YRC Public Data Repository - Protein Structure Prediction

Protein:	TDA3
Organism:	Saccharomyces cerevisiae
Length:	523 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 TDA3.

Description	E-value	Query Range	Subject Range
TDA3_YEAST - Putative oxidoreductase TDA3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TDA3 PE=1 S... TDA3 - Putative protein of unknown function; not an essential gene gi\|151943951 - gi\|151943951\|gb\|EDN62244.1\| conserved protein [Saccharomyces cerevisiae YJM789]	0.0	[1..523]	[1..523]
lcl\|NC_016856.1_... - [gene=dadA] [protein=D-amino acid dehydrogenase small subunit] [protein_id=YP_005237738.1] [location... DADA_SALTY - D-amino acid dehydrogenase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=dadA P... DADA_SALEP - D-amino acid dehydrogenase OS=Salmonella enteritidis PT4 (strain P125109) GN=dadA PE=3 SV=1 DADA_SALDC - D-amino acid dehydrogenase OS=Salmonella dublin (strain CT_02021853) GN=dadA PE=3 SV=1 gi\|197263686, gi... - gi\|197263686\|ref\|ZP_03163760.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... DADA_SALHS - D-amino acid dehydrogenase OS=Salmonella heidelberg (strain SL476) GN=dadA PE=3 SV=1 gi\|167554126, gi... - gi\|205321611\|gb\|EDZ09450.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. ent... DADA_SALNS - D-amino acid dehydrogenase OS=Salmonella newport (strain SL254) GN=dadA PE=3 SV=1 gi\|168462708, gi... - gi\|195634104\|gb\|EDX52456.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. ent... DADA_SALPB - D-amino acid dehydrogenase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=dadA PE=3 SV=1 gi\|168241391, gi... - gi\|205339629\|gb\|EDZ26393.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. ent... gi\|167993252, gi... - gi\|205328690\|gb\|EDZ15454.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. ent... DADA_SALPB - D-amino acid dehydrogenase small subunit OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=... DADA_SALTY - D-amino acid dehydrogenase small subunit OS=Salmonella typhimurium GN=dadA PE=3 SV=1 DADA_SALTY - D-amino acid dehydrogenase small subunit OS=Salmonella typhimurium GN=dadA PE=3 SV=1	6.0E-71	[23..519]	[2..418]
gi\|213581080 - gi\|213581080\|ref\|ZP_03362906.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... gi\|213426622 - gi\|213426622\|ref\|ZP_03359372.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... gi\|213648192 - gi\|213648192\|ref\|ZP_03378245.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... gi\|213612759 - gi\|213612759\|ref\|ZP_03370585.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... gi\|16760693 - gi\|16760693\|ref\|NP_456310.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. en... DADA_SALTI - D-amino acid dehydrogenase OS=Salmonella typhi GN=dadA PE=3 SV=1 gi\|213162932 - gi\|213162932\|ref\|ZP_03348642.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... gi\|29137176, gi\|... - gi\|29141549\|ref\|NP_804891.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp. en... gi\|214002620 - gi\|214002620\|ref\|ZP_03413355.1\| D-amino acid dehydrogenase small subunit [Salmonella enterica subsp.... DADA_SALTI - D-amino acid dehydrogenase small subunit OS=Salmonella typhi GN=dadA PE=3 SV=1	4.0E-70	[23..519]	[2..418]
DADA_ECOL6 - D-amino acid dehydrogenase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=dadA PE... EG11407 - D-amino acid dehydrogenase / D-amino acid dehydrogenase DADA_ECODH - D-amino acid dehydrogenase OS=Escherichia coli (strain K12 / DH10B) GN=dadA PE=3 SV=1 gi\|195938844 - gi\|195938844\|ref\|ZP_03084226.1\| D-amino acid dehydrogenase small subunit [Escherichia coli O157:H7 s... gi\|254792666, gi... - gi\|254792666\|ref\|YP_003077503.1\| D-amino acid dehydrogenase [Escherichia coli O157:H7 str. TW14359],... gi\|254161271, gi... - gi\|254161271\|ref\|YP_003044379.1\| D-amino acid dehydrogenase small subunit [Escherichia coli B str. R... gi\|208808515, gi... - gi\|208808515\|ref\|ZP_03250852.1\| D-amino acid dehydrogenase, small subunit [Escherichia coli O157:H7 ... DADA_ECOSE - D-amino acid dehydrogenase OS=Escherichia coli (strain SE11) GN=dadA PE=3 SV=1 gi\|253773813, gi... - gi\|254288079\|ref\|YP_003053827.1\| D-amino acid dehydrogenase small subunit [Escherichia coli BL21(DE3... gi\|242376969, gi... - gi\|251784696\|ref\|YP_002999000.1\| hypothetical protein B21_01174 [Escherichia coli BL21], gi\|24237696... DADA_ECO8A - D-amino acid dehydrogenase OS=Escherichia coli O8 (strain IAI1) GN=dadA PE=3 SV=1 DADA_ECOBW - D-amino acid dehydrogenase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=dadA PE=3 SV=1 gi\|227836602, gi... - gi\|227886398\|ref\|ZP_04004203.1\| D-amino acid dehydrogenase, small subunit [Escherichia coli 83972], ... gi\|75511775, gi\|... - gi\|75511775\|ref\|ZP_00734404.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... DADA_SHISS - D-amino acid dehydrogenase OS=Shigella sonnei (strain Ss046) GN=dadA PE=3 SV=1 DADA_ECO24 - D-amino acid dehydrogenase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=dadA PE=3 SV=1 DADA_ECO57 - D-amino acid dehydrogenase OS=Escherichia coli O157:H7 GN=dadA PE=2 SV=1 DADA_ECOHS - D-amino acid dehydrogenase OS=Escherichia coli O9:H4 (strain HS) GN=dadA PE=3 SV=1 DADA_ECOLC - D-amino acid dehydrogenase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=dadA PE=3 S... EG11407 - D-amino acid dehydrogenase / D-amino acid dehydrogenase gi\|12514889, gi\|... - gi\|15801411\|ref\|NP_287428.1\| D-amino acid dehydrogenase small subunit [Escherichia coli O157:H7 EDL9... gi\|83587333 - gi\|83587333\|ref\|ZP_00925961.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... gi\|75233914 - gi\|75233914\|ref\|ZP_00718374.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... gi\|75241989 - gi\|75241989\|ref\|ZP_00725783.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... gi\|75212627 - gi\|75212627\|ref\|ZP_00712625.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... gi\|75228277 - gi\|75228277\|ref\|ZP_00714932.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Escherichia col... DADA_ECO55 - D-amino acid dehydrogenase OS=Escherichia coli (strain 55989 / EAEC) GN=dadA PE=3 SV=1 DADA_ECO7I - D-amino acid dehydrogenase OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=dadA PE=3 SV=1 DADA_ECOLU - D-amino acid dehydrogenase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=dadA PE=3 SV=1 gi\|124500659, gi... - gi\|124528427\|ref\|ZP_01699737.1\| D-amino-acid dehydrogenase [Escherichia coli B], gi\|124500659\|gb\|EAY... DADA_ECOLI - D-amino acid dehydrogenase small subunit (EC 1.4.99.1) - Escherichia coli DADA_ECOL6 - D-amino acid dehydrogenase small subunit OS=Escherichia coli O6 GN=dadA PE=2 SV=1 gi\|89108034, gi\|... - gi\|89108034\|ref\|AP_001814.1\| D-amino acid dehydrogenase [Escherichia coli str. K-12 substr. W3110], ... gi\|13361148, gi\|... - gi\|15830938\|ref\|NP_309711.1\| D-amino acid dehydrogenase small subunit [Escherichia coli O157:H7 str.... DADA_ECOL5 - D-amino acid dehydrogenase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=dadA PE=3 SV=1	1.0E-68	[23..519]	[2..418]
DADA1_PSEAE, DAD... - D-amino acid dehydrogenase 1 small subunit OS=Pseudomonas aeruginosa GN=dadA1 PE=3 SV=1, (Q9HTQ0) D-... gi\|107104407 - gi\|107104407\|ref\|ZP_01368325.1\| hypothetical protein PaerPA_01005483 [Pseudomonas aeruginosa PACS2] gi\|218774636, gi... - gi\|218894407\|ref\|YP_002443277.1\| D-amino acid dehydrogenase small subunit [Pseudomonas aeruginosa LE... gi\|115588672, gi... - gi\|53726747\|ref\|ZP_00141786.2\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Pseudomonas aer... gi\|126169932, gi... - gi\|84317827\|ref\|ZP_00966262.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Pseudomonas aer... DADA1_PSEAE - D-amino acid dehydrogenase 1 OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LM... gi\|84323989, gi\|... - gi\|84323989\|ref\|ZP_00972054.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Pseudomonas aer...	2.0E-67	[23..520]	[2..420]
gi\|121550047, gi... - gi\|121585684\|ref\|ZP_01675479.1\| D-amino acid dehydrogenase, small subunit [Vibrio cholerae 2740-80],... gi\|124120219, gi... - gi\|153220655\|ref\|ZP_01951766.1\| D-amino acid dehydrogenase, small subunit [Vibrio cholerae MAK 757],... gi\|153817284, gi... - gi\|153817284\|ref\|ZP_01969951.1\| D-amino acid dehydrogenase, small subunit [Vibrio cholerae NCTC 8457... gi\|229510729, gi... - gi\|229510729\|ref\|ZP_04400208.1\| D-amino acid dehydrogenase small subunit [Vibrio cholerae B33], gi\|2... DADA_VIBCM - D-amino acid dehydrogenase OS=Vibrio cholerae serotype O1 (strain M66-2) GN=dadA PE=3 SV=1 gi\|75831973, gi\|... - gi\|75831973\|ref\|ZP_00761232.1\| COG0665: Glycine/D-amino acid oxidases (deaminating) [Vibrio cholerae... gi\|229357822, gi... - gi\|229505599\|ref\|ZP_04395109.1\| D-amino acid dehydrogenase small subunit [Vibrio cholerae BX 330286]... DADA_VIBCH - D-amino acid dehydrogenase small subunit OS=Vibrio cholerae GN=dadA PE=3 SV=1 gi\|229344565, gi... - gi\|229517850\|ref\|ZP_04407294.1\| D-amino acid dehydrogenase small subunit [Vibrio cholerae RC9], gi\|2... gi\|229608618, gi... - gi\|229608618\|ref\|YP_002879266.1\| D-amino acid dehydrogenase small subunit [Vibrio cholerae MJ-1236],... DADA_VIBCH - D-amino acid dehydrogenase OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) ...	9.0E-67	[24..517]	[4..418]
DADA_YERPG - D-amino acid dehydrogenase OS=Yersinia pestis bv. Antiqua (strain Angola) GN=dadA PE=3 SV=1 gi\|45441749, gi\|... - gi\|45441749\|ref\|NP_993288.1\| D-amino acid dehydrogenase small subunit [Yersinia pestis biovar Microt... DADA_YERPN - D-amino acid dehydrogenase OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=dadA PE=3 SV=1 gi\|22126062, gi\|... - gi\|22126062\|ref\|NP_669485.1\| D-amino acid dehydrogenase small subunit [Yersinia pestis KIM], gi\|2195... gi\|16122380, gi\|... - gi\|218929248\|ref\|YP_002347123.1\| D-amino acid dehydrogenase small subunit [Yersinia pestis CO92], gi... DADA_YERPS - D-amino acid dehydrogenase OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=dadA PE=3 S... gi\|166210888, gi... - gi\|166210888\|ref\|ZP_02236923.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar An... gi\|229894821, gi... - gi\|229894821\|ref\|ZP_04510001.1\| D-amino acid dehydrogenase [Yersinia pestis Pestoides A], gi\|2297022... gi\|167401502, gi... - gi\|167401502\|ref\|ZP_02306999.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar An... gi\|229897565, gi... - gi\|229897565\|ref\|ZP_04512721.1\| D-amino acid dehydrogenase [Yersinia pestis biovar Orientalis str. P... gi\|166962069, gi... - gi\|167420374\|ref\|ZP_02312127.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar Or... gi\|229688776, gi... - gi\|229898210\|ref\|ZP_04513358.1\| D-amino acid dehydrogenase [Yersinia pestis biovar Orientalis str. I... gi\|167426555, gi... - gi\|167426555\|ref\|ZP_02318308.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar Me... gi\|167469586 - gi\|167469586\|ref\|ZP_02334290.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis FV-1] DADA_YERPB - D-amino acid dehydrogenase OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) GN=dadA PE=3 SV... DADA_YERPS - D-amino acid dehydrogenase small subunit OS=Yersinia pseudotuberculosis GN=dadA PE=3 SV=1 DADA_YERP3 - D-amino acid dehydrogenase OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=dadA PE... DADA_YERPE - D-amino acid dehydrogenase OS=Yersinia pestis GN=dadA PE=3 SV=1 gi\|165927751, gi... - gi\|165927751\|ref\|ZP_02223583.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar Or... gi\|149292342, gi... - gi\|149365929\|ref\|ZP_01887964.1\| D-amino acid dehydrogenase small subunit [Yersinia pestis CA88-4125]... gi\|165939392, gi... - gi\|165939392\|ref\|ZP_02227940.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar Or... gi\|166009350, gi... - gi\|166009350\|ref\|ZP_02230248.1\| D-amino acid dehydrogenase, small subunit [Yersinia pestis biovar An... DADA_YERPA - D-amino acid dehydrogenase OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=dadA PE=3 SV=1	1.0E-66	[23..519]	[2..418]
DAD1_RALSO, DADA... - D-amino acid dehydrogenase 1 small subunit OS=Ralstonia solanacearum GN=dadA1 PE=3 SV=1, (Q8Y0W7) D-... DADA1_RALSO - D-amino acid dehydrogenase 1 OS=Ralstonia solanacearum (strain GMI1000) GN=dadA1 PE=3 SV=1	5.0E-66	[23..519]	[2..418]
DADA_KLEAE - D-amino acid dehydrogenase small subunit OS=Klebsiella aerogenes GN=dadA PE=2 SV=1 DADA_ENTAE - D-amino acid dehydrogenase OS=Enterobacter aerogenes GN=dadA PE=2 SV=1	1.0E-64	[23..519]	[2..418]

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Predicted Domain #1

Region A:
Residues: [1-164]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGEDFMHPPF QTYPSKNSEG KKHIVIVGGG IIGCCTAYYL TQHPSFSPST HHITIIESRR  60
   61 IAGGASGKAG GLLASWAFPH QIVPLSFQLH QELSDEYDGE NNWDYRRLTT VSLEADVREE 120
  121 VIENYERLSK KAYNLNVPPP KKRPGYISNK FNIGDSNSSL SSSG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [264-363]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKAMETGAVD LLLGKVVGLK CDEMDCVHSL KYLPSVVKNR RNSRGHAENP DIKLGTIFND  60
   61 ENAKPIEIND IQQIVLSMGP WTSKILKDCP ISGLRAHSVT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.0
Match:	1f8rA_
Description:	L-aminoacid oxidase
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [165-263]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SSLKNDSASN EEEGSDIHVS SSVPSLHSLT NERMRSHTNS ASDLDSVSPV EQLRETNIHN  60
   61 PLPADLDWIR RELVNDWSSL GGTDTTAQLH PYKFTHFIL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.0
Match:	1f8rA_
Description:	L-aminoacid oxidase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [364-523]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IKPSEKTVSP YAILAELKVN DREFFSPEMY ARKDEVYVCG EGDTLVNIPE SSDDVEVVSE  60
   61 KCDELYHYVS KLSPTLSKGH LLRKQACFLP VLNVPTSSGP LIGETNVKDL YIASGHSCWG 120
  121 INNAPATGKL MAEILLDGEA TSAEISSLDP KLYFDATILS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.69897
Match:	1el5A_
Description:	Sarcosine oxidase
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