, hydrolase do 31.3 11 0.00045 16.4 0.6 17 27-43 91-107 (302) 9 3d23_B 3C-like proteinase; mai 30.8 10 0.00042 16.6 0.4 17 27-43 94-110 (302) 10 1u0l_A Probable GTPase ENGC; p 11.3 62 0.0026 12.3 0.9 17 31-47 226-242 (301) No 1 >3a69_A Flagellar HOOK protein FLGE; the bacterial flagellar motor, universal joint, bacterial flagellum, motor protein; 7.10A {Salmonella enterica subsp} Probab=99.11 E-value=2.8e-11 Score=78.09 Aligned_cols=38 Identities=21% Similarity=0.288 Sum_probs=36.0 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 52008999999999999999999999999999999636 Q gi|254780381|r 92 NTVGITNELYKSGHIKYLYELNTKLIKKLNSMVMHVVR 129 (130) Q Consensus 92 n~Vdl~~Em~~~~~~~~~Y~a~~~~~~~~~~~~~~al~ 129 (130) .+|||++||++|+.-|+.|+|+.++|....+||.++|. T Consensus 363 S~V~ldeEmtnli~~Q~aY~A~akvitt~demld~lin 400 (402) T 3a69_A 363 SNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVN 400 (402) T ss_dssp ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 14799999999999999999975266499999999970 No 2 >3a69_A Flagellar HOOK protein FLGE; the bacterial flagellar motor, universal joint, bacterial flagellum, motor protein; 7.10A {Salmonella enterica subsp} Probab=98.17 E-value=1.8e-06 Score=52.45 Aligned_cols=54 Identities=19% Similarity=0.236 Sum_probs=42.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC Q ss_conf 9999999999999999999631001377765332210567665443211346651 Q gi|254780381|r 7 FQIASQHANWLSERQKIVSENIANASTPNYRAKDISSFETILNQNFLMARTHETH 61 (130) Q Consensus 7 f~~~~~~l~~~~~R~~via~NIANadTPgYk~~dv~~F~~~l~~~~~~~~~~~~~ 61 (130) |.++-++|.+++..++|+++||||++||||||+++ .|++.+....-+.++.... T Consensus 2 ~~~a~sGl~A~q~al~vts~NIANaNT~GYsRq~v-~f~~~~~~~~~G~GV~v~~ 55 (402) T 3a69_A 2 FSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTA-SFADMFAGSKVGLGVKVAG 55 (402) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHC-------------------------------- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCC-CHHHHHCCCCCCCCEEEEE T ss_conf 78999999999973578888898777642065702-0777646687767447767 No 3 >1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy, helical reconstruction, structural protein; 4.00A {Salmonella typhimurium} SCOP: e.32.1.1 PDB: 3a5x_A Probab=90.42 E-value=0.44 Score=23.80 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=33.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 2008999999999999999999999999999999636 Q gi|254780381|r 93 TVGITNELYKSGHIKYLYELNTKLIKKLNSMVMHVVR 129 (130) Q Consensus 93 ~Vdl~~Em~~~~~~~~~Y~a~~~~~~~~~~~~~~al~ 129 (130) ..|+.+|++++.+.|+.+|+.++++....+.-+.+|+ T Consensus 455 DaD~a~e~~~l~~~qi~~Qaa~~~laqAn~~~q~vl~ 491 (494) T 1ucu_A 455 DSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLS 491 (494) T ss_dssp CCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred HCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 1409999999999999999999999997526789998 No 4 >1ory_B Flagellin; flagellar chaperone, cytosolic export chaperone, FLIS, FLIC; 2.45A {Aquifex aeolicus} Probab=71.56 E-value=1.2 Score=21.49 Aligned_cols=36 Identities=11% Similarity=0.185 Sum_probs=29.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 200899999999999999999999999999999963 Q gi|254780381|r 93 TVGITNELYKSGHIKYLYELNTKLIKKLNSMVMHVV 128 (130) Q Consensus 93 ~Vdl~~Em~~~~~~~~~Y~a~~~~~~~~~~~~~~al 128 (130) .+|+..||+++.+.++..++...++......-+.+| T Consensus 16 DaD~A~E~~~lak~qIL~qa~~amLaQAN~~~q~vL 51 (55) T 1ory_B 16 NVDFAKEMTEFTKYQIRMQSGVAMLAQANALPQLVL 51 (55) T ss_dssp CHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH T ss_conf 155999999999999999999999999842678999 No 5 >2q6f_A Fragment, infectious bronchitis virus (IBV) main protease; coronavirus, 3C-like proteinase, michael acceptor inhibitor, hydrolase; HET: 3IH; 2.00A {Infectious bronchitis virus} PDB: 2q6d_A* Probab=35.63 E-value=7.4 Score=17.24 Aligned_cols=17 Identities=35% Similarity=0.583 Sum_probs=14.0 Q ss_pred HHHCCCCCCCCCCCCCC Q ss_conf 31001377765332210 Q gi|254780381|r 27 NIANASTPNYRAKDISS 43 (130) Q Consensus 27 NIANadTPgYk~~dv~~ 43 (130) +.+|.+||.|+-+.+.+ T Consensus 92 ~~~N~~TP~y~F~~~kp 108 (309) T 2q6f_A 92 AVANAETPKYKFVKANC 108 (309) T ss_dssp SSCCTTCCSEEECCCCT T ss_pred ECCCCCCCCEEEEECCC T ss_conf 32689998637896378 No 6 >2zu2_A 3C-like proteinase; protease-inhibitor complex, cytoplasm, hydrolase, membrane, metal-binding, protease, ribosomal frameshifting; 1.80A {Human coronavirus 229E} PDB: 1p9s_A Probab=35.09 E-value=7.7 Score=17.16 Aligned_cols=17 Identities=24% Similarity=0.315 Sum_probs=13.8 Q ss_pred HHHCCCCCCCCCCCCCC Q ss_conf 31001377765332210 Q gi|254780381|r 27 NIANASTPNYRAKDISS 43 (130) Q Consensus 27 NIANadTPgYk~~dv~~ 43 (130) +.+|++||.|+-+.+.+ T Consensus 91 ~~~N~~TPky~F~~~kp 107 (302) T 2zu2_A 91 SQTNMHTPRHSFRTLKS 107 (302) T ss_dssp SSCCTTCCSEEECCCCT T ss_pred ECCCCCCCCEEEEECCC T ss_conf 32588998637896478 No 7 >2h2z_A PP1AB, ORF1AB, replicase polyprotein 1AB; main protease, authentic N and C termini, viral protein; 1.60A {Sars coronavirus} PDB: 1uk2_A 1uk3_A 1uk4_A 1z1i_A 2a5a_A 1uj1_A* 2bx3_A 2bx4_A 2c3s_A 2a5i_A 2gt7_A* 2gx4_A* 2gz7_A* 2gz8_A* 2gz9_A 2duc_A 2hob_A* 2v6n_A* 2z3c_A* 2z3d_A* ... Probab=32.57 E-value=7.8 Score=17.13 Aligned_cols=17 Identities=29% Similarity=0.561 Sum_probs=13.7 Q ss_pred HHHCCCCCCCCCCCCCC Q ss_conf 31001377765332210 Q gi|254780381|r 27 NIANASTPNYRAKDISS 43 (130) Q Consensus 27 NIANadTPgYk~~dv~~ 43 (130) +.+|++||.|+-+.+.+ T Consensus 92 ~~~N~~TPky~F~~~kp 108 (306) T 2h2z_A 92 DTSNPKTPKYKFVRIQP 108 (306) T ss_dssp SSCCTTCCEEEECCCCT T ss_pred ECCCCCCCCEEEEECCC T ss_conf 32689998637896378 No 8 >1lvo_A Replicase, hydrolase domain; 3C like, corona, proteinase, chymotrypsin, cysteine histidine DYAD, beta barrel; 1.96A {Transmissible gastroenteritis virus} SCOP: b.47.1.4 PDB: 1p9u_A 2amp_A* Probab=31.32 E-value=11 Score=16.42 Aligned_cols=17 Identities=35% Similarity=0.493 Sum_probs=13.8 Q ss_pred HHHCCCCCCCCCCCCCC Q ss_conf 31001377765332210 Q gi|254780381|r 27 NIANASTPNYRAKDISS 43 (130) Q Consensus 27 NIANadTPgYk~~dv~~ 43 (130) +.+|.+||.|+-+.+.+ T Consensus 91 ~~~N~~TP~y~F~~~kp 107 (302) T 1lvo_A 91 NQVNPNTPEHKFKSIKA 107 (302) T ss_dssp SSCCTTCCCCEECCCCT T ss_pred ECCCCCCCCEEEEECCC T ss_conf 33689999647996378 No 9 >3d23_B 3C-like proteinase; main protease, ATP-binding, cytoplasm, endonuclease, exonuclease, helicase, hydrolase, membrane, metal-binding; HET: 3IH; 2.50A {Human coronavirus HKU1} Probab=30.78 E-value=10 Score=16.56 Aligned_cols=17 Identities=24% Similarity=0.522 Sum_probs=13.7 Q ss_pred HHHCCCCCCCCCCCCCC Q ss_conf 31001377765332210 Q gi|254780381|r 27 NIANASTPNYRAKDISS 43 (130) Q Consensus 27 NIANadTPgYk~~dv~~ 43 (130) +.+|++||.|+-+.+.+ T Consensus 94 ~~~N~~TPky~F~~~kp 110 (302) T 3d23_B 94 SLQNPYTPKYTFGNVKP 110 (302) T ss_dssp SSCCTTCCSEEECCCCT T ss_pred ECCCCCCCCEEEEECCC T ss_conf 32689998637896378 No 10 >1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8 Probab=11.30 E-value=62 Score=12.34 Aligned_cols=17 Identities=24% Similarity=0.458 Sum_probs=0.0 Q ss_pred CCCCCCCCCCCCCHHHH Q ss_conf 13777653322105676 Q gi|254780381|r 31 ASTPNYRAKDISSFETI 47 (130) Q Consensus 31 adTPgYk~~dv~~F~~~ 47 (130) +||||++.-++..++.. T Consensus 226 iDTPG~r~~~l~~~~~~ 242 (301) T 1u0l_A 226 VDTPGFANLEINDIEPE 242 (301) T ss_dssp ESSCSSTTCCCCSSCHH T ss_pred EECCCCCCCCCCCCCHH T ss_conf 96898665677779989 Done!