YRC Public Data Repository - Protein Structure Prediction

Protein:	RELA_ECOLI
Organism:	Escherichia coli
Length:	744 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for RELA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|82402728, gi\|... - gi\|82499307\|ref\|ZP_00884755.1\| RelA/SpoT protein [Caldicellulosiruptor saccharolyticus DSM 8903], gi...	799.0	[0..16]	[743..7]
gi\|10443847 - gi\|10443847\|gb\|AAG17607.1\|AF242653_1 ppGpp synthetase/hydrolase Rel [Geobacillus stearothermophilus]	795.0	[0..13]	[744..8]
gi\|56421113, gi\|... - gi\|56421113\|ref\|YP_148431.1\| GTP pyrophosphokinase (ppGpp synthetase) [Geobacillus kaustophilus HTA4...	793.0	[0..13]	[744..8]
gi\|20516195, gi\|... - gi\|20807650\|ref\|NP_622821.1\| guanosine polyphosphate pyrophosphohydrolase/synthetase [Thermoanaeroba... gi\|20807650 - gi\|20807650\|ref\|NP_622821.1\| Guanosine polyphosphate pyrophosphohydrolase/synthetase [Thermoanaeroba...	793.0	[0..17]	[743..5]
gi\|69247932, gi\|... - gi\|69247932\|ref\|ZP_00604548.1\| RelA/SpoT protein [Enterococcus faecium DO], gi\|68194634\|gb\|EAN09121....	791.0	[0..17]	[743..12]
gi\|88911972, gi\|... - gi\|88931701\|ref\|ZP_01137394.1\| RelA/SpoT protein [Acidothermus cellulolyticus 11B], gi\|88911972\|gb\|E...	787.0	[0..17]	[743..89]
gi\|157162238, gi... - gi\|75196755\|ref\|ZP_00706825.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [E...	784.0	[0..1]	[744..1]
gi\|241903868, gi... - gi\|241903868\|ref\|ZP_04788584.1\| (p)ppGpp synthetase I, SpoT/RelA [Thermoanaerobacter brockii subsp. ... gi\|76797241, gi\|... - gi\|76797241\|ref\|ZP_00779574.1\| RelA/SpoT protein [Thermoanaerobacter ethanolicus ATCC 33223], gi\|765...	784.0	[0..17]	[743..5]
gi\|62129099, gi\|... - gi\|62181466\|ref\|YP_217883.1\| GDP/GTP pyrophosphokinase [Salmonella enterica subsp. enterica serovar ... gi\|224584747, gi... - gi\|224584747\|ref\|YP_002638545.1\| GTP pyrophosphokinase [Salmonella enterica subsp. enterica serovar ... gi\|200388682, gi... - gi\|200388682\|ref\|ZP_03215294.1\| RelA/SpoT family protein [Salmonella enterica subsp. enterica serova... gi\|194445692, gi... - gi\|194445692\|ref\|YP_002042207.1\| GTP diphosphokinase [Salmonella enterica subsp. enterica serovar Ne...	784.0	[0..1]	[743..1]
gi\|187428752, gi... - gi\|75176354\|ref\|ZP_00696498.1\| COG0317: Guanosine polyphosphate pyrophosphohydrolases/synthetases [S...	783.0	[0..1]	[744..1]

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Predicted Domain #1

Region A:
Residues: [1-388]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVAVRSAHIN KAGEFDPEKW IASLGITSQK SCECLAETWA YCLQQTQGHP DASLLLWRGV  60
   61 EMVEILSTLS MDIDTLRAAL LFPLADANVV SEDVLRESVG KSVVNLIHGV RDMAAIRQLK 120
  121 ATHTDSVSSE QVDNVRRMLL AMVDDFRCVV IKLAERIAHL REVKDAPEDE RVLAAKECTN 180
  181 IYAPLANRLG IGQLKWELED YCFRYLHPTE YKRIAKLLHE RRLDREHYIE EFVGHLRAEM 240
  241 KAEGVKAEVY GRPKHIYSIW RKMQKKNLAF DELFDVRAVR IVAERLQDCY AALGIVHTHY 300
  301 RHLPDEFDDY VANPKPNGYQ SIHTVVLGPG GKTVEIQIRT KQMHEDAELG VAAHWKYKEG 360
  361 AAAGGARSGH EDRIAWLRKL IAWQEEMA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	116.0
Match:	1vj7A
Description:	Crystal structure of the bifunctional catalytic fragment of RelSeq, the RelA/SpoT homolog from Streptococcus equisimilis.
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
GTP diphosphokinase activity	1.5953523101767	bayes_pls_golite062009
cyclic-nucleotide phosphodiesterase activity	1.53556412385088	bayes_pls_golite062009
3',5'-cyclic-nucleotide phosphodiesterase activity	1.52960140313397	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.17940277430091	bayes_pls_golite062009
guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	1.1479499593037	bayes_pls_golite062009
diphosphoric monoester hydrolase activity	1.1479499593037	bayes_pls_golite062009
catalytic activity	1.122769147009	bayes_pls_golite062009
nucleotidyltransferase activity	0.92178707322923	bayes_pls_golite062009
hydrolase activity	0.89382287998944	bayes_pls_golite062009
phosphoric diester hydrolase activity	0.874654356902841	bayes_pls_golite062009
transferase activity	0.63270331673446	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.262138492248739	bayes_pls_golite062009
phosphoric ester hydrolase activity	0.196287846714023	bayes_pls_golite062009
3',5'-cyclic-AMP phosphodiesterase activity	0.0897894719596	bayes_pls_golite062009
3',5'-cyclic-GMP phosphodiesterase activity	0.0229959143092802	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [389-562]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DSGEMLDEVR SQVFDDRVYV FTPKGDVVDL PAGSTPLDFA YHIHSDVGHR CIGAKIGGRI  60
   61 VPFTYQLQMG DQIEIITQKQ PNPSRDWLNP NLGYVTTSRG RSKIHAWFRK QDRDKNILAG 120
  121 RQILDDELEH LGISLKEAEK HLLPRYNFND VDELLAAIGG GDIRLNQMVN FLQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.522879
Match:	1qf6A
Description:	Threonyl-tRNA synthetase (ThrRS), C-terminal domain; Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain; Threonyl-tRNA synthetase (ThrRS), second 'additional' domain; Threonyl-tRNA synthetase (ThrRS)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [563-659]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QFNKPSAEEQ DAAALKQLQQ KSYTPQNRSK DNGRVVVEGV GNLMHHIARC CQPIPGDEIV  60
   61 GFITQGRGIS VHRADCEQLA ELRSHAPERI VDAVWGE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.459	a.40.1	Calponin-homology domain, CH-domain
View	Download	0.404	d.131.1	DNA clamp
View	Download	0.383	c.84.1	Phosphoglucomutase, first 3 domains
View	Download	0.646	d.58.26	GHMP Kinase, C-terminal domain
View	Download	0.432	d.58.26	GHMP Kinase, C-terminal domain

Predicted Domain #4

Region A:
Residues: [660-744]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SYSAGYSLVV RVVANDRSGL LRDITTILAN EKVNVLGVAS RSDTKQQLAT IDMTIEIYNL  60
   61 QVLGRVLGKL NQVPDVIDAR RLHGS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.522879
Match:	2f1fA
Description:	Crystal structure of the regulatory subunit of acetohydroxyacid synthase isozyme III from E. coli
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transferase activity, transferring aldehyde or ketonic groups	1.58611270031811	bayes_pls_golite062009
catalytic activity	1.01569611874813	bayes_pls_golite062009
binding	0.162590183060409	bayes_pls_golite062009
transferase activity	0.07375530569672	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: