Query         gi|254780749|ref|YP_003065162.1| lipoprotein signal peptidase transmembrane [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 108
No_of_seqs    112 out of 1642
Neff          6.2 
Searched_HMMs 33803
Date          Wed Jun  1 14:10:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780749.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2k4z_A DSRR; ISCA/SUFA/HESB l  14.2      56  0.0017   13.9   0.6   20   53-72     42-61  (77)
  2 >1stz_A Heat-inducible transcr   9.6 1.2E+02  0.0036   12.2   1.4   14   47-60     18-31  (149)
  3 >1sd4_A Penicillinase represso   7.8 1.5E+02  0.0043   11.8   1.2   19   46-64      9-27  (53)
  4 >3kdr_A HK97 family phage port   7.2 1.5E+02  0.0045   11.7   0.7   11   50-60     43-53  (107)
  5 >1pw4_A Glycerol-3-phosphate t   6.9 1.6E+02  0.0048   11.5   9.8   51   35-91    153-203 (222)
  6 >1qtq_A GLNRS, protein (glutam   6.0      99  0.0029   12.6  -0.7   21   57-79     82-102 (111)
  7 >3b5d_A Multidrug transporter    5.0 2.1E+02  0.0063   10.9   4.9   10    7-16      3-12  (110)
  8 >2bbk_H Methylamine dehydrogen   5.0      93  0.0027   12.8  -1.4   20   50-69     18-37  (54)
  9 >3hzq_A Large-conductance mech   4.2 2.5E+02  0.0073   10.6   6.5   66   37-102     5-82  (82)
 10 >1s28_A ORF1; type III chapero   4.2 2.3E+02  0.0068   10.8   0.1   18   45-62      1-18  (132)

No 1  
>>2k4z_A DSRR; ISCA/SUFA/HESB like fold, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Allochromatium vinosum} (A:1-41,A:90-125)
Probab=14.21  E-value=56  Score=13.89  Aligned_cols=20  Identities=20%  Similarity=0.429  Sum_probs=15.6

Q ss_pred             HHHHHCCCCEEEEEECCCCC
Q ss_conf             89763127577662368154
Q gi|254780749|r   53 HCLYGYVIDYIMIHTQTWSF   72 (108)
Q Consensus        53 R~~~G~VvDfi~~~~~~~~~   72 (108)
                      -+..|.|+||..+.-++++|
T Consensus        42 sLLeg~vlDfveie~g~~hF   61 (77)
T 2k4z_A           42 SLLDQTTLDYVELEPGQFHF   61 (77)
T ss_dssp             HHHTTEEEEEEEEETTEEEE
T ss_pred             CCCCCEEEEEECCCCCCCCE
T ss_conf             40597699886278872787


No 2  
>>1stz_A Heat-inducible transcription repressor HRCA homolog; circe element, structural genomics, BSGC structure funded by NIH; 2.20A {Thermotoga maritima} (A:106-143,A:228-338)
Probab=9.60  E-value=1.2e+02  Score=12.18  Aligned_cols=14  Identities=36%  Similarity=0.672  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             79999989763127
Q gi|254780749|r   47 LGNVVDHCLYGYVI   60 (108)
Q Consensus        47 iGNliDR~~~G~Vv   60 (108)
                      .||++-|+.-|||.
T Consensus        18 ~~~~~~~~~~~~~~   31 (149)
T 1stz_A           18 AGNLLARLTEGYVL   31 (149)
T ss_dssp             HHHHHHHHHTCEEE
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999766674


No 3  
>>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding protein; 2.00A {Staphylococcus aureus} (A:74-126)
Probab=7.84  E-value=1.5e+02  Score=11.78  Aligned_cols=19  Identities=5%  Similarity=0.109  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHCCCCEEE
Q ss_conf             8799999897631275776
Q gi|254780749|r   46 ALGNVVDHCLYGYVIDYIM   64 (108)
Q Consensus        46 aiGNliDR~~~G~VvDfi~   64 (108)
                      ...+++||++.|.+--|+.
T Consensus         9 es~~fl~r~f~Gs~~~lv~   27 (53)
T 1sd4_A            9 TAKTFLNKLYGGDXKSLVL   27 (53)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHH
T ss_conf             9999999995899999999


No 4  
>>3kdr_A HK97 family phage portal protein; PSI, MCSG, structural genomics, protein structure initiative; 2.90A {Corynebacterium diphtheriae} (A:130-236)
Probab=7.23  E-value=1.5e+02  Score=11.70  Aligned_cols=11  Identities=45%  Similarity=0.700  Sum_probs=7.6

Q ss_pred             HHHHHHHHCCC
Q ss_conf             99989763127
Q gi|254780749|r   50 VVDHCLYGYVI   60 (108)
Q Consensus        50 liDR~~~G~Vv   60 (108)
                      -.||++.|||.
T Consensus        43 dvdriingyva   53 (107)
T 3kdr_A           43 DVDRIINGYVA   53 (107)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 5  
>>1pw4_A Glycerol-3-phosphate transporter; transmembrane, inner membrane, major facilitator superfamily, secondary active membrane transporter; 3.30A {Escherichia coli} (A:230-451)
Probab=6.91  E-value=1.6e+02  Score=11.54  Aligned_cols=51  Identities=16%  Similarity=0.137  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999988799999897631275776623681540899999999999999999
Q gi|254780749|r   35 FDIGYILITTGALGNVVDHCLYGYVIDYIMIHTQTWSFAVFNLADLFISIGTCIIIY   91 (108)
Q Consensus        35 ~~i~l~li~gGaiGNliDR~~~G~VvDfi~~~~~~~~~pvFNvAD~~I~iG~~lli~   91 (108)
                      ...|+....+...|.+.=-+.-|.+.|-...     ++ +|-+.=+.-.++.++..+
T Consensus       153 ~~~g~~~~~~~~~g~~~~~~~~~~~~~~~g~-----~~-~~~~~~~~~~i~~~~~~~  203 (222)
T 1pw4_A          153 TAAGFTGLFGYLGGSVAASAIVGYTVDFFGW-----DG-GFMVMIGGSILAVILLIV  203 (222)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSSCS-----HH-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH-----HH-HHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999998586-----99-999999999999999999


No 6  
>>1qtq_A GLNRS, protein (glutaminyl-tRNA synthetase); glutamine, trnaGln, E. coli, complex, ligase/RNA complex; HET: QSI; 2.25A {Escherichia coli} (A:102-212)
Probab=6.02  E-value=99  Score=12.63  Aligned_cols=21  Identities=5%  Similarity=-0.039  Sum_probs=14.6

Q ss_pred             HCCCCEEEEEECCCCCHHHHHHH
Q ss_conf             31275776623681540899999
Q gi|254780749|r   57 GYVIDYIMIHTQTWSFAVFNLAD   79 (108)
Q Consensus        57 G~VvDfi~~~~~~~~~pvFNvAD   79 (108)
                      +.+-||+-++..+  .|+.|+||
T Consensus        82 ~~~~D~Vi~R~dg--~p~Y~laD  102 (111)
T 1qtq_A           82 IVMRDPVLYRIKF--AEHHQTGN  102 (111)
T ss_dssp             GGGSSCEEEEECC--CCBTTTBT
T ss_pred             CEEECCEEEEEEC--CCCCCCCC
T ss_conf             2788888989504--34553123


No 7  
>>3b5d_A Multidrug transporter EMRE; helical membrane protein, multidrug resistance transporter, SMR, antiport, inner membrane, transmembrane; HET: P4P; 3.80A {Escherichia coli K12} PDB: 3b61_A 3b62_A* (A:)
Probab=5.04  E-value=2.1e+02  Score=10.94  Aligned_cols=10  Identities=40%  Similarity=0.494  Sum_probs=3.5

Q ss_pred             HHHHHHHHHH
Q ss_conf             2999999999
Q gi|254780749|r    7 PTILVSIRIL   16 (108)
Q Consensus         7 ~~~~~~~~~~   16 (108)
                      +|++...+++
T Consensus         3 ~w~~L~~Ai~   12 (110)
T 3b5d_A            3 PYIYLGGAIL   12 (110)
T ss_pred             HHHHHHHHHH
T ss_conf             3899999999


No 8  
>>2bbk_H Methylamine dehydrogenase (heavy subunit); electron transport; HET: TRQ; 1.75A {Paracoccus denitrificans} (H:50-103)
Probab=4.97  E-value=93  Score=12.77  Aligned_cols=20  Identities=20%  Similarity=0.305  Sum_probs=15.1

Q ss_pred             HHHHHHHHCCCCEEEEEECC
Q ss_conf             99989763127577662368
Q gi|254780749|r   50 VVDHCLYGYVIDYIMIHTQT   69 (108)
Q Consensus        50 liDR~~~G~VvDfi~~~~~~   69 (108)
                      .+||+-+|.=.||+.++=..
T Consensus        18 ~y~RiArGkR~DYvev~Dp~   37 (54)
T 2bbk_H           18 VFSRIARGERTDYVEVFDPV   37 (54)
T ss_dssp             EEEETTEEEEEEEEEEECTT
T ss_pred             CCCCCCCCCCCCEEEEEECC
T ss_conf             76641014799989999999


No 9  
>>3hzq_A Large-conductance mechanosensitive channel; intermediate state mechanosensitive channel osmoregulation, cell membrane, ION transport; 3.82A {Staphylococcus aureus subsp} (A:33-114)
Probab=4.19  E-value=2.5e+02  Score=10.60  Aligned_cols=66  Identities=14%  Similarity=0.083  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-----------HCCCCEEEEEECCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999887999998976-----------31275776623681540-89999999999999999999940004321
Q gi|254780749|r   37 IGYILITTGALGNVVDHCLY-----------GYVIDYIMIHTQTWSFA-VFNLADLFISIGTCIIIYDDIILQHRQKG  102 (108)
Q Consensus        37 i~l~li~gGaiGNliDR~~~-----------G~VvDfi~~~~~~~~~p-vFNvAD~~I~iG~~lli~~~~~~~~~~k~  102 (108)
                      ++-+.++|+|.+.+.+-+..           |..-.--........|. ..|-.=.++.++.+++++-.-..+-++|+
T Consensus         5 LAVaviiG~AF~~iV~slv~~iI~PlI~~~~g~~~~~~~~~~~~i~yG~fi~aii~FlIia~viFliVk~~nk~~~k~   82 (82)
T 3hzq_A            5 LAIAVVMGAAFNKIICSLVENIIMPLIGKIFGSVDFAKEWSFWGIKYGLFIQSVIDFIIIAFALFIFVKIANTLMKKE   82 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTHHHHHHHSSSCSCCCTTCCCSSCCCTHHHHHHHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999999999999899989998577612211120011068999999999999999999999999986169


No 10 
>>1s28_A ORF1; type III chaperone; 3.00A {Pseudomonas syringae PV} (A:)
Probab=4.19  E-value=2.3e+02  Score=10.77  Aligned_cols=18  Identities=39%  Similarity=0.587  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHCCCCE
Q ss_conf             887999998976312757
Q gi|254780749|r   45 GALGNVVDHCLYGYVIDY   62 (108)
Q Consensus        45 GaiGNliDR~~~G~VvDf   62 (108)
                      ||.-|-.||+.+|--.||
T Consensus         1 ~~~kn~Fd~lvd~l~K~Y   18 (132)
T 1s28_A            1 GAXKNSFDRLIDGLAKDY   18 (132)
T ss_dssp             CHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHC
T ss_conf             905778999999999755


Done!