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

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.689	0.005	glycine hydroxymethyltransferase activity	a.2.7	tRNA-binding arm
View	Download	0.610	0.005	glycine hydroxymethyltransferase activity	a.2.6	Effector domain of the protein kinase pkn/prk1
View	Download	0.872	0.005	glycine hydroxymethyltransferase activity	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.647	0.005	glycine hydroxymethyltransferase activity	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.757	0.005	glycine hydroxymethyltransferase activity	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.565	0.005	glycine hydroxymethyltransferase activity	a.47.2	t-snare proteins
View	Download	0.554	0.005	glycine hydroxymethyltransferase activity	a.7.1	Spectrin repeat
View	Download	0.545	0.005	glycine hydroxymethyltransferase activity	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.530	0.005	glycine hydroxymethyltransferase activity	a.7.5	Tubulin chaperone cofactor A
View	Download	0.500	0.005	glycine hydroxymethyltransferase activity	a.47.2	t-snare proteins
View	Download	0.500	0.005	glycine hydroxymethyltransferase activity	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.489	0.005	glycine hydroxymethyltransferase activity	f.15.1	Small-conductance potassium channel
View	Download	0.488	0.005	glycine hydroxymethyltransferase activity	a.7.8	GAT domain
View	Download	0.466	0.005	glycine hydroxymethyltransferase activity	a.24.9	alpha-catenin/vinculin
View	Download	0.450	0.005	glycine hydroxymethyltransferase activity	d.150.1	4'-phosphopantetheinyl transferase
View	Download	0.424	0.005	glycine hydroxymethyltransferase activity	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.410	0.005	glycine hydroxymethyltransferase activity	a.7.1	Spectrin repeat
View	Download	0.364	0.005	glycine hydroxymethyltransferase activity	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.351	0.005	glycine hydroxymethyltransferase activity	f.17.2	Cytochrome c oxidase subunit II-like, transmembrane region
View	Download	0.351	0.005	glycine hydroxymethyltransferase activity	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.350	0.005	glycine hydroxymethyltransferase activity	a.26.1	4-helical cytokines
View	Download	0.338	0.005	glycine hydroxymethyltransferase activity	a.2.1	GreA transcript cleavage protein, N-terminal domain
View	Download	0.338	0.005	glycine hydroxymethyltransferase activity	a.7.3	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
View	Download	0.337	0.005	glycine hydroxymethyltransferase activity	a.47.2	t-snare proteins
View	Download	0.335	0.005	glycine hydroxymethyltransferase activity	a.25.1	Ferritin-like
View	Download	0.329	0.005	glycine hydroxymethyltransferase activity	a.25.1	Ferritin-like
View	Download	0.328	0.005	glycine hydroxymethyltransferase activity	f.14.1	Voltage-gated potassium channels
View	Download	0.326	0.005	glycine hydroxymethyltransferase activity	a.2.7	tRNA-binding arm
View	Download	0.302	0.005	glycine hydroxymethyltransferase activity	i.11.1	Computational models partly based on NMR data
View	Download	0.298	0.005	glycine hydroxymethyltransferase activity	f.28.1	Nonheme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
View	Download	0.297	0.005	glycine hydroxymethyltransferase activity	d.15.6	Superantigen toxins, C-terminal domain
View	Download	0.296	0.005	glycine hydroxymethyltransferase activity	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.295	0.005	glycine hydroxymethyltransferase activity	a.2.10	Epsilon subunit of F1F0-ATP synthase C-terminal domain
View	Download	0.293	0.005	glycine hydroxymethyltransferase activity	a.7.7	BAG domain
View	Download	0.291	0.005	glycine hydroxymethyltransferase activity	a.25.1	Ferritin-like
View	Download	0.282	0.005	glycine hydroxymethyltransferase activity	a.24.3	Cytochromes
View	Download	0.274	0.005	glycine hydroxymethyltransferase activity	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.268	0.005	glycine hydroxymethyltransferase activity	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.265	0.005	glycine hydroxymethyltransferase activity	a.29.3	Acyl-CoA dehydrogenase C-terminal domain-like
View	Download	0.264	0.005	glycine hydroxymethyltransferase activity	a.22.1	Histone-fold
View	Download	0.252	0.005	glycine hydroxymethyltransferase activity	c.51.1	Anticodon-binding domain of Class II aaRS
View	Download	0.248	0.005	glycine hydroxymethyltransferase activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.241	0.005	glycine hydroxymethyltransferase activity	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.236	0.005	glycine hydroxymethyltransferase activity	a.19.1	Fertilization protein
View	Download	0.221	0.005	glycine hydroxymethyltransferase activity	a.2.7	tRNA-binding arm
View	Download	0.219	0.005	glycine hydroxymethyltransferase activity	a.185.1	Gametocyte protein Pfg27
View	Download	0.217	0.005	glycine hydroxymethyltransferase activity	a.24.4	Hemerythrin
View	Download	0.214	0.005	glycine hydroxymethyltransferase activity	a.22.1	Histone-fold
View	Download	0.211	0.005	glycine hydroxymethyltransferase activity	a.7.1	Spectrin repeat
View	Download	0.210	0.005	glycine hydroxymethyltransferase activity	a.7.1	Spectrin repeat
View	Download	0.209	0.005	glycine hydroxymethyltransferase activity	a.4.1	Homeodomain-like
View	Download	0.207	0.005	glycine hydroxymethyltransferase activity	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.206	0.005	glycine hydroxymethyltransferase activity	a.30.1	ROP protein
View	Download	0.204	0.005	glycine hydroxymethyltransferase activity	a.22.1	Histone-fold
View	Download	0.204	0.005	glycine hydroxymethyltransferase activity	a.29.3	Acyl-CoA dehydrogenase C-terminal domain-like
View	Download	0.202	0.005	glycine hydroxymethyltransferase activity	a.24.3	Cytochromes

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