Query 537021.9.peg.993_1 Match_columns 52 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Wed May 25 04:47:54 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_993.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG2718 Uncharacterized conser 14.3 1.3E+02 0.0033 14.5 2.2 31 3-34 304-334 (423) 2 pfam09054 consensus 13.6 41 0.0011 16.8 -0.5 27 21-47 2-28 (46) 3 KOG4819 consensus 11.6 91 0.0023 15.2 0.7 19 8-26 83-101 (106) 4 cd04877 ACT_TyrR N-terminal AC 10.3 1.8E+02 0.0047 13.8 2.2 25 8-32 35-65 (74) 5 TIGR02062 RNase_B exoribonucle 8.7 42 0.0011 16.8 -1.9 37 4-40 624-662 (664) 6 cd04896 ACT_ACR-like_3 ACT dom 7.6 1.8E+02 0.0046 13.9 1.0 19 2-20 44-62 (75) 7 TIGR02863 spore_sspJ small, ac 6.6 1.7E+02 0.0042 14.0 0.4 17 1-17 1-17 (47) 8 KOG1680 consensus 6.5 2.4E+02 0.0061 13.3 1.1 11 39-49 45-55 (290) 9 pfam10805 DUF2730 Protein of u 6.1 2.3E+02 0.0058 13.4 0.8 14 14-27 91-104 (106) 10 PHA00738 putative HTH transcri 5.7 84 0.0022 15.4 -1.6 25 2-26 3-27 (112) No 1 >COG2718 Uncharacterized conserved protein [Function unknown] Probab=14.31 E-value=1.3e+02 Score=14.53 Aligned_cols=31 Identities=39% Similarity=0.728 Sum_probs=24.3 Q ss_pred EEEECCCCEEEECHHHHHHHHHHHHHEEEEHH Q ss_conf 23312342389815799998612332231264 Q 537021.9.peg.9 3 YFFNQTKGKIIINDQLQLLMENIIKIRYVTQE 34 (52) Q Consensus 3 yffnqtkgkiiindqlqllmeniikiryvtqe 34 (52) +|..|..|--|+..-|. +|++||+-||-..| T Consensus 304 FF~~~esGGTivSSAl~-~m~evi~ErYp~ae 334 (423) T COG2718 304 FFYSQESGGTIVSSALK-LMLEVIKERYPPAE 334 (423) T ss_pred CEEECCCCCEEEHHHHH-HHHHHHHHHCCHHH T ss_conf 02324789768688999-99999970388535 No 2 >pfam09054 consensus Probab=13.62 E-value=41 Score=16.81 Aligned_cols=27 Identities=26% Similarity=0.469 Sum_probs=21.4 Q ss_pred HHHHHHHHEEEEHHHHHHHCEEEEEEE Q ss_conf 986123322312643411246557643 Q 537021.9.peg.9 21 LMENIIKIRYVTQEARSLLGITLIKIN 47 (52) Q Consensus 21 lmeniikiryvtqearsllgitlikin 47 (52) |++|+|-.||+-.+.+---+|..+|-- T Consensus 2 L~D~iilLr~~E~~g~l~R~i~VlK~R 28 (46) T pfam09054 2 LADNVILLRYVELNGELRRALSVLKKR 28 (46) T ss_pred CEEEEEEEEEEEECCEEEEEEEEEEEC T ss_conf 355799898752298999889999932 No 3 >KOG4819 consensus Probab=11.56 E-value=91 Score=15.24 Aligned_cols=19 Identities=47% Similarity=0.707 Sum_probs=15.6 Q ss_pred CCCEEEECHHHHHHHHHHH Q ss_conf 3423898157999986123 Q 537021.9.peg.9 8 TKGKIIINDQLQLLMENII 26 (52) Q Consensus 8 tkgkiiindqlqllmenii 26 (52) -||.--.|||.++|.+-|- T Consensus 83 kKGQPnln~qM~~LL~~Iq 101 (106) T KOG4819 83 KKGQPNLNDQMQLLLKQIQ 101 (106) T ss_pred CCCCCCHHHHHHHHHHHHH T ss_conf 2589867789999999999 No 4 >cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence Probab=10.35 E-value=1.8e+02 Score=13.84 Aligned_cols=25 Identities=40% Similarity=0.550 Sum_probs=18.2 Q ss_pred CCCEEEE------CHHHHHHHHHHHHHEEEE Q ss_conf 3423898------157999986123322312 Q 537021.9.peg.9 8 TKGKIII------NDQLQLLMENIIKIRYVT 32 (52) Q Consensus 8 tkgkiii------ndqlqllmeniikiryvt 32 (52) .+|+|-+ .+++|-||..|-+|.-|+ T Consensus 35 ~~g~IYl~~~~l~f~~~~~Lm~~ir~I~GV~ 65 (74) T cd04877 35 PKGRIYLNFPTIEFEKLQTLMPEIRRIDGVE 65 (74) T ss_pred CCCEEEEECCCCCHHHHHHHHHHHHCCCCCC T ss_conf 6881899778789899999999984789831 No 5 >TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process. Probab=8.69 E-value=42 Score=16.78 Aligned_cols=37 Identities=24% Similarity=0.487 Sum_probs=23.3 Q ss_pred EEECCCCEEEECHHHHHHHHHHHH--HEEEEHHHHHHHC Q ss_conf 331234238981579999861233--2231264341124 Q 537021.9.peg.9 4 FFNQTKGKIIINDQLQLLMENIIK--IRYVTQEARSLLG 40 (52) Q Consensus 4 ffnqtkgkiiindqlqllmeniik--iryvtqearsllg 40 (52) -|||-.|++.|...+-.-...+|+ +-=|-++.||+.| T Consensus 624 ~~n~e~G~v~Ikge~~YKi~D~~~v~LtEv~~~tRSiva 662 (664) T TIGR02062 624 VCNQEEGTVYIKGEVVYKIGDVIEVVLTEVREETRSIVA 662 (664) T ss_pred EEECCCCEEEEEEEEEEEEEEEEEEEEEEEECCCCCEEC T ss_conf 650687638871078986610699998454013450112 No 6 >cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains. Probab=7.62 E-value=1.8e+02 Score=13.88 Aligned_cols=19 Identities=32% Similarity=0.471 Sum_probs=15.1 Q ss_pred CEEEECCCCEEEECHHHHH Q ss_conf 4233123423898157999 Q 537021.9.peg.9 2 AYFFNQTKGKIIINDQLQL 20 (52) Q Consensus 2 ayffnqtkgkiiindqlql 20 (52) ..|+-|++||-|++.+-|- T Consensus 44 dLFv~q~dGkKi~Dp~~q~ 62 (75) T cd04896 44 DLFIVQSDGKKIMDPKKQA 62 (75) T ss_pred EEEEECCCCCCCCCHHHHH T ss_conf 8999727988636989999 No 7 >TIGR02863 spore_sspJ small, acid-soluble spore protein, SspJ family; InterPro: IPR014220 This entry represents a group of small acid-soluble proteins (SASP) from Bacillus sp., which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background .. Probab=6.56 E-value=1.7e+02 Score=14.04 Aligned_cols=17 Identities=41% Similarity=0.682 Sum_probs=11.8 Q ss_pred CCEEEECCCCEEEECHH Q ss_conf 94233123423898157 Q 537021.9.peg.9 1 MAYFFNQTKGKIIINDQ 17 (52) Q Consensus 1 mayffnqtkgkiiindq 17 (52) |..|||..+|+---.++ T Consensus 1 mG~ffnkd~G~~~ek~~ 17 (47) T TIGR02863 1 MGIFFNKDKGKKSEKEK 17 (47) T ss_pred CCCCCCCCCCCCHHHHH T ss_conf 97545544454002457 No 8 >KOG1680 consensus Probab=6.49 E-value=2.4e+02 Score=13.33 Aligned_cols=11 Identities=55% Similarity=0.767 Sum_probs=7.7 Q ss_pred HCEEEEEEEEE Q ss_conf 24655764311 Q 537021.9.peg.9 39 LGITLIKINRL 49 (52) Q Consensus 39 lgitlikinrl 49 (52) -||++|.|||- T Consensus 45 ~~I~lItlNRP 55 (290) T KOG1680 45 NGIALITLNRP 55 (290) T ss_pred CCEEEEEECCH T ss_conf 87689983786 No 9 >pfam10805 DUF2730 Protein of unknown function (DUF2730). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. Probab=6.14 E-value=2.3e+02 Score=13.43 Aligned_cols=14 Identities=57% Similarity=0.838 Sum_probs=8.5 Q ss_pred ECHHHHHHHHHHHH Q ss_conf 81579999861233 Q 537021.9.peg.9 14 INDQLQLLMENIIK 27 (52) Q Consensus 14 indqlqllmeniik 27 (52) ++.|.+||.||-+| T Consensus 91 i~hq~~LLLE~~lk 104 (106) T pfam10805 91 ISHQLELLLENELK 104 (106) T ss_pred HHHHHHHHHHHHHC T ss_conf 88899999999864 No 10 >PHA00738 putative HTH transcription regulator Probab=5.65 E-value=84 Score=15.40 Aligned_cols=25 Identities=36% Similarity=0.530 Sum_probs=20.1 Q ss_pred CEEEECCCCEEEECHHHHHHHHHHH Q ss_conf 4233123423898157999986123 Q 537021.9.peg.9 2 AYFFNQTKGKIIINDQLQLLMENII 26 (52) Q Consensus 2 ayffnqtkgkiiindqlqllmenii 26 (52) .|--|.-++||.-..-|||+.||-+ T Consensus 3 ~ynaN~iraki~RrKIl~LiaENY~ 27 (112) T PHA00738 3 DYNANEIRAKILRKKILELIAENYI 27 (112) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 4118899999999999999999889 Done!