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!