YRC Public Data Repository - Protein Structure Prediction

Protein:	GRE2
Organism:	Saccharomyces cerevisiae
Length:	342 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 GRE2.

Description	E-value	Query Range	Subject Range
gi\|16611766 - gi\|16611766\|gb\|AAL27347.1\|AF402315_2 dTDP-D-glucose 4,6-dehydratase [Shigella boydii]	0.0	[1..338]	[1..337]
gi\|209753446, gi... - pir\|\|A91219 dTDP-glucose 4,6-dehydratase [imported] - Escherichia coli (strain O157:H7, substrain R... gi\|189362621, gi... - gi\|189362621\|gb\|EDU81040.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4486], gi\|... gi\|189365802, gi... - gi\|189365802\|gb\|EDU84218.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4501], gi\|... gi\|13364196, gi\|... - gi\|15833975\|ref\|NP_312748.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7], gi\|13364196\|db... gi\|189358938, gi... - gi\|189358938\|gb\|EDU77357.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4401], gi\|... gi\|168751746, gi... - gi\|188014279\|gb\|EDU52401.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4113], gi\|... gi\|217325882, gi... - gi\|217325882\|ref\|ZP_03441966.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. TW14588]... gi\|209399629, gi... - gi\|209399629\|ref\|YP_002273306.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4115]... gi\|13364196, gi\|... - gi\|15833975\|ref\|NP_312748.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. Sakai], gi\|... gi\|189376800, gi... - gi\|189376800\|gb\|EDU95216.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC508], gi\|1... gi\|189373224, gi... - gi\|189373224\|gb\|EDU91640.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC869], gi\|1... gi\|168780684, gi... - gi\|189001405\|gb\|EDU70391.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4076], gi\|... gi\|168775664, gi... - gi\|187768885\|gb\|EDU32729.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4196], gi\|... gi\|208818281, gi... - gi\|208818281\|ref\|ZP_03258601.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4042],... gi\|208813029, gi... - gi\|208813029\|ref\|ZP_03254358.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4045],... gi\|254595186, gi... - gi\|254795786\|ref\|YP_003080623.1\| dTDP-D-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. TW143... gi\|208725490, gi... - gi\|208805689\|ref\|ZP_03248026.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4206],... gi\|195938077 - gi\|195938077\|ref\|ZP_03083459.1\| dTDP-glucose 4,6-dehydratase [Escherichia coli O157:H7 str. EC4024]	0.0	[2..339]	[3..335]
RMLB_SHIFL - dTDP-glucose 4,6-dehydratase OS=Shigella flexneri GN=rfbB PE=3 SV=2 gi\|24052449, gi\|... - gi\|24113426\|ref\|NP_707936.1\| dTDP-glucose 4,6 dehydratase [Shigella flexneri 2a str. 301], gi\|240524... gi\|30063492, gi\|... - gi\|30063492\|ref\|NP_837663.1\| dTDP-glucose 4,6 dehydratase [Shigella flexneri 2a str. 2457T], gi\|3004...	0.0	[1..340]	[1..339]
gi\|170081671, gi... - gi\|170081671\|ref\|YP_001730991.1\| dTDP-glucose 4,6 dehydratase, NAD(P)-binding [Escherichia coli str.... EG12412 - dTDP-glucose 4,6 dehydratase, NAD(P)-binding / TDP-glucose oxidoreductase-4,6 dehydratase gi\|1736731, gi\|8... - gi\|89108861\|ref\|AP_002641.1\| dTDP-glucose 4,6 dehydratase, NAD(P)-binding [Escherichia coli str. K-1... EG12412 - dTDP-glucose 4,6 dehydratase, NAD(P)-binding / TDP-glucose oxidoreductase-4,6 dehydratase RBB1_ECOLI, RFBB... - dTDP-glucose 4,6-dehydratase (EC 4.2.1.46) - Escherichia coli, (P37759) dTDP-glucose 4,6-dehydratase... gi\|238861014, gi... - gi\|238901231\|ref\|YP_002927027.1\| dTDP-glucose 4,6 dehydratase, NAD(P)-binding [Escherichia coli BW29...	0.0	[1..338]	[1..337]
gi\|213650451 - gi\|213650451\|ref\|ZP_03380504.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|213979614 - gi\|213979614\|ref\|ZP_03406873.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|214001795 - gi\|214001795\|ref\|ZP_03412530.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|213023599 - gi\|213023599\|ref\|ZP_03338046.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|213052826 - gi\|213052826\|ref\|ZP_03345704.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|213425545 - gi\|213425545\|ref\|ZP_03358295.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|56412999, gi\|... - gi\|56412999\|ref\|YP_150074.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica serov... gi\|213585955 - gi\|213585955\|ref\|ZP_03367781.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica se... gi\|197936445, gi... - gi\|198241929\|ref\|YP_002216184.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica s... gi\|204928949, gi... - gi\|204928949\|ref\|ZP_03220092.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica se... gi\|205273021, gi... - gi\|205353240\|ref\|YP_002227041.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica s... gi\|207857533, gi... - gi\|207857533\|ref\|YP_002244184.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica s... gi\|161362587, gi... - gi\|161613223\|ref\|YP_001587188.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica s... gi\|167551043, gi... - gi\|205324063\|gb\|EDZ11902.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica serova... gi\|168818214, gi... - gi\|205344684\|gb\|EDZ31448.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica serova... gi\|197093404, gi... - gi\|197361927\|ref\|YP_002141564.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica s... gi\|16761029 - gi\|16761029\|ref\|NP_456646.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica serov... gi\|25292364, gi\|... - gi\|25292364\|pir\|\|AF0767 dTDP-glucose 4,6-dehydratase [imported] - Salmonella enterica subsp. enteric... gi\|29141275, gi\|... - gi\|29141275\|ref\|NP_804617.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica serov...	0.0	[1..338]	[1..337]
gi\|9957829 - gi\|9957829\|gb\|AAG09509.1\|AF279618_1 dTDP-D-glucose-4,6-dehydratase [Salmonella enterica]	0.0	[1..338]	[1..337]
RMLB_SALTY, RFBB... - dTDP-glucose 4,6-dehydratase OS=Salmonella typhimurium GN=rfbB PE=1 SV=1, dTDP-glucose 4,6-dehydrata... gi\|194443120, gi... - gi\|194443120\|ref\|YP_002041367.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica s... gi\|581654, gi\|13... - gi\|581654\|emb\|CAA40115.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica], gi\|13786958\|pdb\|1G1A\|D... gi\|168466245, gi... - gi\|195631509\|gb\|EDX50069.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica serova... gi\|18655662, gi\|... - gi\|18655664\|pdb\|1KEW\|B Chain B, The Crystal Structure Of Dtdp-D-Glucose 4,6-Dehydratase (Rmlb) From ... gi\|194407940, gi... - gi\|194449636\|ref\|YP_002046147.1\| dTDP-glucose 4,6 dehydratase [Salmonella enterica subsp. enterica s... gi\|205338665, gi... - gi\|205338665\|gb\|EDZ25429.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica serova... gi\|205330442, gi... - gi\|205330442\|gb\|EDZ17206.1\| dTDP-glucose 4,6-dehydratase [Salmonella enterica subsp. enterica serova... RFBB_SALTY - dTDP-glucose 4,6-dehydratase OS=Salmonella typhimurium GN=rfbB PE=1 SV=1 lcl\|NC_016856.1_... - [gene=rfbB] [protein=dTDP-glucose-4,6-dehydratase] [protein_id=YP_005238132.1] [location=complement(... RMLB_SALTY - dTDP-glucose 4,6-dehydratase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=rfbB...	0.0	[1..338]	[1..337]

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Predicted Domain #1

Region A: Residues: [1-84]	1 11 21 31 41 51 \| \| \| \| \| \| 1 MSVFVSGANG FIAQHIVDLL LKEDYKVIGS ARSQEKAENL TEAFGNNPKF SMEVVPDISK 60 61 LDAFDHVFQK HGKDIKIVLH TASP [Run NCBI BLAST on this sequence.]
Region B: Residues: [95-126]	1 11 21 31 41 51 \| \| \| \| \| \| 1 DLLIPAVNGV KGILHSIKKY AADSVERVVL TS [Run NCBI BLAST on this sequence.]
Region C: Residues: [169-194]	1 11 21 31 41 51 \| \| \| \| \| \| 1 KKFAEKAAWE FLEENRDSVK FELTAV [Run NCBI BLAST on this sequence.]
Region D: Residues: [245-261]	1 11 21 31 41 51 \| \| \| \| \| \| 1 VAKAHLVAFQ KRETIGQ [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	1keuA_
Description:	dTDP-glucose 4,6-dehydratase (RmlB)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.79741889688267	bayes_pls_golite062009
steroid dehydrogenase activity	1.75109362865449	bayes_pls_golite062009
steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	1.55012034958204	bayes_pls_golite062009
oxidoreductase activity, acting on CH-OH group of donors	1.03956654822048	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.82673050487418	bayes_pls_golite062009
alcohol dehydrogenase (NAD) activity	0.65743456407889	bayes_pls_golite062009
DNA binding	0.525227236870065	bayes_pls_golite062009
retinol dehydrogenase activity	0.48941662111046	bayes_pls_golite062009
coenzyme binding	0.46570602169425	bayes_pls_golite062009
nucleic acid binding	0.459537641913493	bayes_pls_golite062009
NAD or NADH binding	0.44922383360529	bayes_pls_golite062009
binding	0.429102711245135	bayes_pls_golite062009
transcription regulator activity	0.152651308844322	bayes_pls_golite062009
oxidoreductase activity	0.120113583068184	bayes_pls_golite062009

Predicted Domain #2

Region A: Residues: [85-94]	1 11 21 31 41 51 \| \| \| \| \| \| 1 FCFDITDSER [Run NCBI BLAST on this sequence.]
Region B: Residues: [127-168]	1 11 21 31 41 51 \| \| \| \| \| \| 1 SYAAVFDMAK ENDKSLTFNE ESWNPATWES CQSDPVNAYC GS [Run NCBI BLAST on this sequence.]
Region C: Residues: [195-205]	1 11 21 31 41 51 \| \| \| \| \| \| 1 NPVYVFGPQM F [Run NCBI BLAST on this sequence.]
Region D: Residues: [234-244]	1 11 21 31 41 51 \| \| \| \| \| \| 1 ELFGGYIDVR D [Run NCBI BLAST on this sequence.]
Region E: Residues: [262-272]	1 11 21 31 41 51 \| \| \| \| \| \| 1 RLIVSEARFT M [Run NCBI BLAST on this sequence.]
Region F: Residues: [299-329]	1 11 21 31 41 51 \| \| \| \| \| \| 1 ATHNTLGATL DNKKSKKLLG FKFRNLKETI D [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	1keuA_
Description:	dTDP-glucose 4,6-dehydratase (RmlB)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [206-233]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DKDVKKHLNT SCELVNSLMH LSPEDKIP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [273-298]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QDVLDILNED FPVLKGNIPV GKPGSG

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [330-342]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DTASQILKFE GRI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	1keuA_
Description:	dTDP-glucose 4,6-dehydratase (RmlB)
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

Predicted functions: