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!