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!