Query         gi|254780838|ref|YP_003065251.1| hypothetical protein CLIBASIA_03665 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 103
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 00:06:10 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780838.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG4528 consensus               26.7      51  0.0013   15.5   2.3   41    1-47     85-125 (168)
  2 pfam06706 CTV_P6 Citrus triste  17.4      92  0.0024   14.1   2.9   23    1-26      1-23  (51)
  3 pfam05108 DUF690 Protein of un  17.0      87  0.0022   14.2   1.8   39    2-40     42-88  (481)
  4 PHA01757 hypothetical protein   16.6      97  0.0025   14.0   2.3   35    3-37      8-42  (98)
  5 pfam09348 DUF1990 Domain of un  16.1      64  0.0016   14.9   1.0   24   20-43    104-128 (158)
  6 TIGR01770 NDH_I_N proton-trans  15.2 1.1E+02  0.0027   13.8   3.2   34    4-38    174-209 (491)
  7 PRK12705 hypothetical protein;  13.2      86  0.0022   14.3   1.0   15   64-80    293-307 (485)
  8 COG1190 LysU Lysyl-tRNA synthe  13.2      67  0.0017   14.9   0.4   44   53-97    167-214 (502)
  9 TIGR00048 TIGR00048 radical SA  13.1      62  0.0016   15.0   0.2   22   52-73    311-332 (378)
 10 cd00034 ChSh Chromo Shadow Dom  12.8 1.2E+02  0.0032   13.4   1.9   35   28-69      7-42  (54)

No 1  
>KOG4528 consensus
Probab=26.66  E-value=51  Score=15.50  Aligned_cols=41  Identities=39%  Similarity=0.442  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEE
Q ss_conf             90579999999996336899999987620013661889999998760
Q gi|254780838|r    1 MNSLLFGFLAFLYAYGGSVVFSLFESFFVEKEDGELFIRIMVFEISW   47 (103)
Q Consensus         1 mnsllfgflaflyayggsvvfslfesffvekedgelfirimvfeisw   47 (103)
                      |.+|||-||.-+|-     .|| -|.|||.|+---|-+...+|||+-
T Consensus        85 l~gLLfhFlDe~l~-----~f~-aE~~~V~k~v~ilr~d~~~fei~~  125 (168)
T KOG4528          85 LQGLLFHFLDEWLY-----KFS-AEPFFVPKKVEILRFDQRNFEIAV  125 (168)
T ss_pred             HHHHHHHHHHHHHH-----HCC-CCCEEEEEEEEEEECCCEEEEEEE
T ss_conf             88899999999974-----246-685454424555543441368999


No 2  
>pfam06706 CTV_P6 Citrus tristeza virus 6-kDa protein. This family consists of several Citrus tristeza virus (CTV) 6-kDa, 51 residue long hydrophobic (P6) proteins. The function of this family is unknown.
Probab=17.38  E-value=92  Score=14.08  Aligned_cols=23  Identities=43%  Similarity=0.842  Sum_probs=17.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             90579999999996336899999987
Q gi|254780838|r    1 MNSLLFGFLAFLYAYGGSVVFSLFES   26 (103)
Q Consensus         1 mnsllfgflaflyayggsvvfslfes   26 (103)
                      |....-|||.||-   |-.||+-|..
T Consensus         1 mdcviqgfltflv---giavf~afa~   23 (51)
T pfam06706         1 MDCVIQGFLTFLV---GIAVFCAFAE   23 (51)
T ss_pred             CCHHHHHHHHHHH---HHHHHHHHHH
T ss_conf             9314788999999---9999998630


No 3  
>pfam05108 DUF690 Protein of unknown function (DUF690). This family contains several uncharacterized bacterial membrane proteins.
Probab=16.97  E-value=87  Score=14.22  Aligned_cols=39  Identities=21%  Similarity=0.577  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH--------HHHHCCCCCEEEEEE
Q ss_conf             057999999999633689999998--------762001366188999
Q gi|254780838|r    2 NSLLFGFLAFLYAYGGSVVFSLFE--------SFFVEKEDGELFIRI   40 (103)
Q Consensus         2 nsllfgflaflyayggsvvfslfe--------sffvekedgelfiri   40 (103)
                      -++++|.+.-.-.-+|..++.+|.        ...++||.|.+|+++
T Consensus        42 ra~~~G~vlavl~~aG~~v~gl~~P~~~~g~~~iVv~keTGa~YV~~   88 (481)
T pfam05108        42 RSVALGVVLAIVALIGAALLALIKPQGALGQSAILADRDTGALYVRV   88 (481)
T ss_pred             HHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCEEEECCCCCEEEEE
T ss_conf             24899999999999998560366057988987679967887479998


No 4  
>PHA01757 hypothetical protein
Probab=16.60  E-value=97  Score=13.97  Aligned_cols=35  Identities=29%  Similarity=0.462  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             57999999999633689999998762001366188
Q gi|254780838|r    3 SLLFGFLAFLYAYGGSVVFSLFESFFVEKEDGELF   37 (103)
Q Consensus         3 sllfgflaflyayggsvvfslfesffvekedgelf   37 (103)
                      .-|+||+|..-+.-||.+..-.-..+-||...|-|
T Consensus         8 ~al~gffavtg~l~~sfiigeivhlynekq~nenf   42 (98)
T PHA01757          8 GALYGFFAVTGALSASFIIGEIVHLYNEKQRNENF   42 (98)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88989999998888877799999998276411769


No 5  
>pfam09348 DUF1990 Domain of unknown function (DUF1990). This family of proteins are functionally uncharacterized.
Probab=16.09  E-value=64  Score=14.95  Aligned_cols=24  Identities=33%  Similarity=0.527  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHCC-CCCEEEEEEEEE
Q ss_conf             999998762001-366188999999
Q gi|254780838|r   20 VFSLFESFFVEK-EDGELFIRIMVF   43 (103)
Q Consensus        20 vfslfesffvek-edgelfirimvf   43 (103)
                      ..+-=|+|.||+ +||..+..|..|
T Consensus       104 ~e~GEE~F~Ve~~~dg~V~~~v~af  128 (158)
T pfam09348       104 PERGEERFLVERDDDGRVWYEITAF  128 (158)
T ss_pred             HHCCEEEEEEEECCCCEEEEEEEEE
T ss_conf             1044799999997999099999997


No 6  
>TIGR01770 NDH_I_N proton-translocating NADH-quinone oxidoreductase, chain N; InterPro: IPR010096   This entry describes the 14th (based on Escherichia coli) structural gene, N, of bacterial and chloroplast energy-transducing NADH (or NADPH) dehydrogenases. This entry does not describe any subunit of the mitochondrial complex I (for which the subunit composition is very different), nor NADH dehydrogenases that are not coupled to ion transport. The Enzyme Commission designation 1.6.5.3, for NADH dehydrogenase (ubiquinone), is applied broadly, perhaps unfortunately, even if the quinone is menaquinone (Thermus, Mycobacterium) or plastoquinone (chloroplast). For chloroplast members, the name NADH-plastoquinone oxidoreductase is used for the complex and this protein is designated as subunit 2 or B. This entry also includes a subunit of a related complex in the archaeal methanogen, Methanosarcina mazei, in which F420H2 replaces NADH and 2-hydroxyphenazine replaces the quinone.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=15.18  E-value=1.1e+02  Score=13.76  Aligned_cols=34  Identities=35%  Similarity=0.719  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCEEEE
Q ss_conf             79999999996336899999987620--013661889
Q gi|254780838|r    4 LLFGFLAFLYAYGGSVVFSLFESFFV--EKEDGELFI   38 (103)
Q Consensus         4 llfgflaflyayggsvvfslfesffv--ekedgelfi   38 (103)
                      +||| .|+.|+..||..|+---.++.  ++++.++.+
T Consensus       174 lLfG-~sliYg~tG~~~~~~~~~~~~~~~~~~~~i~~  209 (491)
T TIGR01770       174 LLFG-ISLIYGFTGSLNFEDLLLFLSNLEKNISNILI  209 (491)
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             9999-99999867677799999985211023430310


No 7  
>PRK12705 hypothetical protein; Provisional
Probab=13.20  E-value=86  Score=14.25  Aligned_cols=15  Identities=60%  Similarity=0.919  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             12367776777446542
Q gi|254780838|r   64 RSSYQQRSNILSHRKEI   80 (103)
Q Consensus        64 rssyqqrsnilshrkei   80 (103)
                      |+||-|  |+|.|-.|.
T Consensus       293 RtSyGQ--NvL~HSiEv  307 (485)
T PRK12705        293 RTSYGQ--NVLSHSLEV  307 (485)
T ss_pred             CCCCHH--HHHHHHHHH
T ss_conf             023405--799999999


No 8  
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=13.18  E-value=67  Score=14.86  Aligned_cols=44  Identities=34%  Similarity=0.553  Sum_probs=29.8

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHCCCC
Q ss_conf             998740240001236777677744654212201----371334102366
Q gi|254780838|r   53 YVDLLPFNFASRSSYQQRSNILSHRKEIAIDQR----RTPITQKLSMGN   97 (103)
Q Consensus        53 yvdllpfnfasrssyqqrsnilshrkeiaidqr----rtpitqklsmgn   97 (103)
                      ||||. .|-.+|....+||.|++.-.+-..++-    -||+-|...-|.
T Consensus       167 ylDLi-~N~e~r~~f~~Rs~ii~~iR~fl~~~gFlEVETP~lq~i~GGA  214 (502)
T COG1190         167 YLDLI-VNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPGGA  214 (502)
T ss_pred             HHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCC
T ss_conf             88986-5999999999999999999999987797584160003557873


No 9  
>TIGR00048 TIGR00048 radical SAM enzyme, Cfr family; InterPro: IPR004383 This family of conserved hypothetical proteins groups bacterial proteins of unknown function..
Probab=13.12  E-value=62  Score=15.03  Aligned_cols=22  Identities=36%  Similarity=0.570  Sum_probs=17.9

Q ss_pred             EEEEEEECCCCHHHHHHHHHHH
Q ss_conf             7998740240001236777677
Q gi|254780838|r   52 FYVDLLPFNFASRSSYQQRSNI   73 (103)
Q Consensus        52 fyvdllpfnfasrssyqqrsni   73 (103)
                      --|.|.|||..+-+.|+.-|+-
T Consensus       311 ckvNLIP~NP~~e~~Y~R~s~~  332 (378)
T TIGR00048       311 CKVNLIPFNPFPEADYERPSNE  332 (378)
T ss_pred             CEEEEEECCCCCCCCCCCCCHH
T ss_conf             5040121378798888888088


No 10 
>cd00034 ChSh Chromo Shadow Domain,  found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)
Probab=12.76  E-value=1.2e+02  Score=13.37  Aligned_cols=35  Identities=29%  Similarity=0.407  Sum_probs=0.0

Q ss_pred             HHCCCC-CEEEEEEEEEEEEECCCEEEEEEEECCCCHHHHHHH
Q ss_conf             200136-618899999987603541799874024000123677
Q gi|254780838|r   28 FVEKED-GELFIRIMVFEISWSRGEFYVDLLPFNFASRSSYQQ   69 (103)
Q Consensus        28 fveked-gelfirimvfeiswsrgefyvdllpfnfasrssyqq   69 (103)
                      ++++.| |||     .|-+.|+.|+  .||.|-..|..-.-|.
T Consensus         7 ~a~~~~~GeL-----~fl~kwk~~~--~~lv~ak~an~kcPq~   42 (54)
T cd00034           7 GASKSDDGEL-----TFLAKWKDGQ--ASLVPNKELNVKCPLL   42 (54)
T ss_pred             CEEECCCCEE-----EEEEEECCCC--CCCCCHHHHHHHCCHH
T ss_conf             1153699669-----9999972995--0114488986348599


Done!