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!