Query         gi|254780929|ref|YP_003065342.1| hypothetical protein CLIBASIA_04140 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 408
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 33803
Date          Wed Jun  1 19:59:35 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780929.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2ww8_A RRGA, cell WALL surfac  95.8    0.02 5.8E-07   37.2   5.2   59  326-393   202-267 (269)
  2 >1x9d_A Endoplasmic reticulum   41.5     6.4 0.00019   19.3   0.0   63  295-366   155-227 (305)
  3 >1pp9_C Cytochrome B; cytochro  39.5       5 0.00015   20.0  -0.8   55  206-278    33-87  (101)
  4 >3cx5_C Cytochrome B-C1 comple  35.8     7.4 0.00022   18.9  -0.4   53  205-275    33-85  (106)
  5 >3kp1_E D-ornithine aminomutas  31.7      13 0.00039   17.0   0.3   38   34-78     20-57  (76)
  6 >2ri9_A Mannosyl-oligosacchari  26.0      15 0.00045   16.6  -0.2   78  285-375    19-98  (100)
  7 >2jhn_A ALKA, 3-methyladenine   25.7      39  0.0011   13.7   2.3   33   50-82      6-38  (61)
  8 >3kmp_A SMAD1-MH1; protein-DNA  24.6      20 0.00059   15.8   0.2   15  220-234    94-108 (110)
  9 >2v6z_M DNA polymerase epsilon  23.0      41  0.0012   13.5   1.6   18  315-332    81-98  (99)
 10 >2qjy_A Cytochrome B; cytochro  22.8      18 0.00054   16.1  -0.3   49  207-273    35-83  (104)
 11 >3imo_A Integron cassette prot  22.7      44  0.0013   13.3   2.1   16  379-394    46-61  (133)
 12 >2odp_A Complement C2; C3/C5 c  21.8      46  0.0014   13.2   2.6   55  339-393   156-213 (224)

No 1  
>>2ww8_A RRGA, cell WALL surface anchor family protein; IGG, pilus, CNA_B, adhesin, integrin, cell adhesion; HET: EPE; 1.90A {Streptococcus pneumoniae} (A:221-279,A:318-447,A:506-585)
Probab=95.76  E-value=0.02  Score=37.21  Aligned_cols=59  Identities=19%  Similarity=0.300  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC-------HHHHHHHHCCCCHHEEEECCCCCHHHHHHHHHHHH
Q ss_conf             999998599887511476416899740488742-------02678763059032044258765344789877777
Q gi|254780929|r  326 EKVLQDCHYMHKRHRTGRDAITIFSVGFSPDQD-------TRYTLRQCASDPSKYYEINSDENVMPIAKSLARNV  393 (408)
Q Consensus       326 ekvlqdchymhkrhrtgrdaitifsvgfspdqd-------trytlrqcasdpskyyeinsdenvmpiakslarnv  393 (408)
                      ...+..|-.+..      ..|+||+|||..+-+       .++-|+.|||+|+.||+...   .-.+-+++|+..
T Consensus       202 ~~~~~~c~~~k~------~~i~i~ti~~~~~~~~~~~~~~~~~~l~~cas~~~~y~~~~~---~~~~f~~ia~~~  267 (269)
T 2ww8_A          202 PTRWYYNGNIAP------DGYDVFTVGIGINGDPGTDEATATSFMQSISSKPENYTNVTD---TTKILEQLNRYF  267 (269)
T ss_dssp             HHHHHHHHHTGG------GCCEEEEEEESCCCTTTSCHHHHHHHHHHTSSSGGGEEEESS---GGGHHHHHHHHH
T ss_pred             CEEEEEEEECCC------CCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCEEEECC---CCCEECCCCCCC
T ss_conf             305788752046------763035776771564210023430577566116653264056---651111335541


No 2  
>>1x9d_A Endoplasmic reticulum mannosyl-oligosaccharide 1, 2-alpha-mannosidase; substrate analogue, glycosyl hydrolase; HET: SMD; 1.41A {Homo sapiens} (A:1-125,A:337-516)
Probab=41.51  E-value=6.4  Score=19.28  Aligned_cols=63  Identities=25%  Similarity=0.434  Sum_probs=38.5

Q ss_pred             CCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCC----------CCCHHHHHH
Q ss_conf             3446766770799997345100333028999999998599887511476416899740488----------742026787
Q gi|254780929|r  295 CFPHGASQNKYMLMLAIGNQLSRSSVEKEKIEKVLQDCHYMHKRHRTGRDAITIFSVGFSP----------DQDTRYTLR  364 (408)
Q Consensus       295 cfphgasqnkymlmlaignqlsrssvekekiekvlqdchymhkrhrtgrdaitifsvgfsp----------dqdtrytlr  364 (408)
                      ||--|        |+|+|.++....-.-+--++....|+.+-++..||--. .+|+....+          ..|.+|-||
T Consensus       155 cF~gG--------~~aLg~~~~~~~~~l~~a~~l~~~c~~~y~~~~tGl~P-E~~~~~~~~~~~~~~~~~~~~~~~y~LR  225 (305)
T 1x9d_A          155 CFLPG--------TLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSP-EIVHFNLYPQPGRRDVEVKPADRHNLLR  225 (305)
T ss_dssp             GHHHH--------HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHTSTTSCCC-SEEECCSSCCTTCCSCBCCGGGCCBCCC
T ss_pred             HHHHH--------HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC-EEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             87677--------88760124787679999999999999988624167986-5665346687555666557345577889


Q ss_pred             HH
Q ss_conf             63
Q gi|254780929|r  365 QC  366 (408)
Q Consensus       365 qc  366 (408)
                      --
T Consensus       226 PE  227 (305)
T 1x9d_A          226 PE  227 (305)
T ss_dssp             CH
T ss_pred             CH
T ss_conf             22


No 3  
>>1pp9_C Cytochrome B; cytochrome BC1, membrane protein, heme protein, rieske iron sulfur protein, cytochrome B; HET: BHG HEM HEC SMA UQ CDL PEE; 2.10A {Bos taurus} (C:108-208)
Probab=39.46  E-value=5  Score=20.05  Aligned_cols=55  Identities=36%  Similarity=0.582  Sum_probs=39.5

Q ss_pred             HCHHHHHHHHHHHCCCCCEECCCCHHHHHHHEEEEEEEEEECCCCCHHHHHCCCCCCCHHCCHHHHHHHHHHH
Q ss_conf             0522578988761874320027202344341221125786258621256541864211000608999888741
Q gi|254780929|r  206 LNRNTLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPYSFIKNVFDM  278 (408)
Q Consensus       206 lnrntlvknflsqipyknfcmapyhyssilywavgtltysvdnktttreyykdpyyatwdhfpysfiknvfdm  278 (408)
                      .=..|...|.||.|||-.        ..+..|.-|.  +||||.|-||-+-        -||-..||---..|
T Consensus        33 FWGAtVITNLlSAiPYiG--------~~lV~WiWGG--fsvdnaTLtRFF~--------fHF~lPFii~~~~~   87 (101)
T 1pp9_C           33 FWGATVITNLLSAIPYIG--------TNLVEWIWGG--FSVDKATLTRFFA--------FHFILPFIIMAIAM   87 (101)
T ss_dssp             HHHHHHHHGGGGGSTTTH--------HHHHHHHHTS--SSSCHHHHHHHHH--------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCC--------CCHHHHEECC--CCCCCCHHHHHHH--------HHHHHHHHHHHHHH
T ss_conf             889999999898756587--------5423010357--5787412778999--------99999999999999


No 4  
>>3cx5_C Cytochrome B-C1 complex subunit 8; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} (C:108-213)
Probab=35.79  E-value=7.4  Score=18.86  Aligned_cols=53  Identities=30%  Similarity=0.491  Sum_probs=38.8

Q ss_pred             HHCHHHHHHHHHHHCCCCCEECCCCHHHHHHHEEEEEEEEEECCCCCHHHHHCCCCCCCHHCCHHHHHHHH
Q ss_conf             70522578988761874320027202344341221125786258621256541864211000608999888
Q gi|254780929|r  205 YLNRNTLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPYSFIKNV  275 (408)
Q Consensus       205 ylnrntlvknflsqipyknfcmapyhyssilywavgtltysvdnktttreyykdpyyatwdhfpysfiknv  275 (408)
                      -.=..|...|++|.|||..        .+|..|.-|-  +||||.|-+|-|-        -||-..|+--.
T Consensus        33 SfWgATVITNL~SaiP~iG--------~~iV~wlWGG--fsV~n~TL~RFfs--------lHfllPFii~~   85 (106)
T 3cx5_C           33 SHWGATVITNLFSAIPFVG--------NDIVSWLWGG--FSVSNPTIQRFFA--------LHYLVPFIIAA   85 (106)
T ss_dssp             HHHHHHHHHHGGGGSTTTH--------HHHHHHHHTS--SSSCHHHHHHHHH--------HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCC--------CCCHHHHCCC--CCCCCCHHHHHHH--------HHHHHHHHHHH
T ss_conf             2249999998998728273--------0019886188--7789614759999--------99998999999


No 5  
>>3kp1_E D-ornithine aminomutase S component; 5 aminomutase (OAM); HET: PLP B12 5AD; 2.01A {Clostridium sticklandii} PDB: 3kow_E* 3koy_E* 3koz_E* 3kp0_E* 3kox_E* (E:46-121)
Probab=31.67  E-value=13  Score=17.03  Aligned_cols=38  Identities=37%  Similarity=0.575  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHH
Q ss_conf             999999876677776667899998776520683323667741223
Q gi|254780929|r   34 VAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPKNLYDLREAGRD   78 (408)
Q Consensus        34 vaivdvvvdqvtvmqktawlqevldhviyrtspknlydlreagrd   78 (408)
                      -+||+-|++. -.|-|-|      .|+.||-+.+.--|.||||+.
T Consensus        20 k~iVe~v~~~-gLlgKGA------GhvV~kiak~~~i~i~eAG~~   57 (76)
T 3kp1_E           20 KAIVDKTMDR-GLMGKGA------GHIVYKIAKEKNISVREAGLA   57 (76)
T ss_dssp             HHHHHHHHHT-TCGGGCH------HHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHH-CCCCCCC------CHHHHHHHHHCCCCHHHHHHH
T ss_conf             9999999980-5445775------532235797629988999999


No 6  
>>2ri9_A Mannosyl-oligosaccharide alpha-1,2-mannosidase; alternative conformations, modulation of activity, glycoprotein, glycosidase, hydrolase; HET: NAG NDG MAN MMA; 1.95A {Penicillium citrinum} (A:267-366)
Probab=25.99  E-value=15  Score=16.62  Aligned_cols=78  Identities=13%  Similarity=0.211  Sum_probs=49.9

Q ss_pred             CCEEEECCCC--CCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHH
Q ss_conf             8426413674--34467667707999973451003330289999999985998875114764168997404887420267
Q gi|254780929|r  285 DGQVLTNTNH--CFPHGASQNKYMLMLAIGNQLSRSSVEKEKIEKVLQDCHYMHKRHRTGRDAITIFSVGFSPDQDTRYT  362 (408)
Q Consensus       285 dgqvltntnh--cfphgasqnkymlmlaignqlsrssvekekiekvlqdchymhkrhrtgrdaitifsvgfspdqdtryt  362 (408)
                      +|..-....|  ||--|        |+|+|-.+....-.-+--++....|+.|..+-.||--.- ||  .|.|+++..  
T Consensus        19 ~~~~~p~~~HL~CF~gG--------m~aLGa~~~~~~~~l~~a~~Lt~tC~~~Y~~t~TGl~PE-~~--~f~~~~~~~--   85 (100)
T 2ri9_A           19 NRNYDLSSQHLTCFDGG--------SFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPD-SW--GWDPKKVPS--   85 (100)
T ss_dssp             TTEEECEEETGGGGHHH--------HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHTSSSSCCCS-EE--ECCTTCCCG--
T ss_pred             CCCCCCCCCHHHHHHCH--------HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-EE--CCCCCCCCC--
T ss_conf             88777640058675042--------666266233507789989999999999999747624784-21--466545677--


Q ss_pred             HHHHCCCCHHEEE
Q ss_conf             8763059032044
Q gi|254780929|r  363 LRQCASDPSKYYE  375 (408)
Q Consensus       363 lrqcasdpskyye  375 (408)
                      ...|--++..||-
T Consensus        86 ~~~~~~~~~~~yi   98 (100)
T 2ri9_A           86 DQKEFYEKAGFYI   98 (100)
T ss_dssp             GGHHHHHHHSCEE
T ss_pred             CCCHHCCCCCCEE
T ss_conf             5200034677154


No 7  
>>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A (A:235-295)
Probab=25.68  E-value=39  Score=13.71  Aligned_cols=33  Identities=15%  Similarity=0.286  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHH
Q ss_conf             678999987765206833236677412235789
Q gi|254780929|r   50 TAWLQEVLDHVIYRTSPKNLYDLREAGRDNFIR   82 (408)
Q Consensus        50 tawlqevldhviyrtspknlydlreagrdnfir   82 (408)
                      |.|...++.+.-......+.-++++.+|+.|-+
T Consensus         6 tVWIkrim~~~Y~~~~~~s~~~i~~f~r~~FG~   38 (61)
T 2jhn_A            6 DLGVRRAVSRLYFNGEIQSAEKVREIARERFGR   38 (61)
T ss_dssp             CHHHHHHHHHHHSTTCCCCHHHHHHHHHHHTGG
T ss_pred             CHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
T ss_conf             799999999970888899999999999875666


No 8  
>>3kmp_A SMAD1-MH1; protein-DNA complex, SMAD1, SBE DNA, MH1 domain, beta hairpin, nucleus, transcription; 2.70A {Mus musculus} (A:15-124)
Probab=24.58  E-value=20  Score=15.77  Aligned_cols=15  Identities=40%  Similarity=1.061  Sum_probs=11.5

Q ss_pred             CCCCEECCCCHHHHH
Q ss_conf             743200272023443
Q gi|254780929|r  220 PYKNFCMAPYHYSSI  234 (408)
Q Consensus       220 pyknfcmapyhyssi  234 (408)
                      .....|.-|||||-|
T Consensus        94 ~~~~VC~NPyHy~Rv  108 (110)
T 3kmp_A           94 KQKEVCINPYHYKRV  108 (110)
T ss_dssp             CCSEEECCGGGEEEC
T ss_pred             CCCEEEECCCCHHHC
T ss_conf             998088487217540


No 9  
>>2v6z_M DNA polymerase epsilon subunit 2; DNA replication, DPOE2, transferase, AAA protein family; HET: DNA; NMR {Homo sapiens} (M:)
Probab=22.98  E-value=41  Score=13.50  Aligned_cols=18  Identities=28%  Similarity=0.503  Sum_probs=8.1

Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             003330289999999985
Q gi|254780929|r  315 LSRSSVEKEKIEKVLQDC  332 (408)
Q Consensus       315 lsrssvekekiekvlqdc  332 (408)
                      |+-+-||++-||+.+|+|
T Consensus        81 Lss~~Ier~~iE~AVkEC   98 (99)
T 2v6z_M           81 LSSNMIERSVVEAAVQES   98 (99)
T ss_dssp             CSSSEECHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHC
T ss_conf             981040399999999862


No 10 
>>2qjy_A Cytochrome B; cytochrome B, 8 TM helixces cytochrome C1, 1 C-TERM TM helix rieske; HET: BGL HEM SMA LOP UQ2; 2.40A {Rhodobacter sphaeroides} PDB: 2fyn_A* 2qjk_A* 2qjp_A* 1zrt_C* (A:123-226)
Probab=22.81  E-value=18  Score=16.05  Aligned_cols=49  Identities=29%  Similarity=0.409  Sum_probs=36.3

Q ss_pred             CHHHHHHHHHHHCCCCCEECCCCHHHHHHHEEEEEEEEEECCCCCHHHHHCCCCCCCHHCCHHHHHH
Q ss_conf             5225789887618743200272023443412211257862586212565418642110006089998
Q gi|254780929|r  207 NRNTLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPYSFIK  273 (408)
Q Consensus       207 nrntlvknflsqipyknfcmapyhyssilywavgtltysvdnktttreyykdpyyatwdhfpysfik  273 (408)
                      =..|...|++|.|||-        -.+|..|--|-  |||||.|-+|-+-        -||-..||-
T Consensus        35 WgAtVITnL~saiP~i--------G~~iv~wlwGG--fsV~n~TLnRFFs--------lH~llPfii   83 (104)
T 2qjy_A           35 WGATVITGLFGAIPGI--------GHSIQTWLLGG--PAVDNATLNRFFS--------LHYLLPFVI   83 (104)
T ss_dssp             HHHHHHHHHHHTSTTT--------HHHHHHHHHTS--SSSCHHHHHHHHH--------HHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCC--------CCCHHHEEECC--CCCCCCCHHHHHH--------HHHHHHHHH
T ss_conf             4889998764116868--------87401012365--5578874227899--------999889999


No 11 
>>3imo_A Integron cassette protein; novel, integron protein, argentinean O139 strain, unknown function; 1.80A {Vibrio cholerae O139} (A:)
Probab=22.73  E-value=44  Score=13.33  Aligned_cols=16  Identities=38%  Similarity=0.418  Sum_probs=10.3

Q ss_pred             CCCHHHHHHHHHHHHH
Q ss_conf             7653447898777778
Q gi|254780929|r  379 DENVMPIAKSLARNVI  394 (408)
Q Consensus       379 denvmpiakslarnvi  394 (408)
                      -+||||||+.|+-.|+
T Consensus        46 ~g~V~~IalAL~gAIl   61 (133)
T 3imo_A           46 AGNVEEIALALAGAIL   61 (133)
T ss_dssp             CGGGHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHEE
T ss_conf             1542178998611215


No 12 
>>2odp_A Complement C2; C3/C5 convertase, complement serine protease, human complement system, glycoprotein, SP, VWFA, hydrolase; HET: NAG; 1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A* (A:1-224)
Probab=21.80  E-value=46  Score=13.20  Aligned_cols=55  Identities=9%  Similarity=0.191  Sum_probs=37.4

Q ss_pred             HCCCCCEEEEEEEECCCCCCHHHHHHHHCCCCH---HEEEECCCCCHHHHHHHHHHHH
Q ss_conf             114764168997404887420267876305903---2044258765344789877777
Q gi|254780929|r  339 HRTGRDAITIFSVGFSPDQDTRYTLRQCASDPS---KYYEINSDENVMPIAKSLARNV  393 (408)
Q Consensus       339 hrtgrdaitifsvgfspdqdtrytlrqcasdps---kyyeinsdenvmpiakslarnv  393 (408)
                      -+.....|.||.+|+..+....-.|++.|+.+.   .|+.+.+....-.+...+...+
T Consensus       156 ~~~~~~gi~i~~i~ig~~~~~~~~l~~ia~~~~g~~~~~~~~~~~~l~~~~~~i~~~i  213 (224)
T 2odp_A          156 NQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVS  213 (224)
T ss_dssp             CSTTGGGEEEEEEEESSSCCCHHHHHHHSCCCTTCCCEEEESSHHHHHHHHHHHEECT
T ss_pred             HHHHHCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHHCCC
T ss_conf             9998669779999505865599999998638898724999589899999998750221


Done!