Query         gi|254780549|ref|YP_003064962.1| signal peptide protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 271
No_of_seqs    140 out of 348
Neff          9.0 
Searched_HMMs 23785
Date          Tue May 31 19:46:55 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780549.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1lr0_A TOLA protein; domain-sw  99.9 1.4E-24 5.8E-29  158.1  10.9   94  171-271    23-121 (129)
  2 1tol_A G3P - TOLA, protein (fu  99.7 4.5E-17 1.9E-21  115.3   8.5   88  172-270   126-215 (222)
  3 2grx_C Protein TONB; beta barr  99.3 1.8E-13 7.5E-18   94.8   1.1   82  180-269   141-223 (229)
  4 2k9k_A TONB2; metal transport;  97.9 1.4E-05 5.8E-10   49.8   4.7   76  189-269    26-105 (106)
  5 1u07_A TONB protein; beta-hair  97.7 2.2E-05 9.2E-10   48.7   3.7   71  189-267    11-82  (90)
  6 1bwv_A Rubisco, protein (ribul  22.5     2.4  0.0001   20.0  -4.0   60  209-270   407-481 (493)
  7 1lgh_A LH II, B800/850, light   20.4      29  0.0012   13.8   1.2   21    6-26     26-46  (56)
  8 2oa4_A SIR5; structure, struct  19.3      38  0.0016   13.1   2.7   52  209-261    13-72  (101)
  9 1xrd_A LH-1, light-harvesting   17.4      43  0.0018   12.9   2.6   19    7-25     22-40  (52)
 10 3kfu_F Aspartyl/glutamyl-tRNA(  15.5      48   0.002   12.6   7.9   78  165-243   149-227 (466)

No 1  
>1lr0_A TOLA protein; domain-swapping, TONB, protein transport; 1.91A {Pseudomonas aeruginosa} SCOP: d.212.1.1
Probab=99.92  E-value=1.4e-24  Score=158.10  Aligned_cols=94  Identities=16%  Similarity=0.262  Sum_probs=83.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             00000789999999999622546565553752999999987998185335640588860589999999999999718898
Q gi|254780549|r  171 KRIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFR  250 (271)
Q Consensus       171 ~~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~  250 (271)
                      +..++.+|.++|+++|++||++|.+++  .++.|+|+|+|++||+|.+..++.+||+     +.||++|+|||.+|+||+
T Consensus        23 ~~~~~~~y~~~i~~~I~~~W~~P~~~~--~~~~v~v~i~l~~dG~v~~~~i~~sSG~-----~~~d~aa~~Av~ra~p~p   95 (129)
T 1lr0_A           23 GSEVTGSLDDLIVNLVSQQWRRPPSAR--NGMSVEVLIEMLPDGTITNASVSRSSGD-----KPFDSSAVAAVRNVGRIP   95 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCCTTCC--TTCCEEEEEEECTTSBEEEEEEEECCSC-----HHHHHHHHHHHHHHCBCG
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCCEEEEEEEECCCCCEEEEEECCCCCC-----HHHHHHHHHHHHHHCCCC
T ss_conf             588999999999999998468998778--8978999999989998987551027787-----589999999999852699


Q ss_pred             C----CHHHHHH-CCEEEEEECHHHC
Q ss_conf             8----8467761-2228997444009
Q gi|254780549|r  251 L----SPSTYKS-WRNITLFFVPSKM  271 (271)
Q Consensus       251 ~----p~~~y~~-~~~~~~~F~p~~m  271 (271)
                      .    |++.|+. ||+|+|+|+|++|
T Consensus        96 ~p~~~p~~~y~~~~r~i~l~F~Ped~  121 (129)
T 1lr0_A           96 EMQQLPRATFDSLYRQRRIIFKPEDL  121 (129)
T ss_dssp             GGGGSCHHHHHHHTSEEEEEECHHHH
T ss_pred             CCCCCCHHHHHHHEEEEEEEECHHHC
T ss_conf             99877977874400677899882133


No 2  
>1tol_A G3P - TOLA, protein (fusion protein consisting of minor coat protein, glycine rich linker, TOLA,...; bacteriophage M13, phage infection; 1.85A {Enterobacteria phage M13} SCOP: b.37.1.1 d.212.1.1 PDB: 1s62_A
Probab=99.70  E-value=4.5e-17  Score=115.28  Aligned_cols=88  Identities=16%  Similarity=0.238  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             00007899999999996225465655537529999999879981853356405888605899999999999997188988
Q gi|254780549|r  172 RIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRL  251 (271)
Q Consensus       172 ~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~  251 (271)
                      ......|...|+++|+++|.+|.+.+   +.+|+|+|+|.+||+|+++..  +||+     ..||++|+|||.+ .+||.
T Consensus       126 ~a~i~~Y~~~I~a~I~~~~~~p~~~~---Gk~~~V~I~l~pdG~V~~V~~--sSGd-----~alD~AA~~AVr~-a~fP~  194 (222)
T 1tol_A          126 GADINNYAGQIKSAIESKFYDASSYA---GKTCTLRIKLAPDGMLLDIKP--EGGD-----PALCQAALAAAKL-AKIPK  194 (222)
T ss_dssp             CHHHHHHHHHHHHHHHTTCTTGGGGT---TCCEEEEEEECTTSCEEEEEE--EEEC-----HHHHHHHHHHHHH-CCCCC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCC---CCEEEEEEEECCCCEEEEEEE--CCCC-----HHHHHHHHHHHHH-CCCCC
T ss_conf             36688899999999986268985458---998999999889972987463--6899-----8999999999984-78998


Q ss_pred             CH--HHHHHCCEEEEEECHHH
Q ss_conf             84--67761222899744400
Q gi|254780549|r  252 SP--STYKSWRNITLFFVPSK  270 (271)
Q Consensus       252 p~--~~y~~~~~~~~~F~p~~  270 (271)
                      ||  +.|+.||+|.|+|+|+.
T Consensus       195 pp~~~vye~fr~i~l~F~Ps~  215 (222)
T 1tol_A          195 PPSQAVYEVFKNAPLDFKPAA  215 (222)
T ss_dssp             CSCHHHHHHHTTCEEEEECCC
T ss_pred             CCCHHHHHHHEEEEEEECCCC
T ss_conf             997678665166248988887


No 3  
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Probab=99.32  E-value=1.8e-13  Score=94.78  Aligned_cols=82  Identities=15%  Similarity=0.124  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             999999996225465655537-5299999998799818533564058886058999999999999971889888467761
Q gi|254780549|r  180 AIVRNRVIANWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPSTYKS  258 (271)
Q Consensus       180 ~~ir~~I~~~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~y~~  258 (271)
                      ..++..+..+|.||..++..+ ++.|+|.|.|+.||+|.+..++.+||..     +||++|++||.+..+++-++   ..
T Consensus       141 ~~~~~~~~~~~~yp~~A~r~~~~G~v~V~f~I~~~G~V~~v~i~~SSG~~-----~LD~aAl~avrr~~f~P~~~---~~  212 (229)
T 2grx_C          141 SGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPAN-----MFEREVKNAMRRWRYEPGKP---GS  212 (229)
T ss_dssp             -------CCCCCCCHHHHHHTCCEEECEEEECCTTSCCEEEEECCCSSST-----TSHHHHHHHTTSCCCCTTCC---CS
T ss_pred             CCHHHHHCCCCCCCHHHHHCCCCCEEEEEEEECCCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCC---CC
T ss_conf             15477743387770999976898779999998289989688998668965-----89999999999677889987---87


Q ss_pred             CCEEEEEECHH
Q ss_conf             22289974440
Q gi|254780549|r  259 WRNITLFFVPS  269 (271)
Q Consensus       259 ~~~~~~~F~p~  269 (271)
                      |-.+.|.|+-+
T Consensus       213 ~~~v~i~F~L~  223 (229)
T 2grx_C          213 GIVVNILFKIN  223 (229)
T ss_dssp             CEECCEEECCC
T ss_pred             CEEEEEEEEEC
T ss_conf             65998999989


No 4  
>2k9k_A TONB2; metal transport; NMR {Listonella anguillarum}
Probab=97.85  E-value=1.4e-05  Score=49.84  Aligned_cols=76  Identities=17%  Similarity=0.074  Sum_probs=55.6

Q ss_pred             HCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHH---HHHCCEEEE
Q ss_conf             225465655537-5299999998799818533564058886058999999999999971889888467---761222899
Q gi|254780549|r  189 NWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPST---YKSWRNITL  264 (271)
Q Consensus       189 ~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~---y~~~~~~~~  264 (271)
                      ...||..+...+ .+.|+|+|.++.||.|.+..++.+++..     .|+++|++||.+....|-..+.   -..|..+.+
T Consensus        26 ~P~YP~~A~~~gieG~V~v~f~I~~~G~v~~~~v~~ss~~~-----~fd~aa~~av~~~~f~P~~~~G~pv~~~~~~~~i  100 (106)
T 2k9k_A           26 EPVYPSRALKRGVEGFVTLSFTIDTTGKAVDINVVDANPKR-----MFEREAMQALKKWKYQPQIVDGKAIEQPGQTVTV  100 (106)
T ss_dssp             SCCCCSHHHHHCCCCEEEEEEEEETTTEEEEEEEEEESSSS-----SSHHHHHHHHHHCCCCCCCCSSCCSCEEEEEEEE
T ss_pred             CCCCCHHHHHCCCEEEEEEEEEEECCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEE
T ss_conf             99997999975990499999999289989888998647938-----8999999999976778888098576578799989


Q ss_pred             EECHH
Q ss_conf             74440
Q gi|254780549|r  265 FFVPS  269 (271)
Q Consensus       265 ~F~p~  269 (271)
                      +|+-.
T Consensus       101 ~F~L~  105 (106)
T 2k9k_A          101 EFKIA  105 (106)
T ss_dssp             ECCCC
T ss_pred             EEEEC
T ss_conf             99973


No 5  
>1u07_A TONB protein; beta-hairpin, protein transport; 1.13A {Escherichia coli} SCOP: d.212.1.2 PDB: 2gsk_B* 1ihr_A 1qxx_A
Probab=97.70  E-value=2.2e-05  Score=48.72  Aligned_cols=71  Identities=15%  Similarity=0.183  Sum_probs=50.7

Q ss_pred             HCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCEEEEEEC
Q ss_conf             225465655537-5299999998799818533564058886058999999999999971889888467761222899744
Q gi|254780549|r  189 NWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPSTYKSWRNITLFFV  267 (271)
Q Consensus       189 ~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~y~~~~~~~~~F~  267 (271)
                      .+.||..+...+ .+.|.|+|.++.||+|....++.++|..     .|+++|++|+.+....+-.+   ..+-.+.++|.
T Consensus        11 ~P~YP~~A~~~g~eG~v~v~f~I~~~G~v~~~~v~~s~~~~-----~fd~aa~~av~~~~f~P~~~---~~~~~v~i~F~   82 (90)
T 1u07_A           11 QPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPAN-----MFEREVKNAMRRWRYEPGKP---GSGIVVNILFK   82 (90)
T ss_dssp             CCCCCHHHHHHTCCEEEEEEEEECTTSCEEEEEEEEEESSS-----SSHHHHHHHHTTCEECTTCC---EEEEEEEEEEE
T ss_pred             CCCCCHHHHHCCCEEEEEEEEEEECCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCC---CCCEEEEEEEE
T ss_conf             99886999977993489999999599989799999888976-----89999999998587889997---88889999999


No 6  
>1bwv_A Rubisco, protein (ribulose bisphosphate carboxylase); carbon dioxide fixation, complex (rubisco/reaction intermediate); HET: KCX CAP; 2.40A {Galdieria partita} SCOP: c.1.14.1 d.58.9.1 PDB: 1iwa_A 1bxn_A
Probab=22.54  E-value=2.4  Score=19.99  Aligned_cols=60  Identities=15%  Similarity=0.209  Sum_probs=32.5

Q ss_pred             EECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH--------------HH-CCCCCCHHHHHHCCEEEEEECHHH
Q ss_conf             987998185335640588860589999999999999--------------71-889888467761222899744400
Q gi|254780549|r  209 QLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVI--------------KS-QAFRLSPSTYKSWRNITLFFVPSK  270 (271)
Q Consensus       209 ~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~--------------~~-~p~~~p~~~y~~~~~~~~~F~p~~  270 (271)
                      .|+-.|-+.|.|-  +...+-..+|.+-|+++.|+.              .+ .--+-+..--+.|++|.|+|+.-+
T Consensus       407 il~~GGGi~GHP~--G~aaGa~A~RqA~EA~v~~~~~~~~~a~eg~e~l~e~Ak~~~eL~~Ale~Wg~i~f~~~~~~  481 (493)
T 1bwv_A          407 VLQFGGGTIGHPD--GIQAGATANRVALEAMILARNENRDYLTEGPEILREAAKTCGALRTALDLWKDITFNYTSTD  481 (493)
T ss_dssp             EEECSHHHHTCTT--CHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHCHHHHHHHHHHTTCCCCCCCSS
T ss_pred             EEECCCCCCCCCC--CHHHHHHHHHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHCCHHHHHHHHHHCCCEEECCCCC
T ss_conf             9976875237985--65889999999999999733410445542549999997529899999998667367335787


No 7  
>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=20.37  E-value=29  Score=13.80  Aligned_cols=21  Identities=19%  Similarity=0.309  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCC
Q ss_conf             699999999999999987175
Q gi|254780549|r    6 GLAISMILHVMFLLLLYFNFN   26 (271)
Q Consensus         6 gL~lSi~lH~~li~l~~f~~~   26 (271)
                      -++..+.+|+.++.+-.|+|-
T Consensus        26 v~v~ai~VH~~vlslpg~~w~   46 (56)
T 1lgh_A           26 ATVVAIAVHAAVLAAPGFNWI   46 (56)
T ss_dssp             HHHHHHHHHHHHHHSGGGCHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHH
T ss_conf             999999999998706771088


No 8  
>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3
Probab=19.32  E-value=38  Score=13.14  Aligned_cols=52  Identities=17%  Similarity=0.266  Sum_probs=30.1

Q ss_pred             EECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH--------HHCCCCCCHHHHHHCCE
Q ss_conf             987998185335640588860589999999999999--------71889888467761222
Q gi|254780549|r  209 QLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVI--------KSQAFRLSPSTYKSWRN  261 (271)
Q Consensus       209 ~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~--------~~~p~~~p~~~y~~~~~  261 (271)
                      ...|||+++..--+-.. +.....-.---++.+||.        .|.-|.+.++-|..|..
T Consensus        13 v~~pdG~~~t~adlP~~-~trRWvA~RKa~VV~aV~~G~~S~~EAcrrY~LS~eEf~~W~~   72 (101)
T 2oa4_A           13 VTLPDGSIMTRADLPPA-NTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVS   72 (101)
T ss_dssp             EECSSSCEEETTSSCCS-CCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHH
T ss_pred             EECCCCCCCCCCCCCCC-CCEEECHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             46899981301129996-5603269999999999983845799999883999999999999


No 9  
>1xrd_A LH-1, light-harvesting protein B-880, alpha chain; membrane spanning helix, pigment binding, photosynthesis, membrane protein; NMR {Rhodospirillum rubrum} SCOP: f.3.1.1
Probab=17.43  E-value=43  Score=12.88  Aligned_cols=19  Identities=21%  Similarity=0.621  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999998717
Q gi|254780549|r    7 LAISMILHVMFLLLLYFNF   25 (271)
Q Consensus         7 L~lSi~lH~~li~l~~f~~   25 (271)
                      +++.+.+|.+++.--.|||
T Consensus        22 ~~LAl~IHfiLLSt~rfNW   40 (52)
T 1xrd_A           22 FVLALLIHFILLSTERFNW   40 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCC
T ss_conf             9999999999744676565


No 10 
>3kfu_F Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; ASPRS, gatcab, ATP-binding, aminoacyl-tRNA synthetase, ligas nucleotide-binding, protein biosynthesis, ligase-RNA comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Probab=15.48  E-value=48  Score=12.60  Aligned_cols=78  Identities=15%  Similarity=0.073  Sum_probs=0.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCC-HHHHHHHHHHHHHHH
Q ss_conf             1110000000078999999999962254656555375299999998799818533564058886-058999999999999
Q gi|254780549|r  165 VEKSSRKRIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGT-ELVRRMLRENARKAV  243 (271)
Q Consensus       165 ~~~~~~~~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~-~~~~~~~~~~a~rAi  243 (271)
                      ..+.-........|...|+.-++-.-.-..++.. +.++|.++|++.+.|.-.|.++-.++-+| ....++..--+.|-+
T Consensus       149 TePd~~s~~eA~~~~~~L~~ilr~lgvsd~~mee-GslR~DvNVSir~~g~~~g~RvEiKNlNS~~~v~kAIeyEi~RQ~  227 (466)
T 3kfu_F          149 TEPDLKTPEEARLFLQRIQALVQTLGISDASPEE-GKLRADVNVSVRRVGEPLGTKVEIKNLNSFKSVQRALEYEIRRQT  227 (466)
T ss_dssp             ECTTBCCHHHHHHHHHHHHHHHHHHTSBCCCGGG-TCEEEEEEEEECCSSSSCCCCEEEEEECCHHHHHHHHHHHHHHHH
T ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCCCCCCEEECCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf             0478688999999999999999970877675113-614146505641478877765775166554689999999999999


Done!