Query         gi|254781138|ref|YP_003065551.1| hypothetical protein CLIBASIA_05200 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 178
No_of_seqs    113 out of 799
Neff          7.3 
Searched_HMMs 39220
Date          Mon May 30 05:13:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781138.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG3606 consensus               51.0      19 0.00048   16.5   3.3   53   56-108   135-191 (358)
  2 pfam08970 Sda Sporulation inhi  41.2      18 0.00047   16.6   2.0   14   26-39     22-35  (45)
  3 pfam06500 DUF1100 Alpha/beta h  30.4      41   0.001   14.7   3.4   22  128-152   303-324 (411)
  4 cd08055 gp15 Head-Tail Connect  29.4      43  0.0011   14.6   3.8   37    6-42     25-62  (95)
  5 PRK05077 frsA fermentation/res  26.8      47  0.0012   14.3   3.4   21  129-152   308-328 (414)
  6 COG3541 Predicted nucleotidylt  26.3      47  0.0012   14.3   2.1   30   87-116     6-38  (248)
  7 PHA00662 hypothetical protein   23.9      54  0.0014   14.0  10.3  130   25-168    34-175 (215)
  8 TIGR01159 DRP1 density-regulat  21.0      25 0.00065   15.8  -0.2   12  127-138    23-34  (187)
  9 TIGR01063 gyrA DNA gyrase, A s  20.7      55  0.0014   13.9   1.5   15    4-18    462-476 (864)
 10 KOG3239 consensus               16.8      45  0.0011   14.4   0.3   10  129-138    37-46  (193)

No 1  
>KOG3606 consensus
Probab=50.98  E-value=19  Score=16.55  Aligned_cols=53  Identities=21%  Similarity=0.176  Sum_probs=37.4

Q ss_pred             CEEECCCCCEEE---EEEEECCCCCCEEECCCCCCCCCCEEEEECC-EEEEEECCCC
Q ss_conf             213258773267---8776226774101012224776505899888-6999504664
Q gi|254781138|r   56 GSAPLPDDYIEI---RFLEDNKGNKLDHLPLSISLQKNKGYIITAD-SICVLPISSE  108 (178)
Q Consensus        56 ~~~~lP~d~l~~---~~~~~~~~~~~~~~~~~~~~g~P~~ya~~~~-~l~~~P~~~~  108 (178)
                      -.+++|-||..+   +++-+....-++-.-......+|-.|.|.++ .+.++|..--
T Consensus       135 ~~Is~P~DFRqVSsIIDVDivPEtHRRVRL~khG~ekPLGFYIRDG~SVRVtp~Gle  191 (358)
T KOG3606         135 LSISLPQDFRQVSSIIDVDIVPETHRRVRLHKHGSEKPLGFYIRDGTSVRVTPHGLE  191 (358)
T ss_pred             CCCCCCCCCCEECEEEEECCCCHHHHHEEHHHCCCCCCCEEEEECCCEEEECCCCCC
T ss_conf             422584113300214442226313342005333787874578716846875455532


No 2  
>pfam08970 Sda Sporulation inhibitor A. Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilized by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A).
Probab=41.16  E-value=18  Score=16.59  Aligned_cols=14  Identities=29%  Similarity=0.463  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             79999999999610
Q gi|254781138|r   26 KNFLHRIEVKINRA   39 (178)
Q Consensus        26 ~~FI~~aE~rI~R~   39 (178)
                      ||||.+-+.+|.|+
T Consensus        22 ~DFI~Li~~Ei~RR   35 (45)
T pfam08970        22 PDFIELIKEEIIRR   35 (45)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             89999999999998


No 3  
>pfam06500 DUF1100 Alpha/beta hydrolase of unknown function (DUF1100). This family consists of several hypothetical bacterial proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.
Probab=30.39  E-value=41  Score=14.65  Aligned_cols=22  Identities=18%  Similarity=0.194  Sum_probs=11.5

Q ss_pred             CCCHHHCHHHHHHHHHHHHHHHCCC
Q ss_conf             4301112289999999999974149
Q gi|254781138|r  128 NWLLHRAPDLYLYGLVEEIALWEQK  152 (178)
Q Consensus       128 n~l~~~~pd~~LygaL~eA~~flk~  152 (178)
                      .-...+-|++||..   -|+...|+
T Consensus       303 ~~~~~~~P~MylDv---lASRLG~~  324 (411)
T pfam06500       303 PKKLQKMPKMYLDV---LASRLGKS  324 (411)
T ss_pred             HHHHHHCCHHHHHH---HHHHHCCC
T ss_conf             88774476899999---99873764


No 4  
>cd08055 gp15 Head-Tail Connector Protein gp15 of Bacteriophage SPP1 and similar proteins. The bacteriophage SPP1 gp15 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp16 ring (attached to the tail). Binding of the gp15 and gp16 rings to the portal protein is essential to prevent leakage of packaged DNA. gp15 is a component of the mature phage and its mutation results in defective head-tail joining.
Probab=29.40  E-value=43  Score=14.55  Aligned_cols=37  Identities=11%  Similarity=0.015  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHCCCCCHHHH-HHHHHHHHHHHHHHCCC
Q ss_conf             99999999874265003457-79999999999610374
Q gi|254781138|r    6 ASLLIDVSHYVEKGGFTYLF-KNFLHRIEVKINRALRL   42 (178)
Q Consensus         6 ~~L~~~I~~~l~r~dlt~~I-~~FI~~aE~rI~R~lr~   42 (178)
                      .+.+..|.+|+|++.+...+ |.-+.+|....+|.=--
T Consensus        25 ed~~~~v~dY~n~~~~~~~~~~~~v~lai~~~~~~g~e   62 (95)
T cd08055          25 EDAIEDVLDYCNQTFLPDPLLPTVVKLAVALYNKLGTE   62 (95)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999983863365034468999999999970876


No 5  
>PRK05077 frsA fermentation/respiration switch protein; Reviewed
Probab=26.81  E-value=47  Score=14.29  Aligned_cols=21  Identities=14%  Similarity=0.098  Sum_probs=12.2

Q ss_pred             CCHHHCHHHHHHHHHHHHHHHCCC
Q ss_conf             301112289999999999974149
Q gi|254781138|r  129 WLLHRAPDLYLYGLVEEIALWEQK  152 (178)
Q Consensus       129 ~l~~~~pd~~LygaL~eA~~flk~  152 (178)
                      -...+-|++||..   -|+...|+
T Consensus       308 ~~~~~~P~MylDv---lASRLg~~  328 (414)
T PRK05077        308 DRQQQVPEMYLDV---LASRLGMH  328 (414)
T ss_pred             HHHHHCCHHHHHH---HHHHHCCC
T ss_conf             8887687899999---99874643


No 6  
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=26.34  E-value=47  Score=14.29  Aligned_cols=30  Identities=13%  Similarity=-0.136  Sum_probs=13.5

Q ss_pred             CCCCCEEEEE-CCEEE--EEECCCCCEEEEEEE
Q ss_conf             7765058998-88699--950466415898763
Q gi|254781138|r   87 LQKNKGYIIT-ADSIC--VLPISSEDVVLYYYA  116 (178)
Q Consensus        87 ~g~P~~ya~~-~~~l~--~~P~~~~~~~l~Yy~  116 (178)
                      .|.|..|+.. |...+  +.|+++|+++..|-.
T Consensus         6 ~~v~Il~a~esGS~~yGf~spdSDyDvR~V~i~   38 (248)
T COG3541           6 QGVPILFAGESGSHLYGFPSPDSDYDVRGVHIL   38 (248)
T ss_pred             CCCCEEEEECCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             697679997236433588999876442468867


No 7  
>PHA00662 hypothetical protein
Probab=23.92  E-value=54  Score=13.97  Aligned_cols=130  Identities=13%  Similarity=0.083  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEEEEEC----CC---EEECCCCCEEEEEEEECCCCCCEEECCCCCCCCCCEEEE--
Q ss_conf             779999999999610374201478988724----62---132587732678776226774101012224776505899--
Q gi|254781138|r   25 FKNFLHRIEVKINRALRLREMERKIVLSLV----EG---SAPLPDDYIEIRFLEDNKGNKLDHLPLSISLQKNKGYII--   95 (178)
Q Consensus        25 I~~FI~~aE~rI~R~lr~~~~~~~~t~t~~----~~---~~~lP~d~l~~~~~~~~~~~~~~~~~~~~~~g~P~~ya~--   95 (178)
                      ...+=..+-....|..++..-.+.+.+...    .+   .+.||+|++.++.+...+.....  +.   ...+.-|.+  
T Consensus        34 c~~~Y~~~r~~~L~~~~W~fA~~r~~La~~~~~p~~~~~ay~lP~DcLrv~~v~~~~~~~~~--~~---~~~~~~~~~e~  108 (215)
T PHA00662         34 CARFYDFARDALLELHTWGFATKRAQLAAMGISPPEWRYAYAQPADAIRIVAVLPHGAANIE--AG---IDNAQPFSCEI  108 (215)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEECCCHHHHEEEEEEECCCCCCCC--CC---CCCCCCEEEEE
T ss_conf             99888999999997397454654333430478998764423381571566677238865554--33---34565224430


Q ss_pred             --ECCEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCHHHCHHHHHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHH
Q ss_conf             --8886999504664158987631654335454443011122899999999999-741498889999999999999
Q gi|254781138|r   96 --TADSICVLPISSEDVVLYYYACIPPLTENNPVNWLLHRAPDLYLYGLVEEIA-LWEQKIDKATTASALFQESIK  168 (178)
Q Consensus        96 --~~~~l~~~P~~~~~~~l~Yy~~~~~Ls~~n~tn~l~~~~pd~~LygaL~eA~-~flk~~~~~~~~~~~y~~ai~  168 (178)
                        .|+.|. .=  ..++.+.|..+.+      +++-....+-+++-+.--.+.+ +-..+....+...++|+..+.
T Consensus       109 ~~~G~~I~-td--~~~~~l~Yi~rvt------D~~~fd~~F~~aLa~~LAa~lA~piT~s~~l~~~~~~~~~~~~~  175 (215)
T PHA00662        109 DNTGDIIL-TN--QVNAVARYISRVT------DTNKFDALFVEALAWRLAAMLAGPLTGSAGAAESARCVGAMQIY  175 (215)
T ss_pred             CCCCCEEE-EC--CCCCEEEEEEECC------CHHHCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             56688688-26--9861899998458------80338899999999999999888761987999999999999999


No 8  
>TIGR01159 DRP1 density-regulated protein DRP1; InterPro: IPR005873    This expression of members of this family of proteins is increased at high cell density but not growth arrest. The function of these proteins is unknown ..
Probab=21.05  E-value=25  Score=15.82  Aligned_cols=12  Identities=58%  Similarity=1.126  Sum_probs=9.7

Q ss_pred             CCCCHHHCHHHH
Q ss_conf             443011122899
Q gi|254781138|r  127 VNWLLHRAPDLY  138 (178)
Q Consensus       127 tn~l~~~~pd~~  138 (178)
                      =.||..|||++|
T Consensus        23 k~Wl~~N~p~~y   34 (187)
T TIGR01159        23 KAWLEENAPDLY   34 (187)
T ss_pred             HHHHHCCCHHCC
T ss_conf             666641441002


No 9  
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=20.72  E-value=55  Score=13.91  Aligned_cols=15  Identities=13%  Similarity=0.273  Sum_probs=12.6

Q ss_pred             CHHHHHHHHHHHHCC
Q ss_conf             789999999987426
Q gi|254781138|r    4 DFASLLIDVSHYVEK   18 (178)
Q Consensus         4 ~Y~~L~~~I~~~l~r   18 (178)
                      .|.+|++.|++|.+-
T Consensus       462 E~~~L~~~I~~l~~i  476 (864)
T TIGR01063       462 EYKELLELIADLEDI  476 (864)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999975


No 10 
>KOG3239 consensus
Probab=16.84  E-value=45  Score=14.42  Aligned_cols=10  Identities=60%  Similarity=1.311  Sum_probs=0.0

Q ss_pred             CCHHHCHHHH
Q ss_conf             3011122899
Q gi|254781138|r  129 WLLHRAPDLY  138 (178)
Q Consensus       129 ~l~~~~pd~~  138 (178)
                      ||..||||+|
T Consensus        37 WL~~n~pdly   46 (193)
T KOG3239          37 WLEENHPDLY   46 (193)
T ss_pred             HHHHCCHHHH
T ss_conf             9985083677


Done!