Query         537021.9.peg.691_1
Match_columns 46
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 05:29:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_691.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK02624 psbH photosystem II r  45.3      16 0.00041   18.7   2.2   22   17-38     36-57  (64)
  2 CHL00066 psbH photosystem II p  44.1      17 0.00043   18.5   2.2   22   17-38     48-69  (73)
  3 pfam00737 PsbH Photosystem II   42.1      20  0.0005   18.2   2.3   20   16-35     32-51  (52)
  4 TIGR01717 AMP-nucleosdse AMP n  26.2      27 0.00069   17.5   0.8   14   29-42    329-342 (486)
  5 pfam11435 She2p RNA binding pr  24.9      32 0.00081   17.1   1.0   22   14-35      5-26  (205)
  6 KOG3315 consensus               22.6      24 0.00061   17.8  -0.0   18    8-25    116-133 (191)
  7 pfam05982 DUF897 Domain of unk  19.3      76  0.0019   15.2   2.0   18   12-29     18-35  (327)
  8 COG5128 Transport protein part  18.5      49  0.0012   16.2   0.8   18    8-25    129-146 (208)
  9 TIGR02812 fadR_gamma fatty aci  12.3      38 0.00098   16.7  -1.0   10   24-33    198-207 (275)
 10 TIGR01876 cas_Cas5d CRISPR-ass  11.8      76  0.0019   15.2   0.3   18   28-45    104-124 (235)

No 1  
>PRK02624 psbH photosystem II reaction center protein H; Provisional
Probab=45.27  E-value=16  Score=18.66  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             6899999999974415666568
Q 537021.9.peg.6   17 PLFSRFISIYLLIFNSAIPIKN   38 (46)
Q Consensus        17 plfsrfisiyllifnsaipikn   38 (46)
                      -||.-|..|.|-|+||.+.+.+
T Consensus        36 ~Lf~vfl~iiLeiYNssvlldg   57 (64)
T PRK02624         36 VLFLVFLLIILQIYNQSLLLQG   57 (64)
T ss_pred             HHHHHHHHHHHHHHCCCEEECC
T ss_conf             9999999999999365425437


No 2  
>CHL00066 psbH photosystem II protein H
Probab=44.12  E-value=17  Score=18.53  Aligned_cols=22  Identities=41%  Similarity=0.721  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             6899999999974415666568
Q 537021.9.peg.6   17 PLFSRFISIYLLIFNSAIPIKN   38 (46)
Q Consensus        17 plfsrfisiyllifnsaipikn   38 (46)
                      -||.-|..|.|-|+||.+.+.+
T Consensus        48 ~lfavfl~iiLeiYNsSvlLdg   69 (73)
T CHL00066         48 ALFAVFLSIILEIYNSSVLLDG   69 (73)
T ss_pred             HHHHHHHHHHHHHHCCCEEECC
T ss_conf             9999999999999566336427


No 3  
>pfam00737 PsbH Photosystem II 10 kDa phosphoprotein. This protein is phosphorylated in a light dependent reaction.
Probab=42.15  E-value=20  Score=18.20  Aligned_cols=20  Identities=40%  Similarity=0.632  Sum_probs=16.7

Q ss_pred             CHHHHHHHHHHHHHHCCCCC
Q ss_conf             16899999999974415666
Q 537021.9.peg.6   16 SPLFSRFISIYLLIFNSAIP   35 (46)
Q Consensus        16 splfsrfisiyllifnsaip   35 (46)
                      --||.-|..|.|.|+||.+.
T Consensus        32 m~lf~vFl~iiLeiyNsSvl   51 (52)
T pfam00737        32 MALFAVFLLIILEIYNSSLL   51 (52)
T ss_pred             HHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999999999424223


No 4  
>TIGR01717 AMP-nucleosdse AMP nucleosidase; InterPro: IPR011271   This entry represents the AMP nucleosidase from proteobacteria but also including sequences from Corynebacterium, a Gram-positive organism. The Escherichia coli protein is the most well studied ..
Probab=26.15  E-value=27  Score=17.48  Aligned_cols=14  Identities=29%  Similarity=0.778  Sum_probs=12.2

Q ss_pred             HHCCCCCCCCCCCH
Q ss_conf             44156665688720
Q 537021.9.peg.6   29 IFNSAIPIKNPIPQ   42 (46)
Q Consensus        29 ifnsaipiknpipq   42 (46)
                      |.|..+|..+|||-
T Consensus       329 vLd~~lP~~~PIPA  342 (486)
T TIGR01717       329 VLDTRLPPDIPIPA  342 (486)
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             53765769879876


No 5  
>pfam11435 She2p RNA binding protein She2p. She2p is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation. ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. She2p contains a globular domain consisting of a bundle of five alpha-helices.
Probab=24.91  E-value=32  Score=17.15  Aligned_cols=22  Identities=45%  Similarity=0.662  Sum_probs=17.4

Q ss_pred             EECHHHHHHHHHHHHHHCCCCC
Q ss_conf             3016899999999974415666
Q 537021.9.peg.6   14 SISPLFSRFISIYLLIFNSAIP   35 (46)
Q Consensus        14 sisplfsrfisiyllifnsaip   35 (46)
                      .|.++||++||-|.-+.|.-|.
T Consensus         5 qii~~fs~YiS~yi~~LNkyI~   26 (205)
T pfam11435         5 QIISLFSNYISRYVHILNKYIN   26 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999


No 6  
>KOG3315 consensus
Probab=22.63  E-value=24  Score=17.78  Aligned_cols=18  Identities=44%  Similarity=0.702  Sum_probs=15.0

Q ss_pred             EEEECEEECHHHHHHHHH
Q ss_conf             333121301689999999
Q 537021.9.peg.6    8 ETYHNISISPLFSRFISI   25 (46)
Q Consensus         8 etyhnisisplfsrfisi   25 (46)
                      .||--+.-.||+++|||+
T Consensus       116 ~tYmiid~~pl~n~fISV  133 (191)
T KOG3315         116 RTYMIIDKEPLVNTFISV  133 (191)
T ss_pred             CEEEEECCCCHHHHCEEC
T ss_conf             538997176203310424


No 7  
>pfam05982 DUF897 Domain of unknown function (DUF897). Family of bacterial proteins with unknown function
Probab=19.34  E-value=76  Score=15.22  Aligned_cols=18  Identities=28%  Similarity=0.586  Sum_probs=14.6

Q ss_pred             CEEECHHHHHHHHHHHHH
Q ss_conf             213016899999999974
Q 537021.9.peg.6   12 NISISPLFSRFISIYLLI   29 (46)
Q Consensus        12 nisisplfsrfisiylli   29 (46)
                      +..|..-.++|+|+|||+
T Consensus        18 dL~iP~ai~~~LSiyLLl   35 (327)
T pfam05982        18 DLEIPEAIYETLSLYLLL   35 (327)
T ss_pred             CCCCCHHHHHHHHHHHHH
T ss_conf             787886799999999999


No 8  
>COG5128 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=18.51  E-value=49  Score=16.22  Aligned_cols=18  Identities=44%  Similarity=0.779  Sum_probs=13.2

Q ss_pred             EEEECEEECHHHHHHHHH
Q ss_conf             333121301689999999
Q 537021.9.peg.6    8 ETYHNISISPLFSRFISI   25 (46)
Q Consensus         8 etyhnisisplfsrfisi   25 (46)
                      .+|--..-.|||+||||.
T Consensus       129 ~eYmivDn~plls~FIsv  146 (208)
T COG5128         129 REYMIVDNDPLLSRFISV  146 (208)
T ss_pred             CEEEEECCCHHHHHHHCC
T ss_conf             526886386277877348


No 9  
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=12.32  E-value=38  Score=16.73  Aligned_cols=10  Identities=50%  Similarity=0.693  Sum_probs=7.1

Q ss_pred             HHHHHHHCCC
Q ss_conf             9999744156
Q 537021.9.peg.6   24 SIYLLIFNSA   33 (46)
Q Consensus        24 siyllifnsa   33 (46)
                      .||.|||||-
T Consensus       198 ~iY~LILNgl  207 (275)
T TIGR02812       198 PIYGLILNGL  207 (275)
T ss_pred             CEEEEHCCHH
T ss_conf             2333020010


No 10 
>TIGR01876 cas_Cas5d CRISPR-associated protein Cas5, Dvulg subtype; InterPro: IPR010155   CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum..
Probab=11.81  E-value=76  Score=15.25  Aligned_cols=18  Identities=44%  Similarity=0.717  Sum_probs=13.0

Q ss_pred             HHHCCCCC---CCCCCCHHCC
Q ss_conf             74415666---5688720005
Q 537021.9.peg.6   28 LIFNSAIP---IKNPIPQSLQ   45 (46)
Q Consensus        28 lifnsaip---iknpipqslq   45 (46)
                      +.||..-+   .|.|+|.|||
T Consensus       104 fef~~~r~rPdakrPvPeslq  124 (235)
T TIGR01876       104 FEFNEDRERPDAKRPVPESLQ  124 (235)
T ss_pred             EEECCCCCCCCCCCCCCCHHH
T ss_conf             886288888866788850110


Done!