Query gi|254781041|ref|YP_003065454.1| succinate dehydrogenase protein, cytochrome b subunit [Candidatus Liberibacter asiaticus str. psy62] Match_columns 129 No_of_seqs 106 out of 995 Neff 6.8 Searched_HMMs 13730 Date Wed Jun 1 11:11:26 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781041.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 d1nekc_ f.21.2.2 (C:) Succinat 100.0 0 0 268.3 16.0 126 1-126 2-128 (129) 2 d1nekd_ f.21.2.2 (D:) Succinat 98.6 8.1E-07 5.9E-11 54.1 13.0 75 23-99 11-85 (113) 3 d2bs2c1 f.21.2.1 (C:1-254) Fum 97.3 0.0036 2.6E-07 34.2 12.6 77 22-99 122-198 (254) 4 d2bs2c1 f.21.2.1 (C:1-254) Fum 97.1 0.0057 4.2E-07 33.1 12.0 77 16-92 17-102 (254) 5 d1kf6c_ f.21.2.2 (C:) Fumarate 92.7 0.22 1.6E-05 24.4 6.9 105 8-114 9-118 (130) 6 d1kf6d_ f.21.2.2 (D:) Fumarate 92.4 0.27 1.9E-05 24.0 11.7 104 1-120 1-110 (119) 7 d2pu9b1 b.34.4.3 (B:1-73) Ferr 32.9 5.2 0.00038 16.9 0.4 11 6-16 43-53 (73) 8 d1xrda1 f.3.1.1 (A:1-52) Light 8.5 50 0.0036 11.6 3.9 34 30-63 11-44 (52) 9 d1eg3a2 a.39.1.7 (A:210-306) D 4.4 87 0.0063 10.2 1.7 16 19-34 80-95 (97) 10 d1jh6a_ d.61.1.1 (A:) tRNA spl 3.7 1E+02 0.0076 9.8 1.0 14 5-18 111-124 (181) No 1 >d1nekc_ f.21.2.2 (C:) Succinate dehydrogenase subunit SdhC {Escherichia coli [TaxId: 562]} Probab=100.00 E-value=0 Score=268.26 Aligned_cols=126 Identities=18% Similarity=0.333 Sum_probs=121.0 Q ss_pred CCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 96200498999773510266659999999999999999999999999998516303554675306831699999999999 Q gi|254781041|r 1 MSSIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAV 80 (129) Q Consensus 1 m~~m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~ 80 (129) ++|||+|||+||||||||||+||++||+||+||++++++++++.+++.....+||.|+..+..++++++|++++++++++ T Consensus 2 ~~~~~~~RP~sPhL~iyk~~~t~~~SI~HRisGv~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (129) T d1nekc_ 2 IRNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTAL 81 (129) T ss_dssp CTTCCCCCCBCCCGGGSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHTTSHHHHHHHHHHHHHH T ss_pred CHHCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 11013699999985615732999999999999999999999999999998421117999999997799999999999999 Q ss_pred HHHHHHHHHHHHHHCCHHCC-HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999989999985212335-89999999999999999999999997 Q gi|254781041|r 81 IHHMLGGIRYLIWDVSLCLD-KKIATQMAKINIIASILTVLIVWIIK 126 (129) Q Consensus 81 ~yH~~nGiRHL~wD~g~g~~-~~~~~~s~~~vl~~sil~~~~~~~i~ 126 (129) +||++||+||++||+|+|+| +++++++++++++++++.++..|++. T Consensus 82 ~yH~~nGIRHL~wD~G~g~~~~~~~~~s~~~~~~~si~~s~~~~~~i 128 (129) T d1nekc_ 82 AYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVLV 128 (129) T ss_dssp HHHHHHHHHHHHHHHTSSCCSHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999859999997430234689999999999999999999999997 No 2 >d1nekd_ f.21.2.2 (D:) Succinate dehydrogenase subunit SdhD {Escherichia coli [TaxId: 562]} Probab=98.60 E-value=8.1e-07 Score=54.10 Aligned_cols=75 Identities=21% Similarity=0.193 Sum_probs=61.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHC Q ss_conf 99999999999999999999999999985163035546753068316999999999999999998999998521233 Q gi|254781041|r 23 MFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCL 99 (129) Q Consensus 23 ~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~ 99 (129) .--.+.+|+|++++....+.+.. ......+..|+.+.+.++++..+...........||...|+|+.+-|+-.+. T Consensus 11 ~~~W~~qRvSAv~l~~l~~~~~~--~~~~~~~~~y~~~~~~~~~~~~~il~~l~l~~~~~H~~lGl~~IieDYi~~~ 85 (113) T d1nekd_ 11 VHDFILVRATAIVLTLYIIYMVG--FFATSGELTYEVWIGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKPL 85 (113) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH--HHTTTSSCCHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSH T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH T ss_conf 99999999999999999999999--9998299999999999939499999999999999999970756689955974 No 3 >d2bs2c1 f.21.2.1 (C:1-254) Fumarate reductase respiratory complex cytochrome b subunit, FrdC {Wolinella succinogenes [TaxId: 844]} Probab=97.31 E-value=0.0036 Score=34.17 Aligned_cols=77 Identities=13% Similarity=0.016 Sum_probs=53.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHC Q ss_conf 599999999999999999999999999985163035546753068316999999999999999998999998521233 Q gi|254781041|r 22 TMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCL 99 (129) Q Consensus 22 t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nGiRHL~wD~g~g~ 99 (129) ....|-+-|+||+++.+++....+-+-.. ..+..++.....+.++.....-.....+..+|..||+..+..+.|... T Consensus 122 ~t~~~~~q~~tG~ill~fi~~Hl~~~~~~-~~~~~~~~~~~~~~~~~~~~fY~l~l~av~lH~~~Gl~s~~~~wG~~~ 198 (254) T d2bs2c1 122 DTTLWWIQAMTGFAMFFLGSVHLYIMMTQ-PQTIGPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFD 198 (254) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-GGGCSTTHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 24999999999999999999999999747-667879999999947069999999999999998882999998873047 No 4 >d2bs2c1 f.21.2.1 (C:1-254) Fumarate reductase respiratory complex cytochrome b subunit, FrdC {Wolinella succinogenes [TaxId: 844]} Probab=97.13 E-value=0.0057 Score=33.09 Aligned_cols=77 Identities=13% Similarity=-0.009 Sum_probs=62.5 Q ss_pred EECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC---------CHHHHHHHHHHHHHHHHHHH Q ss_conf 102666599999999999999999999999999985163035546753068---------31699999999999999999 Q gi|254781041|r 16 IYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDG---------SVFEVCLFLYTWAVIHHMLG 86 (129) Q Consensus 16 iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---------~~~k~~~~~~~~~~~yH~~n 86 (129) .-|...++...-+|=+||+++.+++......-.....|||.|+....++.+ ++..+...++..++..|... T Consensus 17 ~~~s~~~~~l~~l~slTGlvL~lFl~~Hm~~n~~il~g~eafn~~a~~l~~~~~~~~~~p~l~~i~~~~l~~~ll~H~~~ 96 (254) T d2bs2c1 17 RKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILLGDNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFL 96 (254) T ss_dssp SCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGTCHHHHHHHHHHTTCTTTSSSCCTHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 67778707999999999999999999999988999819999999999998613334786089999999999999999999 Q ss_pred HHHHHH Q ss_conf 899999 Q gi|254781041|r 87 GIRYLI 92 (129) Q Consensus 87 GiRHL~ 92 (129) |+|-+. T Consensus 97 a~~~~~ 102 (254) T d2bs2c1 97 AMRKFP 102 (254) T ss_dssp HGGGSC T ss_pred HHHHHH T ss_conf 999999 No 5 >d1kf6c_ f.21.2.2 (C:) Fumarate reductase subunit FrdC {Escherichia coli [TaxId: 562]} Probab=92.71 E-value=0.22 Score=24.44 Aligned_cols=105 Identities=10% Similarity=0.143 Sum_probs=70.7 Q ss_pred CCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 89997735102666599999999999999999999999999985163035546753068316999999999999999998 Q gi|254781041|r 8 RPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLGG 87 (129) Q Consensus 8 RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~yH~~nG 87 (129) ||+.++= ++-..-=..-.+.-.|.+....+...+.+++.++..|||+++.+..+..+++.-+.-.....+-.||...= T Consensus 9 R~m~~~W--W~k~~FYr~YMlRE~T~v~~~~f~lvLl~Gl~~L~~g~~aw~~fv~flqnP~vv~lniiaLaa~L~Ha~Tw 86 (130) T d1kf6c_ 9 RPMTSTW--WKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAWAGFVDFLQNPVIVIINLITLAAALLHTKTW 86 (130) T ss_dssp CCCCTTG--GGSSHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHH T ss_pred CCCCCHH--HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH T ss_conf 8787407--65683899999988737999999999999999980587899999999718499999999999999999999 Q ss_pred HHHH--HHHC---CHHCCHHHHHHHHHHHHHH Q ss_conf 9999--9852---1233589999999999999 Q gi|254781041|r 88 IRYL--IWDV---SLCLDKKIATQMAKINIIA 114 (129) Q Consensus 88 iRHL--~wD~---g~g~~~~~~~~s~~~vl~~ 114 (129) ..-. .+.. |...+.+...+.-|.+.+. T Consensus 87 F~l~Pk~m~i~v~~~~~~~~~iv~~~wa~~~~ 118 (130) T d1kf6c_ 87 FELAPKAANIIVKDEKMGPEPIIKSLWAVTVV 118 (130) T ss_dssp HHHGGGGCCCBSSSSBCCSHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 99856765466258607738999999999999 No 6 >d1kf6d_ f.21.2.2 (D:) Fumarate reductase subunit FrdD {Escherichia coli [TaxId: 562]} Probab=92.36 E-value=0.27 Score=23.99 Aligned_cols=104 Identities=11% Similarity=0.051 Sum_probs=66.3 Q ss_pred CCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHCCCHHHHHHHHHCCCHHHHHHH Q ss_conf 96200498999773510266659999999999999999999999999998------516303554675306831699999 Q gi|254781041|r 1 MSSIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCI------ANGEHTLSSLRCYMDGSVFEVCLF 74 (129) Q Consensus 1 m~~m~~~RPlsphL~iyk~~~t~~~SI~HRitGi~l~~~~~~~~~~l~~~------~~~~~~~~~~~~~~~~~~~k~~~~ 74 (129) |.|.+.||--- | +.+-+--.-|..-+...|..+...... ..++.+|+.+..+..++++|.+.. T Consensus 1 m~n~~pKRS~E-------P----i~WgLFgAGGm~~A~~~Pvlill~giLlPlG~~~~~a~~y~~i~aFa~s~iG~l~ll 69 (119) T d1kf6d_ 1 MINPNPKRSDE-------P----VFWGLFGAGGMWSAIIAPVMILLVGILLPLGLFPGDALSYERVLAFAQSFIGRVFLF 69 (119) T ss_dssp CCCSSCCCCSH-------H----HHHHHHHHHHHHHHHTHHHHHHHHHTTGGGTCSSTTTTSHHHHHHHHTSHHHHHHHH T ss_pred CCCCCCCCCCC-------C----CHHEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 99899887789-------8----311234477205899988999999999961267866568999999984479999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999998999998521233589999999999999999999 Q gi|254781041|r 75 LYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVL 120 (129) Q Consensus 75 ~~~~~~~yH~~nGiRHL~wD~g~g~~~~~~~~s~~~vl~~sil~~~ 120 (129) ....--..|-+--++|-+=|++.-... ..++--+++.+.|+ T Consensus 70 ~~i~lplWh~~HRihHglHDlkih~p~-----g~~~fYg~A~l~sv 110 (119) T d1kf6d_ 70 LMIVLPLWCGLHRMHHAMHDLKIHVPA-----GKWVFYGLAAILTV 110 (119) T ss_dssp HHHHHHHHHHHHHHHHHHHHTTCCCTT-----HHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHH T ss_conf 999999999999999988663000363-----04788999999999 No 7 >d2pu9b1 b.34.4.3 (B:1-73) Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain {Synechocystis sp. [TaxId: 1143]} Probab=32.94 E-value=5.2 Score=16.92 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=9.0 Q ss_pred CCCCCCCCCCE Q ss_conf 49899977351 Q gi|254781041|r 6 NNRPLSPHLQI 16 (129) Q Consensus 6 ~~RPlsphL~i 16 (129) +.||+||+|.+ T Consensus 43 kGr~ISanlP~ 53 (73) T d2pu9b1 43 QGRPISANLPV 53 (73) T ss_dssp TTEECCCSSCE T ss_pred CCCEECCCCCE T ss_conf 78595699769 No 8 >d1xrda1 f.3.1.1 (A:1-52) Light-harvesting complex subunits {Rhodospirillum rubrum [TaxId: 1085]} Probab=8.55 E-value=50 Score=11.56 Aligned_cols=34 Identities=12% Similarity=-0.100 Sum_probs=25.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 9999999999999999999985163035546753 Q gi|254781041|r 30 RITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCY 63 (129) Q Consensus 30 RitGi~l~~~~~~~~~~l~~~~~~~~~~~~~~~~ 63 (129) |-+-++++.++.++........++.+.|+-+... T Consensus 11 Rr~lva~~~fL~~LAl~IHfiLLSt~rfNWleg~ 44 (52) T d1xrda1 11 RQALVGLATFLFVLALLIHFILLSTERFNWLEGA 44 (52) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 8999999999999999999998546765654588 No 9 >d1eg3a2 a.39.1.7 (A:210-306) Dystrophin {Human (Homo sapiens) [TaxId: 9606]} Probab=4.40 E-value=87 Score=10.24 Aligned_cols=16 Identities=13% Similarity=0.499 Sum_probs=0.0 Q ss_pred CCHHHHHHHHHHHHHH Q ss_conf 6665999999999999 Q gi|254781041|r 19 LIPTMFVSIVHRITGS 34 (129) Q Consensus 19 ~~~t~~~SI~HRitGi 34 (129) ||.-.+.+.+||+.-+ T Consensus 80 Pq~LvWLp~lHRla~a 95 (97) T d1eg3a2 80 PQSMVWLPVLHRVAAA 95 (97) T ss_dssp CTTTTHHHHHHHHHHH T ss_pred CCCEEHHHHHHHHHHH T ss_conf 9702319999899870 No 10 >d1jh6a_ d.61.1.1 (A:) tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Probab=3.65 E-value=1e+02 Score=9.82 Aligned_cols=14 Identities=29% Similarity=0.617 Sum_probs=0.0 Q ss_pred CCCCCCCCCCCEEC Q ss_conf 04989997735102 Q gi|254781041|r 5 KNNRPLSPHLQIYR 18 (129) Q Consensus 5 ~~~RPlsphL~iyk 18 (129) .++||-.||+|+-+ T Consensus 111 ~~~~~f~PHiTLa~ 124 (181) T d1jh6a_ 111 STTTPYMPHLSLLY 124 (181) T ss_dssp CCCSCCCCEEEEEC T ss_pred CCCCCCCCEEEEEE T ss_conf 66777787288883 Done!