Query         537021.9.peg.15_1
Match_columns 47
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 22 15:58:10 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_15.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11424 DNA-binding transcrip  21.1      76  0.0019   14.6   2.3   33   14-46     65-105 (114)
  2 TIGR01934 MenG_MenH_UbiE ubiqu  19.8      59  0.0015   15.1   1.5   27   17-43    198-224 (242)
  3 pfam12070 DUF3550 Protein of u  18.5      87  0.0022   14.3   2.6   29    6-34     63-91  (512)
  4 cd03186 GST_C_SspA GST_N famil  17.5      76  0.0019   14.5   1.6   19   28-46     43-62  (107)
  5 TIGR00588 ogg 8-oxoguanine DNA  14.5      77   0.002   14.5   1.0   17   12-28    230-246 (379)
  6 TIGR02235 menA_cyano-plnt 1,4-  11.2 1.4E+02  0.0036   13.2   1.5   15   28-42    179-193 (293)
  7 pfam05568 ASFV_J13L African sw   9.5 1.3E+02  0.0033   13.4   0.9   11   29-39     45-55  (189)
  8 PRK10494 hypothetical protein;   9.0 1.7E+02  0.0044   12.7   3.8   27   20-46     36-62  (259)
  9 PRK00753 psbL photosystem II r   8.2 1.7E+02  0.0044   12.7   1.1   12   30-41     27-38  (39)
 10 KOG1589 consensus                7.8 1.2E+02  0.0031   13.5   0.2   10   34-43     77-86  (118)

No 1  
>PRK11424 DNA-binding transcriptional activator TdcR; Provisional
Probab=21.10  E-value=76  Score=14.56  Aligned_cols=33  Identities=39%  Similarity=0.684  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHH--------HHHHHHHHHCCHHHHHCC
Q ss_conf             999999887789999--------999999982461242104
Q 537021.9.peg.1   14 YFAKYLRESTRAFFS--------LATLLYLFSSNFFLSDRF   46 (47)
Q Consensus        14 yfakylrestraffs--------latllylfssnfflsdrf   46 (47)
                      .|..||-|...-|+.        ...|--|...|||-|||-
T Consensus        65 ifsryllenkhlfyqyfkisntgidhleqlinvnffssdrt  105 (114)
T PRK11424         65 IFSRYLLENKHLFYQYFKISNTGIDHLEQLINVNFFSSDRT  105 (114)
T ss_pred             HHHHHHHHCCHHHHHEEEECCCCHHHHHHHHCCCEECCCCC
T ss_conf             99999973223444012313666578998751120116764


No 2  
>TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases; InterPro: IPR004033 A number of methyltransferases have been shown to share regions of similarities . Apart from the ubiquinone/menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the ubiE gene of Escherichia coli), the ubiquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the COQ5 gene of Saccharomyces cerevisiae) and the menaquinone biosynthesis methyltransferases (for example, the C-methyltransferase from the MENH gene of Bacillus subtilis), this family also includes methyltransferases involved in biotin and sterol biosynthesis and in phosphatidylethanolamine methylation.; GO: 0008168 methyltransferase activity.
Probab=19.80  E-value=59  Score=15.11  Aligned_cols=27  Identities=37%  Similarity=0.405  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             999887789999999999982461242
Q 537021.9.peg.1   17 KYLRESTRAFFSLATLLYLFSSNFFLS   43 (47)
Q Consensus        17 kylrestraffslatllylfssnffls   43 (47)
                      .||-||+++|-+-.++--.+.+-=|-+
T Consensus       198 ~YL~eSi~~FP~~~~l~~~~~~aGF~~  224 (242)
T TIGR01934       198 EYLPESIRAFPSQEELAAMLKEAGFEE  224 (242)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf             778899875389889999999738632


No 3  
>pfam12070 DUF3550 Protein of unknown function (DUF3550/UPF0682). This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.
Probab=18.54  E-value=87  Score=14.25  Aligned_cols=29  Identities=31%  Similarity=0.519  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999887789999999999
Q 537021.9.peg.1    6 IHDFLIFLYFAKYLRESTRAFFSLATLLY   34 (47)
Q Consensus         6 ihdfliflyfakylrestraffslatlly   34 (47)
                      |---.--||+.-|||.|...|.+-|...|
T Consensus        63 IASkIgQLYY~yYLRTSet~yL~Eay~FY   91 (512)
T pfam12070        63 IASKIGQLYYHYYLRTSETNYLNEAFVFY   91 (512)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             99999999999888614322567999999


No 4  
>cd03186 GST_C_SspA GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival during nutrient starvation. SspA adopts the GST fold with an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, but it does not bind glutathione (GSH) and lacks GST activity. SspA is highly conserved among gram-negative bacteria. Related proteins found in Neisseria (called RegF), Francisella and Vibrio regulate the expression of virulence factors necessary for pathogenesis.
Probab=17.54  E-value=76  Score=14.55  Aligned_cols=19  Identities=37%  Similarity=0.754  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHCC-HHHHHCC
Q ss_conf             999999998246-1242104
Q 537021.9.peg.1   28 SLATLLYLFSSN-FFLSDRF   46 (47)
Q Consensus        28 slatllylfssn-fflsdrf   46 (47)
                      +|.++.-+|+.+ ||+||.|
T Consensus        43 ~L~~l~p~F~~~pyFmsdEF   62 (107)
T cd03186          43 SLLALAPVFAHKPYFMSEEF   62 (107)
T ss_pred             HHHHHHHHHCCCCCCCCCCC
T ss_conf             99999999804844022652


No 5  
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus.
Probab=14.50  E-value=77  Score=14.53  Aligned_cols=17  Identities=41%  Similarity=0.776  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999887789999
Q 537021.9.peg.1   12 FLYFAKYLRESTRAFFS   28 (47)
Q Consensus        12 flyfakylrestraffs   28 (47)
                      +=|=|+|.+||.|+...
T Consensus       230 ~GYRA~Yi~~tar~l~e  246 (379)
T TIGR00588       230 LGYRARYIRETARALLE  246 (379)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             87540689999999884


No 6  
>TIGR02235 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase; InterPro: IPR011937    This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I . The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility..
Probab=11.16  E-value=1.4e+02  Score=13.20  Aligned_cols=15  Identities=53%  Similarity=0.707  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHCCHHH
Q ss_conf             999999998246124
Q 537021.9.peg.1   28 SLATLLYLFSSNFFL   42 (47)
Q Consensus        28 slatllylfssnffl   42 (47)
                      |++|-+-||.|||+-
T Consensus       179 ~~~TtliLFCsHFHQ  193 (293)
T TIGR02235       179 ALATTLILFCSHFHQ  193 (293)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             899999998423464


No 7  
>pfam05568 ASFV_J13L African swine fever virus J13L protein. This family consists of several African swine fever virus J13L proteins.
Probab=9.45  E-value=1.3e+02  Score=13.36  Aligned_cols=11  Identities=55%  Similarity=0.978  Sum_probs=8.0

Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998246
Q 537021.9.peg.1   29 LATLLYLFSSN   39 (47)
Q Consensus        29 latllylfssn   39 (47)
                      .-.|.|||||.
T Consensus        45 iivliylfssr   55 (189)
T pfam05568        45 IIVLIYLFSSR   55 (189)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999997220


No 8  
>PRK10494 hypothetical protein; Provisional
Probab=8.97  E-value=1.7e+02  Score=12.72  Aligned_cols=27  Identities=26%  Similarity=0.357  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHCC
Q ss_conf             887789999999999982461242104
Q 537021.9.peg.1   20 RESTRAFFSLATLLYLFSSNFFLSDRF   46 (47)
Q Consensus        20 restraffslatllylfssnfflsdrf   46 (47)
                      +...|.+..++.+++++.|+-..+|..
T Consensus        36 ~k~~~~~~~~~~l~l~~~s~~pv~~~L   62 (259)
T PRK10494         36 QKTGKIFISIGWLALLLLSLQPVADRL   62 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999989999999


No 9  
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=8.23  E-value=1.7e+02  Score=12.72  Aligned_cols=12  Identities=58%  Similarity=0.683  Sum_probs=8.2

Q ss_pred             HHHHHHHHCCHH
Q ss_conf             999999824612
Q 537021.9.peg.1   30 ATLLYLFSSNFF   41 (47)
Q Consensus        30 atllylfssnff   41 (47)
                      ..+--||||-||
T Consensus        27 fvl~iLfsSYfF   38 (39)
T PRK00753         27 FVLGILFSSYFF   38 (39)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999998823


No 10 
>KOG1589 consensus
Probab=7.77  E-value=1.2e+02  Score=13.50  Aligned_cols=10  Identities=60%  Similarity=1.032  Sum_probs=0.0

Q ss_pred             HHHHCCHHHH
Q ss_conf             9982461242
Q 537021.9.peg.1   34 YLFSSNFFLS   43 (47)
Q Consensus        34 ylfssnffls   43 (47)
                      +|||-|||+.
T Consensus        77 ~LfsVN~f~~   86 (118)
T KOG1589          77 SLFSVNFFVA   86 (118)
T ss_pred             HHHHHHHHHH
T ss_conf             2467899999


Done!