YRC Public Data Repository - Protein Structure Prediction

Protein:	HEM3
Organism:	Saccharomyces cerevisiae
Length:	327 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 HEM3.

Description	E-value	Query Range	Subject Range
gi\|15833989, gi\|... - gi\|15833989\|ref\|NP_312762.1\| porphobilinogen deaminase [Escherichia coli O157:H7], gi\|13364211\|dbj\|B... gi\|209753312, gi... - gi\|25292187\|pir\|\|A86067 porphobilinogen deaminase [imported] - Escherichia coli (strain O157:H7, su... gi\|15804393, gi\|... - gi\|15804393\|ref\|NP_290433.1\| porphobilinogen deaminase [Escherichia coli O157:H7 EDL933], gi\|1251866... gi\|15833989, gi\|... - gi\|15833989\|ref\|NP_312762.1\| porphobilinogen deaminase [Escherichia coli O157:H7 str. Sakai], gi\|133...	0.0	[1..322]	[8..314]
HEM3_ECODH - Porphobilinogen deaminase OS=Escherichia coli (strain K12 / DH10B) GN=hemC PE=3 SV=1 gi\|89110215, gi\|... - gi\|89110215\|ref\|AP_003995.1\| hydroxymethylbilane synthase [Escherichia coli str. K-12 substr. W3110]... gi\|75197688 - gi\|75197688\|ref\|ZP_00707758.1\| COG0181: Porphobilinogen deaminase [Escherichia coli HS] HEM3_ECOLI - Porphobilinogen deaminase (EC 2.5.1.61) (PBG) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyri... EG10429 - hydroxymethylbilane synthase / Porphobilinogen deaminase; neomycin sensitivity gi\|28373294\|pdb\|... - Chain A, Time-Resolved And Static-Ensemble Structural Chemistry Of Hydroxymethylbilane Synthase HEM3_ECOBW - Porphobilinogen deaminase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=hemC PE=3 SV=1 EG10429 - hydroxymethylbilane synthase / Porphobilinogen deaminase; neomycin sensitivity	0.0	[1..322]	[1..307]
HEM3_VIBCH - Porphobilinogen deaminase OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) G... HEM3_VIBCH - Porphobilinogen deaminase OS=Vibrio cholerae GN=hemC PE=3 SV=2 gi\|75829589, gi\|... - gi\|75829589\|ref\|ZP_00758887.1\| COG0181: Porphobilinogen deaminase [Vibrio cholerae MO10], gi\|1161882... gi\|75828041 - gi\|75828041\|ref\|ZP_00757476.1\| COG0181: Porphobilinogen deaminase [Vibrio cholerae O395] gi\|75814732 - gi\|75814732\|ref\|ZP_00745287.1\| COG0181: Porphobilinogen deaminase [Vibrio cholerae V52]	0.0	[1..324]	[1..309]
gi\|9654520, gi\|1... - gi\|9654520\|gb\|AAF93298.1\| porphobilinogen deaminase [Vibrio cholerae O1 biovar El Tor str. N16961], ... gi\|11269688 - gi\|11269688\|pir\|\|F82362 hydroxymethylbilane synthase (EC 4.3.1.8) [similarity] - Vibrio cholerae (st... gi\|227080356, gi... - gi\|227080356\|ref\|YP_002808907.1\| porphobilinogen deaminase [Vibrio cholerae M66-2], gi\|227008244\|gb\|... gi\|229517035, gi... - gi\|229517035\|ref\|ZP_04406481.1\| porphobilinogen deaminase [Vibrio cholerae RC9], gi\|229346098\|gb\|EEO... gi\|229508398, gi... - gi\|229508398\|ref\|ZP_04397902.1\| porphobilinogen deaminase [Vibrio cholerae BX 330286], gi\|229354671\|... gi\|229369326, gi... - gi\|229606671\|ref\|YP_002877319.1\| porphobilinogen deaminase [Vibrio cholerae MJ-1236], gi\|229369326\|g... gi\|121548017, gi... - gi\|121587718\|ref\|ZP_01677479.1\| porphobilinogen deaminase [Vibrio cholerae 2740-80], gi\|121548017\|gb... gi\|153223867, gi... - gi\|153223867\|ref\|ZP_01954104.1\| porphobilinogen deaminase [Vibrio cholerae MAK 757], gi\|124117978\|gb... gi\|121629433, gi... - gi\|121728303\|ref\|ZP_01681334.1\| porphobilinogen deaminase [Vibrio cholerae V52], gi\|121629433\|gb\|EAX... gi\|227116428, gi... - gi\|227116428\|ref\|YP_002818324.1\| porphobilinogen deaminase [Vibrio cholerae O395], gi\|227011878\|gb\|A... gi\|126510497, gi... - gi\|153818935\|ref\|ZP_01971602.1\| porphobilinogen deaminase [Vibrio cholerae NCTC 8457], gi\|126510497\|... gi\|254851504, gi... - gi\|254851504\|ref\|ZP_05240854.1\| porphobilinogen deaminase [Vibrio cholerae MO10], gi\|254847209\|gb\|EE... gi\|126520151, gi... - gi\|229508921\|ref\|ZP_04398411.1\| porphobilinogen deaminase [Vibrio cholerae B33], gi\|229354038\|gb\|EEO...	0.0	[1..324]	[7..315]
gi\|167470637 - gi\|167470637\|ref\|ZP_02335341.1\| porphobilinogen deaminase [Yersinia pestis FV-1] gi\|153997095, gi... - gi\|153997095\|ref\|ZP_02022228.1\| porphobilinogen deaminase [Yersinia pestis CA88-4125], gi\|149289401\|... gi\|167426299, gi... - gi\|167426299\|ref\|ZP_02318052.1\| porphobilinogen deaminase [Yersinia pestis biovar Mediaevalis str. K... gi\|161484901 - gi\|161484901\|ref\|NP_667719.2\| porphobilinogen deaminase [Yersinia pestis KIM] gi\|165926233, gi... - gi\|165926233\|ref\|ZP_02222065.1\| porphobilinogen deaminase [Yersinia pestis biovar Orientalis str. F1... gi\|161511325 - gi\|161511325\|ref\|NP_994488.2\| porphobilinogen deaminase [Yersinia pestis biovar Microtus str. 91001] gi\|166213633, gi... - gi\|166213633\|ref\|ZP_02239668.1\| porphobilinogen deaminase [Yersinia pestis biovar Antiqua str. B4200... gi\|165989447, gi... - gi\|166011678\|ref\|ZP_02232576.1\| porphobilinogen deaminase [Yersinia pestis biovar Antiqua str. E1979... HEM3_YERP3 - Porphobilinogen deaminase OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=hemC PE=... gi\|166961213, gi... - gi\|167421084\|ref\|ZP_02312837.1\| porphobilinogen deaminase [Yersinia pestis biovar Orientalis str. MG... gi\|167048715, gi... - gi\|167401822\|ref\|ZP_02307310.1\| porphobilinogen deaminase [Yersinia pestis biovar Antiqua str. UG05-... HEM3_YERPP - Porphobilinogen deaminase OS=Yersinia pestis (strain Pestoides F) GN=hemC PE=3 SV=1 gi\|165912924, gi... - gi\|89104220\|ref\|ZP_01176770.1\| COG0181: Porphobilinogen deaminase [Yersinia pestis biovar Orientalis... HEM3_YERPE - Porphobilinogen deaminase OS=Yersinia pestis GN=hemC PE=3 SV=2 gi\|229837182, gi... - gi\|229837182\|ref\|ZP_04457347.1\| hydroxymethylbilane synthase [Yersinia pestis Pestoides A], gi\|22970... gi\|229695908, gi... - gi\|229839542\|ref\|ZP_04459701.1\| hydroxymethylbilane synthase [Yersinia pestis biovar Orientalis str.... gi\|229900105, gi... - gi\|229900105\|ref\|ZP_04515242.1\| hydroxymethylbilane synthase [Yersinia pestis biovar Orientalis str.... HEM3_YERPA - Porphobilinogen deaminase OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=hemC PE=3 SV=1 HEM3_YERPN - Porphobilinogen deaminase OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=hemC PE=3 SV=1 gi\|115349463, gi... - gi\|218930852\|ref\|YP_002348727.1\| porphobilinogen deaminase [Yersinia pestis CO92], gi\|16123984\|ref\|N...	0.0	[1..324]	[1..309]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[1..322]	[1..307]
gi\|16767209, gi\|... - gi\|6960263\|gb\|AAF33453.1\| 89% identity with E. coli porphobilinogen deaminase (HEMC) (SP:P06983); co... lcl\|NC_016856.1_... - [gene=hemC] [protein=porphobilinogen deaminase] [protein_id=YP_005240197.1] [location=complement(415... gi\|194449507, gi... - gi\|194449507\|ref\|YP_002047954.1\| porphobilinogen deaminase [Salmonella enterica subsp. enterica sero... gi\|206710947, gi... - gi\|207859144\|ref\|YP_002245795.1\| porphobilinogen deaminase [Salmonella enterica subsp. enterica sero...	0.0	[1..322]	[6..312]

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Predicted Domain #1

Region A:
Residues: [1-104]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGPETLHIGG RKSKLAVIQS NHVLKLIEEK YPDYDCKVFT LQTLGDQIQF KPLYSFGGKA  60
   61 LWTKELEDHL YHDDPSKKLD LIVHSLKDMP TLLPEGFELG GITK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [209-231]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ALGIEIRKGD TKMMKILDEI CDL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	596.9897
Match:	1pda__
Description:	Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain; Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [105-208]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RVDPTDCLVM PFYSAYKSLD DLPDGGIVGT SSVRRSAQLK RKYPHLKFES VRGNIQTRLQ  60
   61 KLDDPKSPYQ CIILASAGLM RMGLENRITQ RFHSDTMYHA VGQG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [232-327]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NATICCLSER ALMRTLEGGC SVPIGVESKY NEETKKLLLK AIVVDVEGTE AVEDEIEMLI  60
   61 ENVKEDSMAC GKILAERMIA DGAKKILDEI NLDRIK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	596.9897
Match:	1pda__
Description:	Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain; Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
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