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!