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!