Query 537021.9.peg.414_1 Match_columns 45 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 24 19:35:41 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_414.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam04850 Baculo_E66 Baculovir 38.8 6.1 0.00015 21.4 -0.8 20 11-30 303-322 (389) 2 pfam12284 HoxA13_N Hox protein 34.3 15 0.00037 19.4 0.6 18 2-19 74-91 (115) 3 TIGR01298 RNaseT ribonuclease 18.2 57 0.0015 16.3 1.1 18 3-20 6-23 (201) 4 KOG1852 consensus 15.4 36 0.00092 17.3 -0.5 37 2-38 138-184 (223) 5 TIGR01911 HesB_rel_seleno HesB 13.8 48 0.0012 16.7 -0.2 31 11-41 49-80 (93) 6 TIGR00175 mito_nad_idh isocitr 13.5 67 0.0017 15.9 0.5 16 26-41 90-105 (348) 7 TIGR00169 leuB 3-isopropylmala 13.4 53 0.0013 16.5 -0.1 17 24-40 90-106 (370) 8 TIGR02373 photo_yellow photoac 12.9 72 0.0018 15.8 0.5 15 11-25 83-97 (126) 9 cd02861 E_set_proteins_like E 10.9 77 0.002 15.6 0.1 22 2-27 34-55 (82) 10 COG2158 Uncharacterized protei 9.5 1.5E+02 0.0038 14.1 1.2 15 5-23 25-39 (112) No 1 >pfam04850 Baculo_E66 Baculovirus E66 occlusion-derived virus envelope protein. Probab=38.84 E-value=6.1 Score=21.38 Aligned_cols=20 Identities=35% Similarity=0.982 Sum_probs=16.4 Q ss_pred EECCCCEEEEEEEHHHHHHH Q ss_conf 72168146876356999999 Q 537021.9.peg.4 11 NLENGELNCIFEFQFVILKK 30 (45) Q Consensus 11 nlengelncifefqfvilkk 30 (45) .-.+++..|+|+|.+|+||. T Consensus 303 ~t~~~~i~~~fdfP~v~lKd 322 (389) T pfam04850 303 VTNGGNIKCLFDFPYVVLKD 322 (389) T ss_pred EECCCCEEEEEECCEEEEEC T ss_conf 98489689999886999964 No 2 >pfam12284 HoxA13_N Hox protein A13 N terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 306 amino acids in length. The family is found in association with pfam00046. This family is the N terminal of the Hox gene protein involved in formation of the digital arch of the hands and feet as well as in correct genital formation. Mutation of the protein is associated with hand-foot-genital syndrome. Probab=34.29 E-value=15 Score=19.39 Aligned_cols=18 Identities=39% Similarity=1.128 Sum_probs=12.1 Q ss_pred CCCCEEEEEEECCCCEEE Q ss_conf 876102687721681468 Q 537021.9.peg.4 2 SEGYYPCKVNLENGELNC 19 (45) Q Consensus 2 segyypckvnlengelnc 19 (45) .-|||||.++-.+.---| T Consensus 74 GsgYYpCRmsh~~~lksc 91 (115) T pfam12284 74 GSGYYPCRMSHHGGVKSC 91 (115) T ss_pred CCCCCCCEECCCCCCCCC T ss_conf 887456221477774325 No 3 >TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3.1.13 from EC) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases.; GO: 0004540 ribonuclease activity, 0006396 RNA processing. Probab=18.18 E-value=57 Score=16.28 Aligned_cols=18 Identities=33% Similarity=0.669 Sum_probs=15.9 Q ss_pred CCCEEEEEEECCCCEEEE Q ss_conf 761026877216814687 Q 537021.9.peg.4 3 EGYYPCKVNLENGELNCI 20 (45) Q Consensus 3 egyypckvnlengelnci 20 (45) .||||.-|..|.|-+|.- T Consensus 6 RGylPVVvDVET~GfN~~ 23 (201) T TIGR01298 6 RGYLPVVVDVETAGFNAK 23 (201) T ss_pred CCCCCEEEEECCCCCCCH T ss_conf 554434886106776601 No 4 >KOG1852 consensus Probab=15.40 E-value=36 Score=17.33 Aligned_cols=37 Identities=30% Similarity=0.633 Sum_probs=27.6 Q ss_pred CCCCEEEEEEECCCCE----------EEEEEEHHHHHHHHHHHHCCC Q ss_conf 8761026877216814----------687635699999999872130 Q 537021.9.peg.4 2 SEGYYPCKVNLENGEL----------NCIFEFQFVILKKLFDIFGNL 38 (45) Q Consensus 2 segyypckvnlengel----------ncifefqfvilkklfdifgnl 38 (45) |..|+|..|+...... --||...|.--.++||+|.|- T Consensus 138 snkyfpsrvsikessv~klgsvcrrvyrifsha~fhhr~ifdefe~e 184 (223) T KOG1852 138 SNKYFPSRVSIKESSVAKLGSVCRRVYRIFSHAYFHHRKIFDEFENE 184 (223) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 77757753201165588888999999999878888899999874226 No 5 >TIGR01911 HesB_rel_seleno HesB-related (seleno)protein; InterPro: IPR010965 This entry represents a family of small proteins related to HesB and its close homologs, which are likely to be involved in iron-sulphur cluster assembly. Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain.. Probab=13.79 E-value=48 Score=16.67 Aligned_cols=31 Identities=35% Similarity=0.444 Sum_probs=26.8 Q ss_pred EECCCCEEEEEEEHHHHHHHHHHHHCC-CEEE Q ss_conf 721681468763569999999987213-0100 Q 537021.9.peg.4 11 NLENGELNCIFEFQFVILKKLFDIFGN-LRIM 41 (45) Q Consensus 11 nlengelncifefqfvilkklfdifgn-lrim 41 (45) .-||-|+-.|-++.|+|=+.|-|.|+. ..|. T Consensus 49 ~nenD~~~~i~d~~f~ID~~lid~flgef~I~ 80 (93) T TIGR01911 49 KNENDEVVVIKDLTFLIDKSLIDQFLGEFSIS 80 (93) T ss_pred CCCCCEEEEECCEEEEECCHHHHHCCCEEEEE T ss_conf 79997478854427986502453308806998 No 6 >TIGR00175 mito_nad_idh isocitrate dehydrogenase, NAD-dependent; InterPro: IPR004434 Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Mitochondrial NAD-dependent isocitrate dehydrogenases (IDH) resemble prokaryotic NADP-dependent IDH and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent IDH. The mitochondrial NAD-dependent isocitrate dehydrogenase is believed to be an alpha(2)-beta-gamma heterotetramer. All subunits are homologous and belog to this group. The NADP-dependent IDH of Thermus thermophilus strain HB8 resembles these NAD-dependent IDH, except for the residues involved in cofactor specificity, much more closely than it resembles other prokaryotic NADP-dependent IDH, including that of Thermus aquaticus. ; GO: 0004449 isocitrate dehydrogenase (NAD+) activity, 0006099 tricarboxylic acid cycle, 0005739 mitochondrion. Probab=13.50 E-value=67 Score=15.93 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=13.8 Q ss_pred HHHHHHHHHHCCCEEE Q ss_conf 9999999872130100 Q 537021.9.peg.4 26 VILKKLFDIFGNLRIM 41 (45) Q Consensus 26 vilkklfdifgnlrim 41 (45) |.|.|-||+|-|++-. T Consensus 90 ~~LRk~LDLYANVvh~ 105 (348) T TIGR00175 90 VALRKELDLYANVVHC 105 (348) T ss_pred HHHHHHCCCEEEEEEE T ss_conf 6776650710555445 No 7 >TIGR00169 leuB 3-isopropylmalate dehydrogenase; InterPro: IPR004429 Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0009098 leucine biosynthetic process, 0005737 cytoplasm. Probab=13.36 E-value=53 Score=16.47 Aligned_cols=17 Identities=41% Similarity=0.680 Sum_probs=13.6 Q ss_pred HHHHHHHHHHHHCCCEE Q ss_conf 69999999987213010 Q 537021.9.peg.4 24 QFVILKKLFDIFGNLRI 40 (45) Q Consensus 24 qfvilkklfdifgnlri 40 (45) -..-|.|-||.|-|||= T Consensus 90 GLL~lRK~l~LfANLRP 106 (370) T TIGR00169 90 GLLKLRKELDLFANLRP 106 (370) T ss_pred CHHHHHHHCCCCCCCCC T ss_conf 42677753685021475 No 8 >TIGR02373 photo_yellow photoactive yellow protein; InterPro: IPR012130 Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by IPR012743 from INTERPRO is required for its biosynthesis. The modified Cys is in a PAS domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.; GO: 0009881 photoreceptor activity, 0007602 phototransduction, 0018298 protein-chromophore linkage. Probab=12.89 E-value=72 Score=15.76 Aligned_cols=15 Identities=33% Similarity=0.944 Sum_probs=12.2 Q ss_pred EECCCCEEEEEEEHH Q ss_conf 721681468763569 Q 537021.9.peg.4 11 NLENGELNCIFEFQF 25 (45) Q Consensus 11 nlengelncifefqf 25 (45) -..+|.||..|||.| T Consensus 83 gv~~G~ln~mfdy~F 97 (126) T TIGR02373 83 GVASGQLNAMFDYVF 97 (126) T ss_pred CCCCCCCCEEEEEEE T ss_conf 102465213676665 No 9 >cd02861 E_set_proteins_like E or "early" set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. Probab=10.87 E-value=77 Score=15.60 Aligned_cols=22 Identities=32% Similarity=0.844 Sum_probs=0.0 Q ss_pred CCCCEEEEEEECCCCEEEEEEEHHHH Q ss_conf 87610268772168146876356999 Q 537021.9.peg.4 2 SEGYYPCKVNLENGELNCIFEFQFVI 27 (45) Q Consensus 2 segyypckvnlengelncifefqfvi 27 (45) +.|.+-+.+.|+.|+ +||+|++ T Consensus 34 ~~g~w~~~~~L~~G~----y~Ykf~V 55 (82) T cd02861 34 GDGLWVVTVELRPGR----YEYKFVV 55 (82) T ss_pred CCCCEEEEEECCCCC----EEEEEEE T ss_conf 999599999679886----9999999 No 10 >COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only] Probab=9.51 E-value=1.5e+02 Score=14.11 Aligned_cols=15 Identities=47% Similarity=1.378 Sum_probs=0.0 Q ss_pred CEEEEEEECCCCEEEEEEE Q ss_conf 1026877216814687635 Q 537021.9.peg.4 5 YYPCKVNLENGELNCIFEF 23 (45) Q Consensus 5 yypckvnlengelncifef 23 (45) ||||.-.-. ||.|=| T Consensus 25 YYPCHfdgQ----nC~fCy 39 (112) T COG2158 25 YYPCHFDGQ----NCLFCY 39 (112) T ss_pred EECCEECCC----CEEEEE T ss_conf 705323599----455894 Done!