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!