Query gi|254780304|ref|YP_003064717.1| DNA protecting protein DprA [Candidatus Liberibacter asiaticus str. psy62] Match_columns 34 No_of_seqs 116 out of 901 Neff 4.5 Searched_HMMs 39220 Date Sun May 29 15:05:49 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780304.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10736 hypothetical protein; 99.4 6.9E-14 1.8E-18 88.7 4.0 34 1-34 157-190 (364) 2 TIGR00732 dprA DNA protecting 99.4 6.7E-14 1.7E-18 88.8 3.7 34 1-34 119-152 (238) 3 pfam02481 DNA_processg_A DNA r 99.2 1.5E-11 3.7E-16 77.5 3.7 34 1-34 102-135 (210) 4 COG0758 Smf Predicted Rossmann 99.2 1.7E-11 4.3E-16 77.2 3.6 33 1-34 171-203 (350) 5 pfam10706 Aminoglyc_resit Amin 60.7 8.3 0.00021 20.9 2.8 28 4-31 44-71 (174) 6 TIGR02318 phosphono_phnM phosp 41.7 17 0.00043 19.5 1.8 10 24-33 254-263 (391) 7 cd01306 PhnM PhnM is believed 17.8 89 0.0023 16.0 2.0 10 24-33 196-205 (325) 8 KOG2339 consensus 16.3 95 0.0024 15.8 1.9 23 4-26 496-519 (624) 9 COG4830 RPS26B Ribosomal prote 14.6 93 0.0024 15.9 1.5 25 7-33 40-64 (108) 10 pfam08853 DUF1823 Domain of un 11.8 1.7E+02 0.0042 14.7 2.1 28 6-33 70-97 (116) No 1 >PRK10736 hypothetical protein; Provisional Probab=99.44 E-value=6.9e-14 Score=88.74 Aligned_cols=34 Identities=35% Similarity=0.748 Sum_probs=33.0 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 9873881089899999999998399599706998 Q gi|254780304|r 1 MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34 (34) Q Consensus 1 l~~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G 34 (34) ||||+|++||++|++|+++|+++||++|||||+| T Consensus 157 Lg~Gld~iYP~~h~~L~~~I~~~gG~lvSE~pp~ 190 (364) T PRK10736 157 LGNGLNNIYPRRHARLAESIIEQGGALVSEFPLD 190 (364) T ss_pred ECCCCCCCCCHHHHHHHHHHHHCCCEEEECCCCC T ss_conf 5788886187788999999997589086668999 No 2 >TIGR00732 dprA DNA protecting protein DprA; InterPro: IPR003488 The SMF family (DNA processing chain A, dprA) are a group of bacterial proteins. In Helicobacter pylori, dprA is required for natural chromosomal and plasmid transformation .; GO: 0009294 DNA mediated transformation. Probab=99.44 E-value=6.7e-14 Score=88.79 Aligned_cols=34 Identities=38% Similarity=0.715 Sum_probs=32.7 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 9873881089899999999998399599706998 Q gi|254780304|r 1 MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34 (34) Q Consensus 1 l~~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G 34 (34) ||||+|.|||++|++|+++|+++||+||||||++ T Consensus 119 l~~Gld~IYPr~n~~L~~~i~~~GG~llSEy~p~ 152 (238) T TIGR00732 119 LGTGLDQIYPRQNSKLAAKIAEQGGLLLSEYPPD 152 (238) T ss_pred ECCCCCCCCCCHHHHHHHHHHHCCCEEEEECCCC T ss_conf 0466677788327899999997198589620789 No 3 >pfam02481 DNA_processg_A DNA recombination-mediator protein A. The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation. Probab=99.18 E-value=1.5e-11 Score=77.53 Aligned_cols=34 Identities=53% Similarity=0.908 Sum_probs=32.6 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 9873881089899999999998399599706998 Q gi|254780304|r 1 MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34 (34) Q Consensus 1 l~~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G 34 (34) |++|+|.+||++|++|+++|++++|++|||||+| T Consensus 102 l~~Gl~~~yP~~n~~l~~~I~~~~GlliSE~~p~ 135 (210) T pfam02481 102 LGTGLDRIYPKENRKLAEEIAEQGGLLLSEYPPG 135 (210) T ss_pred ECCCCCCCCCHHHHHHHHHHHHCCCCEEECCCCC T ss_conf 4577561263565999999998699087617988 No 4 >COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion] Probab=99.17 E-value=1.7e-11 Score=77.23 Aligned_cols=33 Identities=52% Similarity=0.762 Sum_probs=31.2 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC Q ss_conf 9873881089899999999998399599706998 Q gi|254780304|r 1 MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34 (34) Q Consensus 1 l~~GiD~iYP~~n~~L~~~I~~~gG~liSE~P~G 34 (34) +|+|+|++||++|++|+++|+++| ++|||||++ T Consensus 171 l~~Gld~iYP~~n~~l~~~i~~~g-~liSEypp~ 203 (350) T COG0758 171 LATGLDKIYPRENIKLAEKIAENG-LLISEYPPD 203 (350) T ss_pred ECCCCCCCCCHHHHHHHHHHHHCC-EEEEECCCC T ss_conf 717777608746599999997568-687636999 No 5 >pfam10706 Aminoglyc_resit Aminoglycoside-2''-adenylyltransferase. This family is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents. Probab=60.66 E-value=8.3 Score=20.93 Aligned_cols=28 Identities=21% Similarity=0.304 Sum_probs=24.2 Q ss_pred CCCCCCCHHHHHHHHHHHHHCCEEEEEC Q ss_conf 3881089899999999998399599706 Q gi|254780304|r 4 GLDCLYPPENRNLLEEIWDNGGIAISEI 31 (34) Q Consensus 4 GiD~iYP~~n~~L~~~I~~~gG~liSE~ 31 (34) -||.+||.+++.-|+.++.+=|..++|. T Consensus 44 DIDl~~P~d~~ae~~~ll~~~g~~i~eq 71 (174) T pfam10706 44 DIDLTFPGDRHAEFECLLHAFGGVITEQ 71 (174) T ss_pred CCCCCCCCHHHHHHHHHHHHCCCEEEEE T ss_conf 7111376244789999999748888664 No 6 >TIGR02318 phosphono_phnM phosphonate metabolism protein PhnM; InterPro: IPR012696 This family consists of proteins from in the PhnM family. PhnM is a protein associated with phosphonate utilization in a number of bacterial species. Pseudomonas stutzeri WM88, has a related protein that is part of a system for the oxidation of phosphites (another form of reduced phosphorous compound), which is not contained in this entry.. Probab=41.74 E-value=17 Score=19.46 Aligned_cols=10 Identities=50% Similarity=0.737 Sum_probs=8.5 Q ss_pred CCEEEEECCC Q ss_conf 9959970699 Q gi|254780304|r 24 GGIAISEIPF 33 (34) Q Consensus 24 gG~liSE~P~ 33 (34) -|..|||||- T Consensus 254 ~Gv~isEFPt 263 (391) T TIGR02318 254 LGVTISEFPT 263 (391) T ss_pred CCCEEEECHH T ss_conf 7826740423 No 7 >cd01306 PhnM PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage of alkylphosphonates, which are utilized as sole phosphorus sources by many bacteria. Probab=17.83 E-value=89 Score=15.98 Aligned_cols=10 Identities=50% Similarity=0.720 Sum_probs=8.2 Q ss_pred CCEEEEECCC Q ss_conf 9959970699 Q gi|254780304|r 24 GGIAISEIPF 33 (34) Q Consensus 24 gG~liSE~P~ 33 (34) -|+-|||||. T Consensus 196 ~G~~IaEFPt 205 (325) T cd01306 196 LGVVISEFPT 205 (325) T ss_pred CCCEEEECCC T ss_conf 7986853521 No 8 >KOG2339 consensus Probab=16.34 E-value=95 Score=15.84 Aligned_cols=23 Identities=26% Similarity=0.679 Sum_probs=19.0 Q ss_pred CCCCCCCHHH-HHHHHHHHHHCCE Q ss_conf 3881089899-9999999983995 Q gi|254780304|r 4 GLDCLYPPEN-RNLLEEIWDNGGI 26 (34) Q Consensus 4 GiD~iYP~~n-~~L~~~I~~~gG~ 26 (34) |.|++||+.- .+.+.+|+...|+ T Consensus 496 G~dv~YPkn~~~~~Y~e~l~~d~l 519 (624) T KOG2339 496 GFDVIYPKNEIAQWYVELLKEDGL 519 (624) T ss_pred CCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 867506672788999999986088 No 9 >COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis] Probab=14.55 E-value=93 Score=15.87 Aligned_cols=25 Identities=12% Similarity=0.204 Sum_probs=18.6 Q ss_pred CCCCHHHHHHHHHHHHHCCEEEEECCC Q ss_conf 108989999999999839959970699 Q gi|254780304|r 7 CLYPPENRNLLEEIWDNGGIAISEIPF 33 (34) Q Consensus 7 ~iYP~~n~~L~~~I~~~gG~liSE~P~ 33 (34) .+|-.--..++.++ ++ |+++|||+. T Consensus 40 ~i~s~Ve~a~~rdL-~~-asIy~~y~v 64 (108) T COG4830 40 AIRSPVEAAAARDL-SE-ASIYSEYAV 64 (108) T ss_pred ECCCCCCHHHHHHH-HH-CEEEEEEEC T ss_conf 42576667888777-53-613567751 No 10 >pfam08853 DUF1823 Domain of unknown function (DUF1823). This presumed domain is functionally uncharacterized. Probab=11.77 E-value=1.7e+02 Score=14.66 Aligned_cols=28 Identities=29% Similarity=0.307 Sum_probs=22.5 Q ss_pred CCCCCHHHHHHHHHHHHHCCEEEEECCC Q ss_conf 8108989999999999839959970699 Q gi|254780304|r 6 DCLYPPENRNLLEEIWDNGGIAISEIPF 33 (34) Q Consensus 6 D~iYP~~n~~L~~~I~~~gG~liSE~P~ 33 (34) -+--|++|++|..+-+.-.|--|.|+-+ T Consensus 70 TRSIPke~KQlLK~~LgFkGYki~el~P 97 (116) T pfam08853 70 TRSIPKEHKQLLKEQLGFKGYKIGELYP 97 (116) T ss_pred HCCCCHHHHHHHHHHCCCCCEEECCCCC T ss_conf 1148888899999744878645457273 Done!