Query         gi|254780471|ref|YP_003064884.1| cytochrome o ubiquinol oxidase subunit IV [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 119
No_of_seqs    101 out of 264
Neff          4.7 
Searched_HMMs 23785
Date          Mon May 30 11:32:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780471.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2bg9_B Acetylcholine receptor   24.8      29  0.0012   13.7   9.1   25   85-109   339-363 (370)
  2 3aag_A General glycosylation p  23.8      30  0.0013   13.6   2.1   19    9-27     52-70  (291)
  3 1lgh_A LH II, B800/850, light   17.4      42  0.0018   12.8   3.8   30   35-68      9-38  (56)
  4 1ydl_A TFIIH, general transcri  15.0      12 0.00049   15.9  -1.9   15    7-21      3-17  (79)
  5 1m56_D Cytochrome C oxidase; m  14.8      38  0.0016   13.0   0.6   15    4-18      3-17  (51)
  6 2zjs_Y Preprotein translocase   13.8      52  0.0022   12.3   5.6   53   51-103   117-170 (434)
  7 2onk_C Molybdate/tungstate ABC  11.2      64  0.0027   11.8   3.2   15    1-15      1-15  (284)
  8 3eam_A GLR4197 protein; pentam  10.6      66  0.0028   11.7   9.0   23   22-44    225-247 (317)
  9 2f2f_C CDT C, cytolethal diste  10.5      46  0.0019   12.6   0.0   23   17-39      1-23  (186)
 10 3f4m_A Tumor necrosis factor,    9.9      71   0.003   11.5   2.7   55   25-84     71-126 (161)

No 1  
>2bg9_B Acetylcholine receptor protein, beta chain; ION channel/receptor, ION channel, electron microscopy, ION transport, postsynaptic membrane; 4.00A {Torpedo marmorata}
Probab=24.78  E-value=29  Score=13.69  Aligned_cols=25  Identities=20%  Similarity=0.656  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999998511304
Q gi|254780471|r   85 IFTIIMVAICFVGSMWVMYHLNNNM  109 (119)
Q Consensus        85 ~Ft~~ii~iiv~GSiWIM~~l~~nM  109 (119)
                      +|-.+.+++.+.|++.|..+-.+|-
T Consensus       339 ~~~~~~~~~~~i~t~~i~~~~~~~~  363 (370)
T 2bg9_B          339 LFLYIFITMCSIGTFSIFLDASHNV  363 (370)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHEEEECCCCC
T ss_conf             9999999999998885074077789


No 2  
>3aag_A General glycosylation pathway protein; multidomain, transferase; HET: MLY; 2.80A {Campylobacter jejuni RM1221}
Probab=23.82  E-value=30  Score=13.58  Aligned_cols=19  Identities=16%  Similarity=0.083  Sum_probs=15.9

Q ss_pred             CCCCCCCCHHHHHHHHHHH
Q ss_conf             8777888525689999999
Q gi|254780471|r    9 MNMHSYGTKKQCLVGFILS   27 (119)
Q Consensus         9 ~~~~~hgs~k~yliGFiLs   27 (119)
                      +|+..|.+.+.|.++++|+
T Consensus        52 ~DGg~h~g~~~y~va~~ls   70 (291)
T 3aag_A           52 VDGGXHLGXDNFFPSFALS   70 (291)
T ss_dssp             CBTTBCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHC
T ss_conf             2586333227788888747


No 3  
>1lgh_A LH II, B800/850, light harvesting complex II; bacteriochlorophyll, dexter energy transfer, foerster exciton transfer mechanism; HET: BCL LYC DET HTO; 2.40A {Phaeospirillum molischianum} SCOP: f.3.1.1
Probab=17.38  E-value=42  Score=12.79  Aligned_cols=30  Identities=13%  Similarity=0.294  Sum_probs=21.4

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999806578846999999999999999999999
Q gi|254780471|r   35 FGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFF   68 (119)
Q Consensus        35 F~lV~~~~~~~~~~~~~~I~~~Av~Qi~VqL~~F   68 (119)
                      ||+|..    |.+.+.++.+..+++-+.||.+-|
T Consensus         9 iWlVvN----PaTWL~pi~~av~v~ai~VH~~vl   38 (56)
T 1lgh_A            9 IWLVIN----PSTWLPVIWIVATVVAIAVHAAVL   38 (56)
T ss_dssp             HHHHSC----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEC----CHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999977----415489999999999999999987


No 4  
>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A
Probab=15.04  E-value=12  Score=15.87  Aligned_cols=15  Identities=47%  Similarity=0.642  Sum_probs=9.5

Q ss_pred             CCCCCCCCCCHHHHH
Q ss_conf             898777888525689
Q gi|254780471|r    7 HNMNMHSYGTKKQCL   21 (119)
Q Consensus         7 h~~~~~~hgs~k~yl   21 (119)
                      |.+..+||||.|+.+
T Consensus         3 ~~~~~~~~~~~KGvL   17 (79)
T 1ydl_A            3 HHHHHHSHGTRKGML   17 (79)
T ss_dssp             ------CCCCCCCEE
T ss_pred             CCCCCCCCCCCCEEE
T ss_conf             543432358866489


No 5  
>1m56_D Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.23.8.1 PDB: 1m57_D*
Probab=14.80  E-value=38  Score=13.04  Aligned_cols=15  Identities=27%  Similarity=0.361  Sum_probs=10.4

Q ss_pred             CCCCCCCCCCCCCHH
Q ss_conf             888898777888525
Q gi|254780471|r    4 DNIHNMNMHSYGTKK   18 (119)
Q Consensus         4 ~~~h~~~~~~hgs~k   18 (119)
                      |+.|...+|.||++-
T Consensus         3 ~HkH~~~~H~hGeMD   17 (51)
T 1m56_D            3 DHSHPAHGHVAGSMD   17 (51)
T ss_dssp             -------CCCTTCSC
T ss_pred             CCCCCCCCCCCCCCC
T ss_conf             665665567788532


No 6  
>2zjs_Y Preprotein translocase SECY subunit; translocon, SEC, protein-conducting-channel, membrane, protein transport, translocation, transmembrane, transport; 3.20A {Thermus thermophilus} PDB: 2zqp_Y
Probab=13.78  E-value=52  Score=12.25  Aligned_cols=53  Identities=11%  Similarity=-0.036  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999704778765025-99999999999999999999998
Q gi|254780471|r   51 LTIVLCAIAQIIVHLVFFLHMSTKVEDGWS-IMAMIFTIIMVAICFVGSMWVMY  103 (119)
Q Consensus        51 ~~I~~~Av~Qi~VqL~~FLHl~~~~~~~~n-~~a~~Ft~~ii~iiv~GSiWIM~  103 (119)
                      .+.+.+|++|..+....+...+.+.-.... .....|...++..++.||.-+|+
T Consensus       117 ~ltl~~a~iqa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~Gs~~l~w  170 (434)
T 2zjs_Y          117 IGGIALGAFQGFFLATAFLGAEGGRFLLPGWSPGPFFWFVVVVTQVAGIALLLW  170 (434)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSSSTTBCTTCCSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999998535787435214680378999999999999999999


No 7  
>2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: f.58.1.1
Probab=11.16  E-value=64  Score=11.79  Aligned_cols=15  Identities=33%  Similarity=0.425  Sum_probs=6.2

Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             987888898777888
Q gi|254780471|r    1 MKYDNIHNMNMHSYG   15 (119)
Q Consensus         1 m~~~~~h~~~~~~hg   15 (119)
                      |.|.+.|.++.|+-|
T Consensus         1 ~~~~~~~~~~~~~~g   15 (284)
T 2onk_C            1 MGHHHHHHHHHHSSG   15 (284)
T ss_dssp             ---------------
T ss_pred             CCCCCCCCCCCCCCC
T ss_conf             975322210235678


No 8  
>3eam_A GLR4197 protein; pentameric ligand-gated ION-channel, membrane protein, transport protein; HET: LMT PC1; 2.90A {Gloeobacter violaceus} PDB: 3ehz_A 3lsv_A 3ei0_A
Probab=10.62  E-value=66  Score=11.68  Aligned_cols=23  Identities=22%  Similarity=0.434  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999999999999999806578
Q gi|254780471|r   22 VGFILSLILTIIPFGIVMKGFFL   44 (119)
Q Consensus        22 iGFiLsiiLT~iaF~lV~~~~~~   44 (119)
                      +++....+||.++|-.+..+.+|
T Consensus       225 ~~l~it~lL~~~~~~~~~~~~lP  247 (317)
T 3eam_A          225 VTLVVSTLIAHIAFNILVETNLP  247 (317)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             EEEEEHHHHHHHHHHHHHHHHCC
T ss_conf             79996599999999998874489


No 9  
>2f2f_C CDT C, cytolethal distending toxin C; actinobacillus actinomycetemcomitans, oligomerization, stability and toxic activity; 2.40A {Aggregatibacter actinomycetemcomitans} SCOP: b.42.2.1
Probab=10.51  E-value=46  Score=12.56  Aligned_cols=23  Identities=35%  Similarity=0.514  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             25689999999999999999998
Q gi|254780471|r   17 KKQCLVGFILSLILTIIPFGIVM   39 (119)
Q Consensus        17 ~k~yliGFiLsiiLT~iaF~lV~   39 (119)
                      +|+|++-|.++++++.....-..
T Consensus         1 mkK~~i~f~~~l~~~~~s~~~~~   23 (186)
T 2f2f_C            1 MKKYLLSFLLSMILTLTSHAESN   23 (186)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             93248999999997511455468


No 10 
>3f4m_A Tumor necrosis factor, alpha-induced protein 8- like protein 2; TIPE2, immune homeostasis, tnfaip8, immune system; 1.70A {Homo sapiens}
Probab=9.88  E-value=71  Score=11.53  Aligned_cols=55  Identities=18%  Similarity=0.332  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHH
Q ss_conf             99999999999999806578846999999999999999999999704778765025-9999
Q gi|254780471|r   25 ILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWS-IMAM   84 (119)
Q Consensus        25 iLsiiLT~iaF~lV~~~~~~~~~~~~~~I~~~Av~Qi~VqL~~FLHl~~~~~~~~n-~~a~   84 (119)
                      .-.+.+|+++|+=|-+. + +++.+...+--|  -+.+-|++ ==|++.+|.+|.| ++.+
T Consensus        71 ~~~~amt~iSFyevdfT-f-D~~~L~~~L~ec--r~~L~~lV-~~HLT~KS~~RI~~VF~~  126 (161)
T 3f4m_A           71 LRQGAMTALSFGEVDFT-F-EAAVLAGLLTEC--RDVLLELV-EHHLTPKSHGRIRHVFDH  126 (161)
T ss_dssp             HHHHHHHHHHHTSTTSC-C-CHHHHHHHHHHH--HHHHHHHH-TTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCEE-E-CHHHHHHHHHHH--HHHHHHHH-HHHCCHHHHHHHHHHHHC
T ss_conf             99888998522011134-2-699999999999--99999999-876876357679999860


Done!