YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|224499816
Organism:	Listeria monocytogenes Finland 1998
Length:	738 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 gi|224499816.

Description	E-value	Query Range	Subject Range
gi\|254824418 - gi\|254824418\|ref\|ZP_05229419.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL J1-194] gi\|226224124, gi... - gi\|226224124\|ref\|YP_002758231.1\| (p)ppGpp synthetase [Listeria monocytogenes Clip81459], gi\|22587658... gi\|254878988 - gi\|254878988\|ref\|ZP_05251698.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL J2-071] gi\|46907751, gi\|... - gi\|46907751\|ref\|YP_014140.1\| GTP pyrophosphokinase [Listeria monocytogenes str. 4b F2365], gi\|468810... gi\|254852146 - gi\|254852146\|ref\|ZP_05241494.1\| (p)ppGpp synthetase [Listeria monocytogenes FSL R2-503] gi\|133735221, gi... - gi\|254931458\|ref\|ZP_05264817.1\| (p)ppGpp synthetase [Listeria monocytogenes HPB2262], gi\|153202446\|r...	861.0	[0..1]	[738..1]
gi\|16414045, gi\|... - pir\|\|AE1627 (p)ppGpp synthetase homolog relA [imported] - Listeria innocua (strain Clip11262), gi\|16... gi\|16800626 - gi\|16800626\|ref\|NP_470894.1\| hypothetical protein lin1558 [Listeria innocua Clip11262]	856.0	[0..1]	[738..1]
gi\|14325225 - gi\|14325225\|dbj\|BAB60670.1\| Rel [Listeria monocytogenes]	854.0	[0..1]	[738..1]
gi\|47094426, gi\|... - gi\|47094426\|ref\|ZP_00232112.1\| GTP pyrophosphokinase [Listeria monocytogenes str. 4b H7858], gi\|4701...	849.0	[0..16]	[738..2]
gi\|10443847 - gi\|10443847\|gb\|AAG17607.1\|AF242653_1 ppGpp synthetase/hydrolase Rel [Geobacillus stearothermophilus]	838.0	[0..1]	[738..1]
gi\|56421113, gi\|... - gi\|56421113\|ref\|YP_148431.1\| GTP pyrophosphokinase (ppGpp synthetase) [Geobacillus kaustophilus HTA4...	838.0	[0..1]	[738..1]
RELA_BACSU - GTP pyrophosphokinase OS=Bacillus subtilis GN=relA PE=3 SV=3 gi\|221324224 - gi\|221324224\|ref\|ZP_03605518.1\| GTP pyrophosphokinase [Bacillus subtilis subsp. subtilis str. SMY] gi\|221319943 - gi\|221319943\|ref\|ZP_03601237.1\| GTP pyrophosphokinase [Bacillus subtilis subsp. subtilis str. JH642] gi\|221315022 - gi\|221315022\|ref\|ZP_03596827.1\| GTP pyrophosphokinase [Bacillus subtilis subsp. subtilis str. NCIB 3... RELA_BACSU - GTP pyrophosphokinase OS=Bacillus subtilis (strain 168) GN=relA PE=3 SV=3	833.0	[0..1]	[738..1]
gi\|52349121, gi\|... - gi\|52786619\|ref\|YP_092448.1\| RelA [Bacillus licheniformis ATCC 14580], gi\|52349121\|gb\|AAU41755.1\| Re...	832.0	[0..1]	[738..1]
RELA_BACSU - GTP pyrophosphokinase OS=Bacillus subtilis GN=relA PE=3 SV=2 gi\|2635224, gi\|1... - gi\|2635224\|emb\|CAB14719.1\| GTP pyrophosphokinase [Bacillus subtilis subsp. subtilis str. 168], gi\|16...	829.0	[0..1]	[738..1]
gi\|69247932, gi\|... - gi\|69247932\|ref\|ZP_00604548.1\| RelA/SpoT protein [Enterococcus faecium DO], gi\|68194634\|gb\|EAN09121....	828.0	[0..1]	[737..1]

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Predicted Domain #1

Region A:
Residues: [1-391]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKEQNLTAE QVIDMASHYM NQEHLALVKK AYEFARDSHK EQFRKSGEPY IIHPIQVAGI  60
   61 LVELKMDPST VASGFLHDVV EDTPVTLADL EEVFGSEVAM LVDGVTKLGK IKYKSHEEQQ 120
  121 AENHRKMFIA MAQDIRVILI KLADRLHNMR TLKHLPVEKQ RRIANETLEI FAPLAHRLGI 180
  181 SRVKWELEDT ALRYLNPQQY YRIVHLMKQK RDARERYLHD VIDGVNENLD ELNIQADISG 240
  241 RPKHIYSIYR KMSEQNKQFN EIYDLLAVRI VVSSIKDCYA VLGIIHTRWK PMPGRFKDYI 300
  301 AMPKSNMYQS IHTTVIGPQG EPLEVQIRTH EMHQIAEYGV AAHWAYKEGK VVNSKTSFDN 360
  361 KLTWFREILE YQNESDNAEE FMESLKLDLF S

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	133.0
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: [392-653]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DVVYVFTPKG DVYELPNGSV PLDFAYRVHT EIGNKTIGAK INGKIVTLDY KLKTGDIIDI  60
   61 LTSKHSYGPS RDWLKLVQTS QARNKIKQFF KRQAKEENVE KGRDLVEKEI RQLGFEPKKI 120
  121 MAAENLRKLA DKLNFSHEDD LFAAVGYNGI TALQVANRLT EKLRKERELE AETEKLLTQS 180
  181 ENKPSNSDAN NEKLKIKHNA GVVVQGVGNL LIRLSRCCNP VPGDDIVGYI TKGRGISIHR 240
  241 QDCPNVQAIE PERLIEVDWE DA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	35.0
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: [654-738]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DSQAKNDYNV DIEIYGYNRN GLLNDILQVI NSLTSNINGV NAKVDNNKMA TLVVTLQIHN  60
   61 INHLQRVVDK IKQIPDVYTV RRLMN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.39794
Match:	2fgcA
Description:	Crystal structure of Acetolactate synthase- small subunit from Thermotoga maritima
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: