Query 537021.9.peg.683_1 Match_columns 37 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 24 23:32:15 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_683.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01408 Ube1 ubiquitin-activ 37.9 9.6 0.00024 20.3 0.1 25 11-35 125-149 (1033) 2 pfam06801 consensus 28.3 22 0.00057 18.6 0.7 27 5-31 45-71 (96) 3 pfam08902 DUF1848 Domain of un 26.6 31 0.00078 17.9 1.1 17 9-25 71-87 (264) 4 pfam05311 Baculo_PP31 Baculovi 24.7 4 0.0001 22.1 -3.7 18 1-18 87-107 (267) 5 PTZ00007 (NAP-L) nucleosome as 18.6 48 0.0012 17.0 0.8 21 7-27 154-174 (360) 6 TIGR00653 GlnA glutamine synth 10.5 29 0.00075 18.0 -2.1 22 3-24 315-336 (486) 7 pfam11094 UL11 Membrane-associ 9.4 1.2E+02 0.003 15.1 0.6 12 26-37 14-25 (39) 8 pfam12538 FtsK_SpoIIIE_N DNA t 9.2 1.4E+02 0.0035 14.8 0.9 16 21-36 88-103 (111) 9 PRK13743 conjugal transfer pro 9.2 29 0.00073 18.0 -2.6 13 1-13 81-93 (140) 10 pfam00956 NAP Nucleosome assem 8.6 2.3E+02 0.0059 13.7 2.0 25 8-32 108-132 (237) No 1 >TIGR01408 Ube1 ubiquitin-activating enzyme E1; InterPro: IPR000011 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation , , . Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade . The E1 enzyme is responsible for activating ubiquitin, the first step in ubiquitinylation. The E1 enzyme hydrolyses ATP and adenylates the C-terminal glycine residue of ubiquitin, and then links this residue to the active site cysteine of E1, yielding a ubiquitin-thioester and free AMP. To be fully active, E1 must non-covalently bind to and adenylate a second ubiquitin molecule. The E1 enzyme can then transfer the thioester-linked ubiquitin molecule to a cysteine residue on the ubiquitin-conjugating enzyme, E2, in an ATP-dependent reaction.; GO: 0008641 small protein activating enzyme activity, 0006464 protein modification process, 0006512 ubiquitin cycle. Probab=37.91 E-value=9.6 Score=20.29 Aligned_cols=25 Identities=36% Similarity=0.638 Sum_probs=20.9 Q ss_pred EEEEEEEEECHHHHCCCCEEEECCC Q ss_conf 3799997500553167872653147 Q 537021.9.peg.6 11 FSLIFQFTINEYCRSNRNSITFSSG 35 (37) Q Consensus 11 fslifqftineycrsnrnsitfssg 35 (37) .||--|..||.||||+.-.|.|-+. T Consensus 125 ~~l~~q~einDfchs~~PPIafi~A 149 (1033) T TIGR01408 125 ISLEKQLEINDFCHSQQPPIAFIKA 149 (1033) T ss_pred CCHHHHHCCCCHHCCCCCCCEEEEC T ss_conf 7514420002010267377105521 No 2 >pfam06801 consensus Probab=28.30 E-value=22 Score=18.57 Aligned_cols=27 Identities=41% Similarity=0.507 Sum_probs=19.8 Q ss_pred HHCCCCEEEEEEEEECHHHHCCCCEEE Q ss_conf 420240379999750055316787265 Q 537021.9.peg.6 5 LKKAKSFSLIFQFTINEYCRSNRNSIT 31 (37) Q Consensus 5 lkkaksfslifqftineycrsnrnsit 31 (37) |-|-|-|.--.--|-|+||.+|..-|. T Consensus 45 llkmklfptnilgtcn~yct~nsdc~g 71 (96) T pfam06801 45 LLKMKLFPTNILGTCNDYCTSNSDCIG 71 (96) T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCEEE T ss_conf 887622551201114541157878445 No 3 >pfam08902 DUF1848 Domain of unknown function (DUF1848). This family of proteins are functionally uncharacterized. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of pfam04055. Probab=26.56 E-value=31 Score=17.90 Aligned_cols=17 Identities=35% Similarity=0.802 Sum_probs=14.1 Q ss_pred CCEEEEEEEEECHHHHC Q ss_conf 40379999750055316 Q 537021.9.peg.6 9 KSFSLIFQFTINEYCRS 25 (37) Q Consensus 9 ksfslifqftineycrs 25 (37) ..+...||||||.|-+. T Consensus 71 ~gy~~yfq~Tit~Y~~~ 87 (264) T pfam08902 71 RGYPYYFQFTLTPYGRD 87 (264) T ss_pred CCCCEEEEEEECCCCCC T ss_conf 69856999985799865 No 4 >pfam05311 Baculo_PP31 Baculovirus 33KDa late protein (PP31). Autographa californica nuclear polyhedrosis virus (AcMNPV) pp31 is a nuclear phosphoprotein that accumulates in the virogenic stroma, which is the viral replication centre in the infected-cell nucleus, binds to DNA, and serves as a late expression factor. Probab=24.70 E-value=4 Score=22.07 Aligned_cols=18 Identities=56% Similarity=1.064 Sum_probs=13.6 Q ss_pred CCHHHHC---CCCEEEEEEEE Q ss_conf 9034420---24037999975 Q 537021.9.peg.6 1 MWNILKK---AKSFSLIFQFT 18 (37) Q Consensus 1 mwnilkk---aksfslifqft 18 (37) |||+.|- ++.|-.||.|+ T Consensus 87 MWN~mK~~~~~k~Fv~IFD~m 107 (267) T pfam05311 87 MWNLMKSQSEAKPFVDIFDFM 107 (267) T ss_pred HHHHHHCCCCCCHHHHHHHHH T ss_conf 999985372203199998899 No 5 >PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional Probab=18.58 E-value=48 Score=16.97 Aligned_cols=21 Identities=29% Similarity=0.524 Sum_probs=16.6 Q ss_pred CCCCEEEEEEEEECHHHHCCC Q ss_conf 024037999975005531678 Q 537021.9.peg.6 7 KAKSFSLIFQFTINEYCRSNR 27 (37) Q Consensus 7 kaksfslifqftineycrsnr 27 (37) |..+|.|.|.|.-|+|-.... T Consensus 154 k~egF~L~F~F~pNpyFsNsv 174 (360) T PTZ00007 154 KKEGFILSFHFASNPFFSNSV 174 (360) T ss_pred CCCCEEEEEECCCCCCCCCCE T ss_conf 567648999748997666761 No 6 >TIGR00653 GlnA glutamine synthetase, type I; InterPro: IPR004809 Glutamine synthetase type I (or glutamate-ammonia ligase) has a dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. Escherichia coli, Synechocystis sp. (strain PCC 6803) , Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon S. acidocaldarius differs from that in E. coli in that it is not regulated by adenylation. ; GO: 0004356 glutamate-ammonia ligase activity, 0009399 nitrogen fixation, 0005737 cytoplasm. Probab=10.54 E-value=29 Score=17.99 Aligned_cols=22 Identities=41% Similarity=0.543 Sum_probs=18.9 Q ss_pred HHHHCCCCEEEEEEEEECHHHH Q ss_conf 3442024037999975005531 Q 537021.9.peg.6 3 NILKKAKSFSLIFQFTINEYCR 24 (37) Q Consensus 3 nilkkaksfslifqftineycr 24 (37) -|||.||++.-+--=|.|-|-| T Consensus 315 GiLkHA~AL~A~tNPTvNSYKR 336 (486) T TIGR00653 315 GILKHAKALAAFTNPTVNSYKR 336 (486) T ss_pred HHHHHHHHHHHHHCCCCCCCCC T ss_conf 0877778888976566055223 No 7 >pfam11094 UL11 Membrane-associated tegument protein. The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment. UL11 is acylated which is crucial for lipid raft association. Probab=9.42 E-value=1.2e+02 Score=15.14 Aligned_cols=12 Identities=50% Similarity=0.725 Sum_probs=9.4 Q ss_pred CCCEEEECCCCC Q ss_conf 787265314769 Q 537021.9.peg.6 26 NRNSITFSSGEI 37 (37) Q Consensus 26 nrnsitfssgei 37 (37) .||-++-++||. T Consensus 14 R~N~LvT~~Gev 25 (39) T pfam11094 14 RRNVLVTSSGEV 25 (39) T ss_pred ECCEEECCCCCE T ss_conf 168898058868 No 8 >pfam12538 FtsK_SpoIIIE_N DNA transporter. This domain family is found in bacteria, and is typically between 107 and 121 amino acids in length. The family is found in association with pfam01580. The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division. Probab=9.21 E-value=1.4e+02 Score=14.84 Aligned_cols=16 Identities=44% Similarity=0.515 Sum_probs=13.5 Q ss_pred HHHHCCCCEEEECCCC Q ss_conf 5531678726531476 Q 537021.9.peg.6 21 EYCRSNRNSITFSSGE 36 (37) Q Consensus 21 eycrsnrnsitfssge 36 (37) -|+-++|.+|+||+.+ T Consensus 88 vY~~g~~~~itis~~~ 103 (111) T pfam12538 88 VYDIGDRDEITISSEE 103 (111) T ss_pred EEECCCCEEEEECCCC T ss_conf 9945886699967897 No 9 >PRK13743 conjugal transfer protein TrbF; Provisional Probab=9.17 E-value=29 Score=18.04 Aligned_cols=13 Identities=54% Similarity=0.976 Sum_probs=9.1 Q ss_pred CCHHHHCCCCEEE Q ss_conf 9034420240379 Q 537021.9.peg.6 1 MWNILKKAKSFSL 13 (37) Q Consensus 1 mwnilkkaksfsl 13 (37) |||||-.|-.+.| T Consensus 81 mWNilMYaIPytL 93 (140) T PRK13743 81 MWNILMYAIPYTL 93 (140) T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999999 No 10 >pfam00956 NAP Nucleosome assembly protein (NAP). NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity. They affect the transcription of many genes. Probab=8.60 E-value=2.3e+02 Score=13.75 Aligned_cols=25 Identities=36% Similarity=0.606 Sum_probs=17.7 Q ss_pred CCCEEEEEEEEECHHHHCCCCEEEE Q ss_conf 2403799997500553167872653 Q 537021.9.peg.6 8 AKSFSLIFQFTINEYCRSNRNSITF 32 (37) Q Consensus 8 aksfslifqftineycrsnrnsitf 32 (37) ..+|.|.|.|.-|+|-....-+-+| T Consensus 108 ~~~f~l~F~F~~N~yF~N~~L~K~y 132 (237) T pfam00956 108 KKGFKLIFHFAPNPYFTNEVLTKTY 132 (237) T ss_pred CCCEEEEEEECCCCCCCCCEEEEEE T ss_conf 7736999996678776565699999 Done!