YRC Public Data Repository - Protein Structure Prediction

Protein:	SDHD_ECOLI
Organism:	Escherichia coli
Length:	442 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 SDHD_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|189366338, gi... - gi\|189366338\|gb\|EDU84754.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4501], gi\|168763... gi\|188017246, gi... - gi\|188017246\|gb\|EDU55368.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4113], gi\|168748... gi\|13362715, gi\|... - gi\|15832499\|ref\|NP_311272.1\| D-serine dehydratase [Escherichia coli O157:H7 str. Sakai], gi\|13362715... gi\|254593728, gi... - gi\|254794328\|ref\|YP_003079165.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. TW14359], gi\|... gi\|189372865, gi... - gi\|189372865\|gb\|EDU91281.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC869], gi\|1687872... gi\|168780326, gi... - gi\|189001880\|gb\|EDU70866.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4076], gi\|168780... gi\|168772802, gi... - gi\|187771214\|gb\|EDU35058.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4196], gi\|168772... gi\|168770934, gi... - gi\|189360248\|gb\|EDU78667.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4486], gi\|168770... gi\|209747728, gi... - pir\|\|G85878 D-serine dehydratase (deaminase) [imported] - Escherichia coli (strain O157:H7, substrai... gi\|15802909, gi\|... - gi\|15802909\|ref\|NP_288936.1\| D-serine dehydratase [Escherichia coli O157:H7 EDL933], gi\|12516733\|gb\|... SDHD_ECO57 - D-serine dehydratase OS=Escherichia coli O157:H7 GN=dsdA PE=3 SV=1 gi\|208740136, gi... - gi\|208820013\|ref\|ZP_03260333.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4042], gi\|20... gi\|208813879, gi... - gi\|208813879\|ref\|ZP_03255208.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4045], gi\|20... gi\|208727157, gi... - gi\|208807356\|ref\|ZP_03249693.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. EC4206], gi\|20... gi\|195938719 - gi\|195938719\|ref\|ZP_03084101.1\| D-serine dehydratase [Escherichia coli O157:H7 str. EC4024] gi\|217326787, gi... - gi\|217326787\|ref\|ZP_03442870.1\| D-serine ammonia-lyase [Escherichia coli O157:H7 str. TW14588], gi\|2... SDHD_ECO5E - D-serine dehydratase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=dsdA PE=3 SV=1	345.0	[0..1]	[442..1]
gi\|194428614, gi... - gi\|75210158\|ref\|ZP_00710330.1\| COG3048: D-serine dehydratase [Escherichia coli B171], gi\|194428614\|r...	343.0	[0..1]	[442..1]
SDHD_ECO24 - D-serine dehydratase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=dsdA PE=3 SV=1 gi\|253772725, gi... - gi\|254289120\|ref\|YP_003054868.1\| D-serine dehydratase [Escherichia coli BL21(DE3)], gi\|253978427\|gb\|... gi\|194424693, gi... - gi\|83588370\|ref\|ZP_00926995.1\| COG3048: D-serine dehydratase [Escherichia coli 101-1], gi\|194435965\|... gi\|251785711, gi... - gi\|251785711\|ref\|YP_003000015.1\| hypothetical protein B21_02237 [Escherichia coli BL21], gi\|24237798... gi\|254162359, gi... - gi\|254162359\|ref\|YP_003045467.1\| D-serine dehydratase [Escherichia coli B str. REL606], gi\|253974260... SDHD_ECO8A - D-serine dehydratase OS=Escherichia coli O8 (strain IAI1) GN=dsdA PE=3 SV=1 gi\|75259810, gi\|... - gi\|75259810\|ref\|ZP_00731112.1\| COG3048: D-serine dehydratase [Escherichia coli E22], gi\|193062412\|re... gi\|193069723, gi... - gi\|75235556\|ref\|ZP_00719747.1\| COG3048: D-serine dehydratase [Escherichia coli E110019], gi\|19306972... gi\|75231344, gi\|... - gi\|75231344\|ref\|ZP_00717732.1\| COG3048: D-serine dehydratase [Escherichia coli B7A], gi\|191165484\|re... SDHD_ECOHS - D-serine dehydratase OS=Escherichia coli O9:H4 (strain HS) GN=dsdA PE=3 SV=1	343.0	[0..1]	[442..1]
SDHD_SHIDS - D-serine dehydratase OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=dsdA PE=3 SV=1	342.0	[0..1]	[442..1]
SDHD_SHIF8 - D-serine dehydratase OS=Shigella flexneri serotype 5b (strain 8401) GN=dsdA PE=3 SV=1	342.0	[0..1]	[442..1]
SDHD2_ECOUT - D-serine dehydratase 2 OS=Escherichia coli (strain UTI89 / UPEC) GN=dsdA2 PE=3 SV=1 SDHD2_ECOL5 - D-serine dehydratase 2 OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=dsdA2 PE=3 SV=1 gi\|190908934, gi... - gi\|75242296\|ref\|ZP_00726058.1\| COG3048: D-serine dehydratase [Escherichia coli F11], gi\|191170710\|re... gi\|23954265 - gi\|23954265\|emb\|CAD42063.1\| hypothetical protein [Escherichia coli]	341.0	[0..1]	[441..1]
gi\|145806 - gi\|145806\|gb\|AAA87975.1\| D-serine deaminase	341.0	[0..1]	[442..1]
SDHD_SHISS - D-serine dehydratase OS=Shigella sonnei (strain Ss046) GN=dsdA PE=3 SV=1	341.0	[0..1]	[442..1]
gi\|24052799, gi\|... - gi\|24113727\|ref\|NP_708237.1\| D-serine dehydratase [Shigella flexneri 2a str. 301], gi\|24052799\|gb\|AA... gi\|30042028, gi\|... - gi\|30063773\|ref\|NP_837944.1\| D-serine dehydratase [Shigella flexneri 2a str. 2457T], gi\|30042028\|gb\|... SDHD_SHIFL - D-serine dehydratase OS=Shigella flexneri GN=dsdA PE=3 SV=1	340.0	[0..1]	[442..1]

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Predicted Domain #1

Region A:
Residues: [1-442]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MENAKMNSLI AQYPLVKDLV ALKETTWFNP GTTSLAEGLP YVGLTEQDVQ DAHARLSRFA  60
   61 PYLAKAFPET AATGGIIESE LVAIPAMQKR LEKEYQQPIS GQLLLKKDSH LPISGSIKAR 120
  121 GGIYEVLAHA EKLALEAGLL TLDDDYSKLL SPEFKQFFSQ YSIAVGSTGN LGLSIGIMSA 180
  181 RIGFKVTVHM SADARAWKKA KLRSHGVTVV EYEQDYGVAV EEGRKAAQSD PNCFFIDDEN 240
  241 SRTLFLGYSV AGQRLKAQFA QQGRIVDADN PLFVYLPCGV GGGPGGVAFG LKLAFGDHVH 300
  301 CFFAEPTHSP CMLLGVHTGL HDQISVQDIG IDNLTAADGL AVGRASGFVG RAMERLLDGF 360
  361 YTLSDQTMYD MLGWLAQEEG IRLEPSALAG MAGPQRVCAS VSYQQMHGFS AEQLRNTTHL 420
  421 VWATGGGMVP EEEMNQYLAK GR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.0
Match:	1jbqA
Description:	Cystathionine beta-synthase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
cysteine synthase activity	3.05516621034881	bayes_pls_golite062009
catalytic activity	2.76038225023173	bayes_pls_golite062009
lyase activity	2.54165185299539	bayes_pls_golite062009
carbon-oxygen lyase activity	1.52790731142158	bayes_pls_golite062009
ammonia-lyase activity	0.943946746392831	bayes_pls_golite062009
carbon-nitrogen lyase activity	0.8463142805916	bayes_pls_golite062009
L-threonine ammonia-lyase activity	0.57533596285038	bayes_pls_golite062009
tryptophan synthase activity	0.44169275450925	bayes_pls_golite062009
threonine synthase activity	0.19129755094699	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: