Query         gi|254780982|ref|YP_003065395.1| putative homoserine/homoserine lactoneefflux protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 202
No_of_seqs    115 out of 3554
Neff          8.3 
Searched_HMMs 33803
Date          Wed Jun  1 21:18:29 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780982.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1h2s_A Sensory rhodopsin II;   20.1      46  0.0014   12.7   9.5   28  150-177   194-221 (225)
  2 >3ffr_A Phosphoserine aminotra  12.4      75  0.0022   11.6   2.1   21   18-38      8-28  (111)
  3 >1jb0_L Photosystem 1 reaction  12.0      78  0.0023   11.6   7.6   87   44-130    12-101 (116)
  4 >1rzh_L Reaction center protei  11.7      80  0.0024   11.5   3.1   79   57-135    44-128 (167)
  5 >1xio_A Anabaena sensory rhodo  10.0      92  0.0027   11.2  12.1   23  153-175   202-224 (261)
  6 >3ddl_A Xanthorhodopsin; carot   7.8 1.2E+02  0.0034   10.7  12.6   22  153-174   232-253 (273)
  7 >2yuj_A Ubiquitin fusion degra   6.8 1.3E+02  0.0038   10.5   0.8   12  116-127    14-25  (75)
  8 >3ixz_A Potassium-transporting   6.6 1.3E+02  0.0039   10.4   8.6   78   18-95     32-112 (140)
  9 >2zxe_G FXYD10, phospholemman-   6.0 1.4E+02  0.0043   10.2   3.7   20   73-92     21-40  (74)
 10 >1zc1_A Ubiquitin fusion degra   5.9 1.5E+02  0.0043   10.2   0.6   12  116-127    13-24  (87)

No 1  
>>1h2s_A Sensory rhodopsin II; membrane protein, menbrane protein complex, signal transduction; HET: BOG RET; 1.93A {Natronomonas pharaonis} (A:)
Probab=20.09  E-value=46  Score=12.68  Aligned_cols=28  Identities=14%  Similarity=0.222  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999605
Q gi|254780982|r  150 SLTMVSVDAMVLMTFSLICSKLRTLFSS  177 (202)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (202)
                      .......+......+.....+.++...+
T Consensus       194 ~i~y~ilDv~~K~~Fg~~ll~~~~~~~~  221 (225)
T 1h2s_A          194 VALIVYLDLVTKVGFGFIALDAAATLRA  221 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             8999999999999999999999972610


No 2  
>>3ffr_A Phosphoserine aminotransferase SERC; YP_677612.1, structural genomics, joint center for structural genomics, JCSG; HET: LLP MSE P33; 1.75A {Cytophaga hutchinsonii atcc 33406} (A:1-13,A:266-363)
Probab=12.41  E-value=75  Score=11.63  Aligned_cols=21  Identities=19%  Similarity=0.199  Sum_probs=10.6

Q ss_pred             HCCCHHHHHHHHHHHHHHHHH
Q ss_conf             489947999999998310288
Q gi|254780982|r   18 SAPGPGNILTINHALQHGWRP   38 (202)
Q Consensus        18 ~~PGP~~~~~i~~~~~~G~~~   38 (202)
                      .+|||++..--.+....-.|+
T Consensus         8 ~~~~~~~~~~Rh~~~a~~lr~   28 (111)
T 3ffr_A            8 FTPGPSGIRKQTEEKAALINT   28 (111)
T ss_dssp             ECSSSCHHHHHHHHHHHHHHH
T ss_pred             ECCCCCHHHHHHHHHHHHHHH
T ss_conf             017992589999999999999


No 3  
>>1jb0_L Photosystem 1 reaction centre subunit XI; membrane protein, multiprotein-pigment complex, photosynthesis; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} (L:39-154)
Probab=12.01  E-value=78  Score=11.56  Aligned_cols=87  Identities=17%  Similarity=0.157  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             999977669999999977755307478886768999999999999741246---77871013567888999987898632
Q gi|254780982|r   44 LGQETAVFIIMLSITMGTKFLSQLAYTMLIIKFLGVAWLIYSAWSAWYSPF---NDLPLGEIPLSSKSKLFVKGFITDIT  120 (202)
Q Consensus        44 ~G~~~g~~~~~~~~~~g~~~l~~~~~~~~~l~~~G~~yL~~lg~~~~~~~~---~~~~~~~~~~~~~~~~f~~G~~v~l~  120 (202)
                      +|++-|+.++-=.+.+|=--=.+....--.+.-+|...++-.+..++-...   .+.+.++-..+..++.|..||++.-.
T Consensus        12 iGmAHGYfL~GPf~~lGPLRnt~~a~laGllsaiglv~IlT~~Ls~Yg~~s~~~~~~~~d~l~t~~GW~~Ft~GF~iGg~   91 (116)
T 1jb0_L           12 VGMAHGYFLIGPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQFTAGFFVGAM   91 (116)
T ss_dssp             HHHHHHHHHTHHHHHHSTTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCSSCGGGSHHHHHHHHHHHHHHHH
T ss_pred             HHHHCEEEEECHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             72320001556377617776736889989999999999999999996167778899982102270069887202132125


Q ss_pred             CCHHHHHHHH
Q ss_conf             7425788786
Q gi|254780982|r  121 NGKAWAFFMA  130 (202)
Q Consensus       121 NPka~~f~~~  130 (202)
                      ---.+.+++.
T Consensus        92 GGa~~Ay~Ll  101 (116)
T 1jb0_L           92 GSAFVAFFLL  101 (116)
T ss_dssp             HHHHHHHHHH
T ss_pred             CHHHHHHHHH
T ss_conf             2899999999


No 4  
>>1rzh_L Reaction center protein L chain; bacterial photosynthesis, proton transfer pathway, revertant, X-RAY crystallography; HET: BCL BPH BPB U10 SPO LDA HTO CDL; 1.80A {Rhodobacter sphaeroides} (L:115-281)
Probab=11.66  E-value=80  Score=11.50  Aligned_cols=79  Identities=11%  Similarity=0.075  Sum_probs=46.3

Q ss_pred             HHHHHH--HHHCCH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHH-H--HHHHHHCCCHHHHHHHH
Q ss_conf             999777--553074-78886768999999999999741246778710135678889999-8--78986327425788786
Q gi|254780982|r   57 ITMGTK--FLSQLA-YTMLIIKFLGVAWLIYSAWSAWYSPFNDLPLGEIPLSSKSKLFV-K--GFITDITNGKAWAFFMA  130 (202)
Q Consensus        57 ~~~g~~--~l~~~~-~~~~~l~~~G~~yL~~lg~~~~~~~~~~~~~~~~~~~~~~~~f~-~--G~~v~l~NPka~~f~~~  130 (202)
                      ..++..  -+..+| ....+--.+|+..+.-+-=....+..+..+++|.++......|. +  |.-++..|-+-+.++++
T Consensus        44 ~~~~~~~~N~~ynPfHml~i~f~fg~al~~AmHG~~Vls~~~~g~~eE~~~~~~~~tffr~~ig~~~~~~~ih~l~~flA  123 (167)
T 1rzh_L           44 SNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHENTFFRDLVGYSIGTLGIHRLGLLLS  123 (167)
T ss_dssp             HHHHHTTSCGGGCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSTTCCCCCHHHHHHHHHHHHSBCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHCEEEECHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCEECCHHHCCCHHHHCEEECCCCCHHHHHHHHHH
T ss_conf             77765613256676998889998622999986335377302789980505754412132111001036306699999999


Q ss_pred             HHHHH
Q ss_conf             66765
Q gi|254780982|r  131 MVPAY  135 (202)
Q Consensus       131 ~~~~f  135 (202)
                      +.|.+
T Consensus       124 ~~~~~  128 (167)
T 1rzh_L          124 LSAVF  128 (167)
T ss_dssp             HHHHH
T ss_pred             HHHHH
T ss_conf             99999


No 5  
>>1xio_A Anabaena sensory rhodopsin; signaling protein, photoreceptor; HET: RET PEE; 2.00A {Nostoc SP} (A:)
Probab=10.03  E-value=92  Score=11.20  Aligned_cols=23  Identities=9%  Similarity=-0.015  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999996
Q gi|254780982|r  153 MVSVDAMVLMTFSLICSKLRTLF  175 (202)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~  175 (202)
                      +...+......+....-...+..
T Consensus       202 y~ilDi~~K~~Fg~~ll~~~~~~  224 (261)
T 1xio_A          202 FCLLPFFSKVGFSFLDLHGLRNL  224 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999999999999999997741


No 6  
>>3ddl_A Xanthorhodopsin; carotenoid, ION pump, light-harvesting, antenna, retinal, transport protein; HET: SXN UNL RET PX4 PCW; 1.90A {Salinibacter ruber} (A:)
Probab=7.76  E-value=1.2e+02  Score=10.70  Aligned_cols=22  Identities=5%  Similarity=0.167  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999
Q gi|254780982|r  153 MVSVDAMVLMTFSLICSKLRTL  174 (202)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~  174 (202)
                      +...+......+.......+++
T Consensus       232 y~ilDi~aK~~fg~~l~~~~~~  253 (273)
T 3ddl_A          232 YTIADVLAKAGYGVLIYNIAKA  253 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999998


No 7  
>>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens} (A:116-190)
Probab=6.80  E-value=1.3e+02  Score=10.45  Aligned_cols=12  Identities=50%  Similarity=0.307  Sum_probs=8.7

Q ss_pred             HHHHCCCHHHHH
Q ss_conf             986327425788
Q gi|254780982|r  116 ITDITNGKAWAF  127 (202)
Q Consensus       116 ~v~l~NPka~~f  127 (202)
                      +.++.|||+++=
T Consensus        14 F~~i~npkavLE   25 (75)
T 2yuj_A           14 FLDITNPKAVLE   25 (75)
T ss_dssp             HHHSSCHHHHHH
T ss_pred             CCCCCCHHHHHH
T ss_conf             535664899999


No 8  
>>3ixz_A Potassium-transporting ATPase alpha; ION pump, H+, K+-ATPase, P-type ATPase, membrane protein, hydrolase, aluminium fluoride, ATP-binding; 6.50A {Sus scrofa} PDB: 1iwc_A 1iwf_A (A:344-380,A:764-866)
Probab=6.58  E-value=1.3e+02  Score=10.39  Aligned_cols=78  Identities=17%  Similarity=0.111  Sum_probs=38.3

Q ss_pred             HCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH-HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             489947999999998310288--9999999997766999999-9977755307478886768999999999999741246
Q gi|254780982|r   18 SAPGPGNILTINHALQHGWRP--NKILILGQETAVFIIMLSI-TMGTKFLSQLAYTMLIIKFLGVAWLIYSAWSAWYSPF   94 (202)
Q Consensus        18 ~~PGP~~~~~i~~~~~~G~~~--~~~~~~G~~~g~~~~~~~~-~~g~~~l~~~~~~~~~l~~~G~~yL~~lg~~~~~~~~   94 (202)
                      =+-|-.|+..+-.+++.||+-  .++-.+...+...+..... ..+.-.-...|-.-.-+-|+....-..-++..-..++
T Consensus        32 etlG~vnFssIv~aI~eGR~i~~Nikk~i~~~Ls~ni~~vl~~l~~~i~~~~~pltp~qiL~inli~d~lpalaL~~e~~  111 (140)
T 3ixz_A           32 ETLGSTNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPYLIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKA  111 (140)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             88615888899999999999999999999999999999999999999983311368999999999999999998506888


Q ss_pred             C
Q ss_conf             7
Q gi|254780982|r   95 N   95 (202)
Q Consensus        95 ~   95 (202)
                      .
T Consensus       112 ~  112 (140)
T 3ixz_A          112 E  112 (140)
T ss_pred             C
T ss_conf             8


No 9  
>>2zxe_G FXYD10, phospholemman-like protein; membrane protein, ION pump, ATPase, K+ binding, haloacid dehydrogenease superfamily, phosphate analogue; HET: CLR NAG NDG; 2.40A {Squalus acanthias} PDB: 3a3y_G* (G:)
Probab=5.98  E-value=1.4e+02  Score=10.21  Aligned_cols=20  Identities=10%  Similarity=0.052  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHC
Q ss_conf             67689999999999997412
Q gi|254780982|r   73 IIKFLGVAWLIYSAWSAWYS   92 (202)
Q Consensus        73 ~l~~~G~~yL~~lg~~~~~~   92 (202)
                      +-.++-+..|.-+|+-++.+
T Consensus        21 igGLi~A~vLfi~GI~iilS   40 (74)
T 2zxe_G           21 VVGLIVAAVLCVIGIIILLA   40 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHC
T ss_conf             20069999999999999993


No 10 
>>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae} (A:122-208)
Probab=5.94  E-value=1.5e+02  Score=10.20  Aligned_cols=12  Identities=33%  Similarity=0.235  Sum_probs=8.3

Q ss_pred             HHHHCCCHHHHH
Q ss_conf             986327425788
Q gi|254780982|r  116 ITDITNGKAWAF  127 (202)
Q Consensus       116 ~v~l~NPka~~f  127 (202)
                      +.++.|||+++=
T Consensus        13 F~~i~npKavLE   24 (87)
T 1zc1_A           13 FLDISDPKAVLE   24 (87)
T ss_dssp             HHTSSCHHHHHH
T ss_pred             CCCCCCHHHHHH
T ss_conf             446566899999


Done!