Query         gi|254780692|ref|YP_003065105.1| hypothetical protein CLIBASIA_02895 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 72
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 20:01:25 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780692.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4591 LolE ABC-type transpor  55.9      10 0.00025   19.2   2.5   21    6-26     36-56  (408)
  2 TIGR00263 trpB tryptophan synt  46.1     5.6 0.00014   20.5  -0.0   43   24-66    136-180 (412)
  3 pfam06388 DUF1075 Protein of u  41.5      32 0.00083   16.5   3.4   39    7-45    100-140 (146)
  4 KOG1469 consensus               35.4      22 0.00055   17.4   1.6   43   23-65    282-324 (392)
  5 pfam04111 APG6 Autophagy prote  23.0      52  0.0013   15.5   1.7   18   47-64    326-343 (356)
  6 TIGR02002 PTS-II-BC-glcB PTS s  16.7      93  0.0024   14.2   1.9   19    3-21    147-165 (518)
  7 pfam12297 EVC2_like Ellis van   15.9   1E+02  0.0026   14.0   2.2   22    2-23     73-94  (429)
  8 COG4220 Phage DNA packaging pr  13.7 1.2E+02   0.003   13.6   2.2   29   24-52     67-95  (174)
  9 COG1398 OLE1 Fatty-acid desatu  13.5 1.2E+02  0.0031   13.6   2.2   20    3-22    167-186 (289)
 10 COG5438 Predicted multitransme  11.7 1.4E+02  0.0035   13.3   2.3   21    3-23    183-203 (385)

No 1  
>COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]
Probab=55.93  E-value=10  Score=19.19  Aligned_cols=21  Identities=43%  Similarity=0.779  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHCCHHHHHHH
Q ss_conf             899999999983132567877
Q gi|254780692|r    6 GIIFTIICLYMMNGYQKEKKD   26 (72)
Q Consensus         6 giiftiiclymmngyqkekkd   26 (72)
                      |+..-|+-+.+|||.|+|-.+
T Consensus        36 gV~~LIv~lsvmnGf~~el~~   56 (408)
T COG4591          36 GVAVLIVVLSVMNGFQKELEN   56 (408)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999988567999984


No 2  
>TIGR00263 trpB tryptophan synthase, beta subunit; InterPro: IPR006654   Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan , :  L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H_2O  It has two functional domains, each found in bacteria and plants on a separate subunit: alpha chain (IPR002028 from INTERPRO) is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and beta chain is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together on a single multifunctional protein .   The beta chain of the enzyme, represented here, requires pyridoxal-phosphate as a cofactor. The pyridoxal-phosphate group is attached to a lysine residue. The region around this lysine residue also contains two histidine residues which are part of the pyridoxal-phosphate binding site.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process.
Probab=46.08  E-value=5.6  Score=20.47  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHHHHCC
Q ss_conf             8778887733688773389873--032455669999998751028
Q gi|254780692|r   24 KKDIERTRLNIERTRLTCEEAR--HTQDENLTKACKDELKNIKSN   66 (72)
Q Consensus        24 kkdiertrlniertrltceear--htqdenltkackdelkniksn   66 (72)
                      .+|+||-+||+.|-||---+--  +.-...|-.||.+-|..--||
T Consensus       136 a~DV~RQ~pNVFRMellGA~V~pV~sGs~TLKDA~N~AlrDWv~~  180 (412)
T TIGR00263       136 AEDVERQKPNVFRMELLGAKVVPVTSGSGTLKDAVNEALRDWVTS  180 (412)
T ss_pred             CCCHHHCCCCHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             613514577523451377868330157870378999999874136


No 3  
>pfam06388 DUF1075 Protein of unknown function (DUF1075). This family consists of several eukaryotic proteins of unknown function.
Probab=41.47  E-value=32  Score=16.54  Aligned_cols=39  Identities=28%  Similarity=0.502  Sum_probs=25.8

Q ss_pred             HHHHHH-HHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999-99983-1325678778887733688773389873
Q gi|254780692|r    7 IIFTII-CLYMM-NGYQKEKKDIERTRLNIERTRLTCEEAR   45 (72)
Q Consensus         7 iiftii-clymm-ngyqkekkdiertrlniertrltceear   45 (72)
                      |.+||| |++|+ .|-|--|..---|.+|+|+-.---|||.
T Consensus       100 i~lT~igC~~mvi~GKkA~kr~es~t~~Nlekka~~reeaa  140 (146)
T pfam06388       100 IALTVVGCIIMVISGKKAAERHESLTSMNLEKKAKWNEEAA  140 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999998336664445287753899987717876


No 4  
>KOG1469 consensus
Probab=35.44  E-value=22  Score=17.45  Aligned_cols=43  Identities=35%  Similarity=0.433  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHC
Q ss_conf             7877888773368877338987303245566999999875102
Q gi|254780692|r   23 EKKDIERTRLNIERTRLTCEEARHTQDENLTKACKDELKNIKS   65 (72)
Q Consensus        23 ekkdiertrlniertrltceearhtqdenltkackdelkniks   65 (72)
                      -.+||...|..||.+||-.-+|-|.-|.--.|+.|.|+.-||-
T Consensus       282 ~~~diA~sRveiEqaRLLvLkAAh~mD~~G~k~Ak~~iAMiKv  324 (392)
T KOG1469         282 VAHDIAESRVEIEQARLLVLKAAHSMDTLGNKGAKKEIAMIKV  324 (392)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHEEEEEE
T ss_conf             9999998776766524434236666652064234212002331


No 5  
>pfam04111 APG6 Autophagy protein Apg6. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.
Probab=23.00  E-value=52  Score=15.50  Aligned_cols=18  Identities=50%  Similarity=0.486  Sum_probs=12.8

Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             324556699999987510
Q gi|254780692|r   47 TQDENLTKACKDELKNIK   64 (72)
Q Consensus        47 tqdenltkackdelknik   64 (72)
                      .+||+-|+|||--|-|.|
T Consensus       326 N~de~WTkAlK~mLtnlK  343 (356)
T pfam04111       326 NSDEQWTKALKFMLTNLK  343 (356)
T ss_pred             CCCCHHHHHHHHHHHHHH
T ss_conf             775379999999999899


No 6  
>TIGR02002 PTS-II-BC-glcB PTS system, glucose-specific IIBC component; InterPro: IPR011299   This entry represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport . Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name 'PTS system, glucose-specific IIABC component' while the Bacillus subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains . This group is most closely related to the N-acetylglucosamine-specific PTS enzymes (IPR010974 from INTERPRO).; GO: 0005355 glucose transmembrane transporter activity, 0015758 glucose transport, 0016021 integral to membrane.
Probab=16.68  E-value=93  Score=14.17  Aligned_cols=19  Identities=32%  Similarity=0.646  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHCCHH
Q ss_conf             5778999999999831325
Q gi|254780692|r    3 FLGGIIFTIICLYMMNGYQ   21 (72)
Q Consensus         3 flggiiftiiclymmngyq   21 (72)
                      -+||||--+|.-||-|-|-
T Consensus       147 VFGGII~Ga~AA~cYNrFy  165 (518)
T TIGR02002       147 VFGGIIVGAVAAYCYNRFY  165 (518)
T ss_pred             CCHHHHHHHHHHHHHCCCC
T ss_conf             5037999999999837532


No 7  
>pfam12297 EVC2_like Ellis van Creveld protein 2 like protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Probab=15.94  E-value=1e+02  Score=13.96  Aligned_cols=22  Identities=18%  Similarity=0.484  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             2577899999999983132567
Q gi|254780692|r    2 EFLGGIIFTIICLYMMNGYQKE   23 (72)
Q Consensus         2 eflggiiftiiclymmngyqke   23 (72)
                      -|+.+|+.|..|++.|+-+|--
T Consensus        73 af~vsiVlt~~~~f~l~rt~~~   94 (429)
T pfam12297        73 AFLVSIVLTLLAFFLLGRTRCL   94 (429)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999999999999874110


No 8  
>COG4220 Phage DNA packaging protein, Nu1 subunit of terminase [DNA replication, recombination, and repair]
Probab=13.75  E-value=1.2e+02  Score=13.63  Aligned_cols=29  Identities=34%  Similarity=0.397  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             87788877336887733898730324556
Q gi|254780692|r   24 KKDIERTRLNIERTRLTCEEARHTQDENL   52 (72)
Q Consensus        24 kkdiertrlniertrltceearhtqdenl   52 (72)
                      .+|+|--+.-+||+|||-+.|-.++-+|-
T Consensus        67 ~~dvee~~~~~er~rLt~aQad~q~Lkna   95 (174)
T COG4220          67 RDDVEELREARERHRLTRAQADAQELKNA   95 (174)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             22189999999999988998778999879


No 9  
>COG1398 OLE1 Fatty-acid desaturase [Lipid metabolism]
Probab=13.52  E-value=1.2e+02  Score=13.60  Aligned_cols=20  Identities=20%  Similarity=0.456  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHCCHHH
Q ss_conf             57789999999998313256
Q gi|254780692|r    3 FLGGIIFTIICLYMMNGYQK   22 (72)
Q Consensus         3 flggiiftiiclymmngyqk   22 (72)
                      .+++|++..+|+|.++||-.
T Consensus       167 ~l~~i~~~l~~~~~~gg~~g  186 (289)
T COG1398         167 LLMQIVLPLFIGYALGGWLG  186 (289)
T ss_pred             HHHHHHHHHHHHHHHCCHHH
T ss_conf             99988899999999633577


No 10 
>COG5438 Predicted multitransmembrane protein [Function unknown]
Probab=11.71  E-value=1.4e+02  Score=13.30  Aligned_cols=21  Identities=38%  Similarity=0.643  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHCCHHHH
Q ss_conf             577899999999983132567
Q gi|254780692|r    3 FLGGIIFTIICLYMMNGYQKE   23 (72)
Q Consensus         3 flggiiftiiclymmngyqke   23 (72)
                      +...++++++-|+|.+|+.+.
T Consensus       183 ii~~viit~~tL~~v~g~n~K  203 (385)
T COG5438         183 IILCVIITAITLFMVNGINKK  203 (385)
T ss_pred             HHHHHHHHHHHHHHHCCCCHH
T ss_conf             999999999999861585299


Done!