YRC Public Data Repository - Protein Structure Prediction

Protein:	SHM1
Organism:	Saccharomyces cerevisiae
Length:	490 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 ...	2.0E-92	[1..490]	[1..490]
gi\|46432983, gi\|... - gi\|68489015\|ref\|XP_711664.1\| hypothetical protein CaO19.8922 [Candida albicans SC5314], gi\|46432983\|... orf19.8922 - SHM1 CGDID:CAL0003822 Assembly 19, Contig19-20110 (28076, 29557) CDS, translated using codon table 1...	6.0E-91	[5..490]	[11..493]
GLYM_CANAX - Serine hydroxymethyltransferase, mitochondrial OS=Candida albicans GN=SHM1 PE=3 SV=1	1.0E-87	[5..490]	[11..493]
CG3011-PA - This gene is referred to in FlyBase by the symbol Dmel\CG3011 (CG3011, FBgn0029823). It is a protein... gi\|220959690, gi... - gi\|220959690\|gb\|ACL92388.1\| CG3011-PA [synthetic construct], gi\|220951154\|gb\|ACL88120.1\| CG3011-PA [...	2.0E-87	[26..488]	[74..533]
GLYM_ASHGO - Serine hydroxymethyltransferase, mitochondrial OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / ... GLYM_ASHGO - Serine hydroxymethyltransferase, mitochondrial OS=Ashbya gossypii GN=SHM1 PE=3 SV=1	5.0E-87	[4..490]	[11..497]
gi\|42549295, gi\|... - gi\|46127945\|ref\|XP_388526.1\| hypothetical protein FG08350.1 [Gibberella zeae PH-1], gi\|42549295\|gb\|E...	1.0E-86	[4..488]	[8..499]
GLYM_PEA - Serine hydroxymethyltransferase, mitochondrial OS=Pisum sativum PE=1 SV=1	2.0E-86	[1..488]	[21..508]
GLYC4_ARATH - Serine hydroxymethyltransferase 4 OS=Arabidopsis thaliana GN=SHM4 PE=1 SV=1	2.0E-86	[23..488]	[2..461]
gi\|42542754 - gi\|42542754\|gb\|AAH66496.1\| Shmt1 protein [Danio rerio]	4.0E-86	[22..488]	[12..477]

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Predicted Domain #1

Region A:
Residues: [1-490]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFPRASALAK CMATVHRRGL LTSGAQSLVS KPVSEGDPEM FDILQQERHR QKHSITLIPS  60
   61 ENFTSKAVMD LLGSELQNKY SEGYPGERYY GGNEIIDKSE SLCQARALEL YGLDPAKWGV 120
  121 NVQPLSGAPA NLYVYSAIMN VGERLMGLDL PDGGHLSHGY QLKSGTPISF ISKYFQSMPY 180
  181 HVDHTTGLID YDNLQVLAKA FRPKVIVAGT SAYSRLIDYA RFKEISQGCG AYLMSDMAHI 240
  241 SGLVAANVVP SPFEHSDIVT TTTHKSLRGP RGAMIFFRKG IKSVTKKGKE IPYELEKKIN 300
  301 FSVFPGHQGG PHNHTIGAMA VALKQAMSPE FKEYQQKIVD NSKWFAQELT KMGYKLVSGG 360
  361 TDNHLIVIDL SGTQVDGARV ETILSALNIA ANKNTIPGDK SALFPSGLRI GTPAMTTRGF 420
  421 GREEFSQVAK YIDSAVKLAE NLKTLEPTTK LDARSRLNEF KKLCNESSEV AALSGEISKW 480
  481 VGQYPVPGDI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	82.69897
Match:	1ls3A_
Description:	Serine hydroxymethyltransferase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
L-aspartate:2-oxoglutarate aminotransferase activity	3.359406422625	bayes_pls_golite062009
glycine dehydrogenase (decarboxylating) activity	3.2128372762799	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-NH2 group of donors, disulfide as acceptor	3.2128372762799	bayes_pls_golite062009
transferase activity	2.59075614411581	bayes_pls_golite062009
5-aminolevulinate synthase activity	2.47911083054773	bayes_pls_golite062009
catalytic activity	2.29878871754893	bayes_pls_golite062009
O-phospho-L-serine:2-oxoglutarate aminotransferase activity	2.1692959843619	bayes_pls_golite062009
transcription regulator activity	1.67701710033155	bayes_pls_golite062009
DNA binding	1.4774443071095	bayes_pls_golite062009
nucleic acid binding	1.39741122443159	bayes_pls_golite062009
transferase activity, transferring nitrogenous groups	1.28316822767388	bayes_pls_golite062009
transaminase activity	1.24990480711889	bayes_pls_golite062009
transferase activity, transferring acyl groups	1.19150094103499	bayes_pls_golite062009
transcription factor activity	1.15775909410582	bayes_pls_golite062009
N-succinyltransferase activity	1.14675852378654	bayes_pls_golite062009
binding	1.09053123792737	bayes_pls_golite062009
structural molecule activity	0.754675308623467	bayes_pls_golite062009
methyltransferase activity	0.681623261233707	bayes_pls_golite062009
vitamin binding	0.66463470119531	bayes_pls_golite062009
protein binding	0.613130945854863	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	0.60304280865376	bayes_pls_golite062009
L-allo-threonine aldolase activity	0.500744432308415	bayes_pls_golite062009
glycine hydroxymethyltransferase activity	0.271623203801431	bayes_pls_golite062009
pyridoxal phosphate binding	0.16957228630576	bayes_pls_golite062009
vitamin B6 binding	0.16957228630576	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: