YRC Public Data Repository - Protein Structure Prediction

Protein:	SHM1
Organism:	Saccharomyces cerevisiae
Length:	565 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 SHM1.

Description	E-value	Query Range	Subject Range
SHM1 - Mitochondrial serine hydroxymethyltransferase, converts serine to glycine plus 5,10 methylenetetrahy... GLYM_YEAST - Serine hydroxymethyltransferase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28... gi\|151946650 - gi\|151946650\|gb\|EDN64872.1\| serine hydroxymethyltransferase [Saccharomyces cerevisiae YJM789] gi\|190408586 - gi\|190408586\|gb\|EDV11851.1\| serine hydroxymethyltransferase, mitochondrial precursor [Saccharomyces ...	0.0	[76..565]	[1..490]
GLYC_SHEEP - Serine hydroxymethyltransferase, cytosolic OS=Ovis aries GN=SHMT1 PE=1 SV=3	0.0	[89..563]	[7..480]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[89..563]	[7..480]
GLYM_PEA - Serine hydroxymethyltransferase, mitochondrial OS=Pisum sativum PE=1 SV=1	0.0	[104..563]	[52..508]
GLYM_SOLTU - Serine hydroxymethyltransferase, mitochondrial OS=Solanum tuberosum PE=2 SV=1	0.0	[104..563]	[52..508]
GLYC4_ARATH - Serine hydroxymethyltransferase 4 OS=Arabidopsis thaliana GN=SHM4 PE=1 SV=1	0.0	[101..565]	[5..463]
gi\|157928568, gi... - gi\|157928568\|gb\|ABW03580.1\| serine hydroxymethyltransferase 1 (soluble) [synthetic construct], gi\|12... gi\|119576041, gi... - gi\|14124914\|gb\|AAH07979.1\| Serine hydroxymethyltransferase 1 (soluble) [Homo sapiens], gi\|119576045\|...	0.0	[90..563]	[8..479]

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Predicted Domain #1

Region A:
Residues: [1-92]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MILSVICWFL VHCLFCPPSV QEIEYKKDSL FFFRYFAYWW SMRKKILKAI ASWRRANYQK  60
   61 SSSRHFHIES HSLSIMFPRA SALAKCMATV HR

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.872	0.005	glycine hydroxymethyltransferase activity	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac

Predicted Domain #2

Region A:
Residues: [93-137]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RGLLTSGAQS LVSKPVSEGD PEMFDILQQE RHRQKHSITL IPSEN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [411-565]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKIVDNSKWF AQELTKMGYK LVSGGTDNHL IVIDLSGTQV DGARVETILS ALNIAANKNT  60
   61 IPGDKSALFP SGLRIGTPAM TTRGFGREEF SQVAKYIDSA VKLAENLKTL EPTTKLDARS 120
  121 RLNEFKKLCN ESSEVAALSG EISKWVGQYP VPGDI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1562.0
Match:	1cj0A_
Description:	Serine hydroxymethyltransferase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [138-410]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FTSKAVMDLL GSELQNKYSE GYPGERYYGG NEIIDKSESL CQARALELYG LDPAKWGVNV  60
   61 QPLSGAPANL YVYSAIMNVG ERLMGLDLPD GGHLSHGYQL KSGTPISFIS KYFQSMPYHV 120
  121 DHTTGLIDYD NLQVLAKAFR PKVIVAGTSA YSRLIDYARF KEISQGCGAY LMSDMAHISG 180
  181 LVAANVVPSP FEHSDIVTTT THKSLRGPRG AMIFFRKGIK SVTKKGKEIP YELEKKINFS 240
  241 VFPGHQGGPH NHTIGAMAVA LKQAMSPEFK EYQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1562.0
Match:	1cj0A_
Description:	Serine hydroxymethyltransferase
Matching Structure (courtesy of the PDB):

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