YRC Public Data Repository - Protein Structure Prediction

Protein:	MDE1
Organism:	Saccharomyces cerevisiae
Length:	244 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 MDE1.

Description	E-value	Query Range	Subject Range
MTNB_YEAST - Methylthioribulose-1-phosphate dehydratase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ... MDE1 - 5'-methylthioribulose-1-phosphate dehydratase; acts in the methionine salvage pathway; potential Smt...	2.0E-64	[1..244]	[1..244]
gi\|7705724, gi\|4... - gi\|7705724\|ref\|NP_057041.1\| APAF1 interacting protein [Homo sapiens], gi\|4680697\|gb\|AAD27738.1\|AF132...	1.0E-53	[9..234]	[17..238]
MTNB_DROSI - Probable methylthioribulose-1-phosphate dehydratase OS=Drosophila simulans GN=GD17142 PE=3 SV=1 gi\|220948664, gi... - gi\|220958120\|gb\|ACL91603.1\| CG11134-PA [synthetic construct], gi\|220948664\|gb\|ACL86875.1\| CG11134-PA... MTNB_DROSE - Probable methylthioribulose-1-phosphate dehydratase OS=Drosophila sechellia GN=GM17635 PE=3 SV=1 FBpp0304097, CG1... - This gene is referred to in FlyBase by the symbol Dmel\CG11134 (CG11134, FBgn0030518). It is a prote...	3.0E-49	[14..229]	[12..222]
gi\|218350263, gi... - gi\|218693531\|ref\|YP_002401198.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli 55989], gi\|218... ARAD_ECOLI - L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (Phosphoribulose isomerase) - Escherichia coli gi\|89106945, gi\|... - gi\|89106945\|ref\|AP_000725.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli str. K-12 substr. ... gi\|124530630, gi... - gi\|124530630\|ref\|ZP_01701214.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli B], gi\|12449905... gi\|254037477, gi... - gi\|254037477\|ref\|ZP_04871554.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia sp. 1_1_43], gi\|2268... EG10055 - L-ribulose-5-phosphate 4-epimerase / L-ribulose-5-phosphate 4-epimerase gi\|75234300, gi\|... - gi\|75234300\|ref\|ZP_00718678.1\| COG0235: Ribulose-5-phosphate 4-epimerase and related epimerases and ... EG10055 - L-ribulose-5-phosphate 4-epimerase / L-ribulose-5-phosphate 4-epimerase gi\|157065210, gi... - gi\|75194280\|ref\|ZP_00704350.1\| COG0235: Ribulose-5-phosphate 4-epimerase and related epimerases and ... gi\|169756511, gi... - gi\|170021583\|ref\|YP_001726537.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli ATCC 8739], gi... gi\|191167766, gi... - gi\|75229088\|ref\|ZP_00715668.1\| COG0235: Ribulose-5-phosphate 4-epimerase and related epimerases and ...	1.0E-48	[13..239]	[2..214]
gi\|18655680, gi\|... - gi\|225433\|prf\|\|1303258C operon araD, gi\|18655685\|pdb\|1JDI\|F Chain F, Crystal Structure Of L-Ribulose... gi\|251783625, gi... - gi\|251783625\|ref\|YP_002997929.1\| hypothetical protein B21_00062 [Escherichia coli BL21], gi\|24237589... gi\|253976294, gi... - gi\|254286987\|ref\|YP_003052735.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli BL21(DE3)], gi... gi\|253972085, gi... - gi\|254160184\|ref\|YP_003043292.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli B str. REL606]... gi\|194439393, gi... - gi\|83585215\|ref\|ZP_00923865.1\| COG0235: Ribulose-5-phosphate 4-epimerase and related epimerases and ...	4.0E-48	[13..239]	[2..214]
gi\|168771283, gi... - gi\|189359915\|gb\|EDU78334.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4486... gi\|168764062, gi... - gi\|189365876\|gb\|EDU84292.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4501... gi\|189357097, gi... - gi\|189357097\|gb\|EDU75516.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4401... gi\|188014527, gi... - gi\|188014527\|gb\|EDU52649.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4113... gi\|81239615, gi\|... - gi\|82775467\|ref\|YP_401814.1\| L-ribulose-5-phosphate 4-epimerase [Shigella dysenteriae Sd197], gi\|812... gi\|209746824, gi... - pir\|\|A85488 L-ribulose-5-phosphate 4-epimerase - Escherichia coli (strain O157:H7, substrain EDL933... gi\|217326432, gi... - gi\|217326432\|ref\|ZP_03442516.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. TW... gi\|209157864, gi... - gi\|209396464\|ref\|YP_002268669.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. E... gi\|15799745, gi\|... - gi\|15799745\|ref\|NP_285757.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 EDL933], g... gi\|254590599, gi... - gi\|254791199\|ref\|YP_003076036.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. T... gi\|13359521, gi\|... - gi\|15829319\|ref\|NP_308092.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7], gi\|13359... gi\|189376356, gi... - gi\|189376356\|gb\|EDU94772.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC508]... gi\|168789586, gi... - gi\|189370832\|gb\|EDU89248.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC869]... gi\|168781944, gi... - gi\|189000393\|gb\|EDU69379.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4076... gi\|168776903, gi... - gi\|187767752\|gb\|EDU31596.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC4196... gi\|13359521, gi\|... - gi\|15829319\|ref\|NP_308092.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. Sakai... gi\|208742052, gi... - gi\|208821929\|ref\|ZP_03262249.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC... gi\|208734268, gi... - gi\|208812991\|ref\|ZP_03254320.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC... gi\|208727914, gi... - gi\|208808113\|ref\|ZP_03250450.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC... gi\|195939277 - gi\|195939277\|ref\|ZP_03084659.1\| L-ribulose-5-phosphate 4-epimerase [Escherichia coli O157:H7 str. EC...	5.0E-48	[13..239]	[2..214]
ARAD_GEOSE - L-ribulose-5-phosphate 4-epimerase OS=Geobacillus stearothermophilus GN=araD PE=3 SV=1	9.0E-48	[13..231]	[2..207]

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Predicted Domain #1

Region A:
Residues: [1-244]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSQDVLIHS DDPCHPANLI CTLCKQFFHN NWCTGTGGGI SIKDPNTNYY YLAPSGVQKE  60
   61 KMIPEDLFVM DAQTLEYLRS PKLYKPSACT PLFLACYQKK NAGAIIHTHS QNAVICSLLF 120
  121 GDEFRIANIE QIKAIPSGKV DPVTKKPMAL SFFDTLKIPI IENMAHEDEL IDDLHKTFKD 180
  181 YPDTCAVIVR RHGIFVWGPT IDKAKIFNEA IDYLMELAIK MYQMGIPPDC GIGEEKKHLK 240
  241 MASP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	129.0
Match:	1jdiA_
Description:	L-ribulose-5-phosphate 4-epimerase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.89539096965643	bayes_pls_golite062009
catalytic activity	1.58067730905989	bayes_pls_golite062009
protein binding	0.401574215469404	bayes_pls_golite062009
lyase activity	0.114082266751758	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: