Query         537021.9.peg.873_1
Match_columns 41
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 01:27:47 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_873.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02728 spore_gerQ spore coa  36.3      31 0.00078   17.4   2.5   31    7-39      2-32  (82)
  2 pfam05748 Rubella_E1 Rubella m  27.7      26 0.00067   17.8   1.0   14   18-31    405-418 (496)
  3 pfam09671 Spore_GerQ Spore coa  27.2      12  0.0003   19.5  -0.9   33    6-40      3-35  (81)
  4 pfam03068 PAD Protein-arginine  20.3      34 0.00086   17.2   0.3   21    8-28    122-142 (385)
  5 pfam00608 Adeno_shaft Adenovir  16.4      81  0.0021   15.3   1.5   15   14-28      1-15  (30)
  6 TIGR02668 moaA_archaeal probab  15.9      46  0.0012   16.6   0.2   19   11-38    272-290 (324)
  7 KOG0983 consensus               11.5 1.5E+02  0.0037   14.0   1.7   17   22-38    149-165 (391)
  8 pfam02262 Cbl_N CBL proto-onco  10.2      91  0.0023   15.1   0.3   13   14-26     26-38  (130)
  9 pfam06973 DUF1297 Domain of un  10.1 1.1E+02  0.0028   14.7   0.7   21    9-29     56-84  (188)
 10 TIGR01958 nuoE_fam NADH-quinon   9.4 1.2E+02  0.0029   14.6   0.6   15    5-19     99-113 (153)

No 1  
>TIGR02728 spore_gerQ spore coat protein GerQ; InterPro: IPR014099   Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase..
Probab=36.27  E-value=31  Score=17.44  Aligned_cols=31  Identities=35%  Similarity=0.649  Sum_probs=25.1

Q ss_pred             EEEECCCCCEEEECCCCCEEEEEEEEECCCCCC
Q ss_conf             642021121689628998079999995154554
Q 537021.9.peg.8    7 EMRQSTIDGKLKLNTSPPYTVTCFLTFENATDY   39 (41)
Q Consensus         7 emrqstidgklklntsppytvtcfltfenatdy   39 (41)
                      -..||-|..-|.+|-..  +.|.+.||||....
T Consensus         2 P~~~SyiENILR~NRG~--~aT~Y~Tf~N~~~~   32 (82)
T TIGR02728         2 PVEQSYIENILRMNRGK--TATVYMTFENSKEW   32 (82)
T ss_pred             CCCCCEEEEEEECCCCC--EEEEEEEEECCCCC
T ss_conf             87521001000116886--15789885088000


No 2  
>pfam05748 Rubella_E1 Rubella membrane glycoprotein E1. Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus. The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa). In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins. The E1 has been shown to be a type 1 membrane protein, rich in cysteine residues with extensive i
Probab=27.69  E-value=26  Score=17.76  Aligned_cols=14  Identities=57%  Similarity=0.914  Sum_probs=11.6

Q ss_pred             EECCCCCEEEEEEE
Q ss_conf             96289980799999
Q 537021.9.peg.8   18 KLNTSPPYTVTCFL   31 (41)
Q Consensus        18 klntsppytvtcfl   31 (41)
                      -|||.|||.|.|--
T Consensus       405 llntpppyqvscgg  418 (496)
T pfam05748       405 LLNTPPPYQVSCGG  418 (496)
T ss_pred             HHCCCCCEEEECCC
T ss_conf             50699970640478


No 3  
>pfam09671 Spore_GerQ Spore coat protein (Spore_GerQ). Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=27.18  E-value=12  Score=19.52  Aligned_cols=33  Identities=33%  Similarity=0.639  Sum_probs=25.8

Q ss_pred             EEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCC
Q ss_conf             76420211216896289980799999951545547
Q 537021.9.peg.8    6 IEMRQSTIDGKLKLNTSPPYTVTCFLTFENATDYN   40 (41)
Q Consensus         6 iemrqstidgklklntsppytvtcfltfenatdyn   40 (41)
                      +.+.||-|..-|+||....  .|.+.||||...+|
T Consensus         3 lp~eqSyieNILRlN~GK~--~T~y~Tfenn~eWn   35 (81)
T pfam09671         3 LPLEQSYIENILRLNRGKQ--ATVYMTFENNSEWG   35 (81)
T ss_pred             CCHHHHHHHHHHHHCCCCE--EEEEEEECCCHHHH
T ss_conf             7327999998997627854--89999975866762


No 4  
>pfam03068 PAD Protein-arginine deiminase (PAD). Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes EC:3.5.3.15 catalyse the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-arginine + H2O <= Protein L-citrulline + NH3. Several types are recognized (and included in the family) on the basis of molecular mass, substrate specificity, and tissue localisation. The expression of type I PAD is known to be under the control of oestrogen.
Probab=20.31  E-value=34  Score=17.22  Aligned_cols=21  Identities=38%  Similarity=0.411  Sum_probs=15.8

Q ss_pred             EEECCCCCEEEECCCCCEEEE
Q ss_conf             420211216896289980799
Q 537021.9.peg.8    8 MRQSTIDGKLKLNTSPPYTVT   28 (41)
Q Consensus         8 mrqstidgklklntsppytvt   28 (41)
                      ..-+++|.-=.|.+|||||+.
T Consensus       122 ~~~~slDSfGNLEvsPPvt~~  142 (385)
T pfam03068       122 AGVSGLDSFGNLEVSPPVTVR  142 (385)
T ss_pred             CCCCCCCCCCCCCCCCCCCCC
T ss_conf             775443145761337971237


No 5  
>pfam00608 Adeno_shaft Adenoviral fibre protein (repeat/shaft region). There is no separation between signal and noise. Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, rather than the 'shaft' region represented by this family. The alignment of this family contains two copies of a fifteen residue repeat found in the 'shaft' region of adenoviral fibre proteins.
Probab=16.40  E-value=81  Score=15.34  Aligned_cols=15  Identities=53%  Similarity=0.709  Sum_probs=10.2

Q ss_pred             CCEEEECCCCCEEEE
Q ss_conf             216896289980799
Q 537021.9.peg.8   14 DGKLKLNTSPPYTVT   28 (41)
Q Consensus        14 dgklklntsppytvt   28 (41)
                      ++.|.+++++|.+++
T Consensus         1 ~~~L~l~~g~gL~v~   15 (30)
T pfam00608         1 NNSLSLNTGPGLTVT   15 (30)
T ss_pred             CCCEECCCCCCEEEE
T ss_conf             972000369983785


No 6  
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485    This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=15.92  E-value=46  Score=16.57  Aligned_cols=19  Identities=58%  Similarity=0.824  Sum_probs=12.8

Q ss_pred             CCCCCEEEECCCCCEEEEEEEEECCCCC
Q ss_conf             2112168962899807999999515455
Q 537021.9.peg.8   11 STIDGKLKLNTSPPYTVTCFLTFENATD   38 (41)
Q Consensus        11 stidgklklntsppytvtcfltfenatd   38 (41)
                      -|.|||||         ||.|--+|-.|
T Consensus       272 lT~DGkLK---------tCLlR~D~~~d  290 (324)
T TIGR02668       272 LTSDGKLK---------TCLLRNDNLVD  290 (324)
T ss_pred             ECCCCCCC---------CCCCCCCCCCC
T ss_conf             52366224---------54144779667


No 7  
>KOG0983 consensus
Probab=11.46  E-value=1.5e+02  Score=14.05  Aligned_cols=17  Identities=47%  Similarity=0.774  Sum_probs=13.4

Q ss_pred             CCCEEEEEEEEECCCCC
Q ss_conf             99807999999515455
Q 537021.9.peg.8   22 SPPYTVTCFLTFENATD   38 (41)
Q Consensus        22 sppytvtcfltfenatd   38 (41)
                      .-||-|+||-.|-..+|
T Consensus       149 dcpyIV~c~GyFi~n~d  165 (391)
T KOG0983         149 DCPYIVQCFGYFITNTD  165 (391)
T ss_pred             CCCEEEEEEEEEEECCH
T ss_conf             99723113457862760


No 8  
>pfam02262 Cbl_N CBL proto-oncogene N-terminal domain 1. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. Cbl_N is comprised of 3 structural domains of which this is the first - a four helix bundle.
Probab=10.22  E-value=91  Score=15.08  Aligned_cols=13  Identities=46%  Similarity=0.874  Sum_probs=9.7

Q ss_pred             CCEEEECCCCCEE
Q ss_conf             2168962899807
Q 537021.9.peg.8   14 DGKLKLNTSPPYT   26 (41)
Q Consensus        14 dgklklntsppyt   26 (41)
                      +-||.|..||||-
T Consensus        26 ~Prl~LKnSPP~i   38 (130)
T pfam02262        26 SPKLNLKNSPPFI   38 (130)
T ss_pred             CCCCCCCCCCCHH
T ss_conf             9763346799369


No 9  
>pfam06973 DUF1297 Domain of unknown function (DUF1297). This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme.
Probab=10.13  E-value=1.1e+02  Score=14.67  Aligned_cols=21  Identities=43%  Similarity=0.757  Sum_probs=15.1

Q ss_pred             EECCCCC--------EEEECCCCCEEEEE
Q ss_conf             2021121--------68962899807999
Q 537021.9.peg.8    9 RQSTIDG--------KLKLNTSPPYTVTC   29 (41)
Q Consensus         9 rqstidg--------klklntsppytvtc   29 (41)
                      .||.+||        .|+++-.|.|+|+-
T Consensus        56 ~esniDg~~Rlpa~~Ql~~~~~p~~vvvG   84 (188)
T pfam06973        56 YESNLDGLVRLPAKQQLELNIEPTYVVVG   84 (188)
T ss_pred             EECCCHHHHCCCCHHHHHCCCCCCEEEEC
T ss_conf             23260344228827786168986079988


No 10 
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit; InterPro: IPR002023   Respiratory-chain NADH dehydrogenase (ubiquinone) (1.6.5.3 from EC) ,  (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to , : Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase  ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0006118 electron transport.
Probab=9.43  E-value=1.2e+02  Score=14.57  Aligned_cols=15  Identities=33%  Similarity=0.567  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCEEEE
Q ss_conf             676420211216896
Q 537021.9.peg.8    5 AIEMRQSTIDGKLKL   19 (41)
Q Consensus         5 aiemrqstidgklkl   19 (41)
                      +|...++|-|||++|
T Consensus        99 gi~~gEtT~DG~F~l  113 (153)
T TIGR01958        99 GIKPGETTPDGRFTL  113 (153)
T ss_pred             CCCCCCCCCCCCEEE
T ss_conf             866773479971798


Done!