YRC Public Data Repository - Protein Structure Prediction

Protein:	ALKB_ECOLI
Organism:	Escherichia coli
Length:	216 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 ALKB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|74312733, gi\|... - gi\|74312733\|ref\|YP_311152.1\| DNA repair system specific for alkylated DNA [Shigella sonnei Ss046], g...	228.0	[0..1]	[216..1]
gi\|189365342, gi... - gi\|189365342\|gb\|EDU83758.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4501]... gi\|168767836, gi... - gi\|189362800\|gb\|EDU81219.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4486]... gi\|187771131, gi... - gi\|187771131\|gb\|EDU34975.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4196]... gi\|189002134, gi... - gi\|189002134\|gb\|EDU71120.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4076]... gi\|254593511, gi... - gi\|254794111\|ref\|YP_003078948.1\| oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA ... gi\|168749619, gi... - gi\|188016117\|gb\|EDU54239.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4113]... gi\|168754963, gi... - gi\|189357628\|gb\|EDU76047.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4401]... gi\|209765664, gi... - pir\|\|G85860 DNA repair system specific for alkylated DNA [imported] - Escherichia coli (strain O157:... gi\|15802765, gi\|... - gi\|15802765\|ref\|NP_288792.1\| DNA repair system specific for alkylated DNA [Escherichia coli O157:H7 ... gi\|13362570, gi\|... - gi\|15832355\|ref\|NP_311128.1\| alkylated DNA repair protein [Escherichia coli O157:H7], gi\|13362570\|db... gi\|13362570, gi\|... - gi\|15832355\|ref\|NP_311128.1\| alkylated DNA repair protein [Escherichia coli O157:H7 str. Sakai], gi\|... gi\|208821524, gi... - gi\|208821524\|ref\|ZP_03261844.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4... gi\|209159819, gi... - gi\|209398419\|ref\|YP_002271625.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC... gi\|217327520, gi... - gi\|217327520\|ref\|ZP_03443603.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. TW1... gi\|189372948, gi... - gi\|189372948\|gb\|EDU91364.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC869],... gi\|195935593 - gi\|195935593\|ref\|ZP_03080975.1\| alkylated DNA repair protein [Escherichia coli O157:H7 str. EC4024] gi\|208727465, gi... - gi\|208807664\|ref\|ZP_03250001.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4... gi\|208733654, gi... - gi\|208812377\|ref\|ZP_03253706.1\| alkylated DNA repair protein AlkB [Escherichia coli O157:H7 str. EC4...	227.0	[0..1]	[216..1]
gi\|124526381, gi... - gi\|124526381\|ref\|ZP_01698334.1\| alkylated DNA repair protein AlkB [Escherichia coli B], gi\|124501852... gi\|75514424, gi\|... - gi\|75514424\|ref\|ZP_00736702.1\| COG3145: Alkylated DNA repair protein [Escherichia coli 53638], gi\|18... gi\|187428676, gi... - gi\|75176157\|ref\|ZP_00696315.1\| COG3145: Alkylated DNA repair protein [Shigella boydii BS512], gi\|187... gi\|169754402, gi... - gi\|170019474\|ref\|YP_001724428.1\| alkylated DNA repair protein AlkB [Escherichia coli ATCC 8739], gi\|...	227.0	[0..1]	[216..1]
gi\|190904556, gi... - gi\|75231450\|ref\|ZP_00717819.1\| COG3145: Alkylated DNA repair protein [Escherichia coli B7A], gi\|1911... gi\|75187008, gi\|... - gi\|75187008\|ref\|ZP_00700275.1\| COG3145: Alkylated DNA repair protein [Escherichia coli E24377A], gi\|... gi\|218554781, gi... - gi\|218554781\|ref\|YP_002387694.1\| oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA ... gi\|218352557, gi... - gi\|218695825\|ref\|YP_002403492.1\| oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA ...	227.0	[0..1]	[216..1]
gi\|193062349, gi... - gi\|75259684\|ref\|ZP_00730986.1\| COG3145: Alkylated DNA repair protein [Escherichia coli E22], gi\|1930... gi\|194427195, gi... - gi\|75211628\|ref\|ZP_00711707.1\| COG3145: Alkylated DNA repair protein [Escherichia coli B171], gi\|194...	227.0	[0..1]	[216..1]
gi\|82776184, gi\|... - gi\|82776184\|ref\|YP_402533.1\| DNA repair system specific for alkylated DNA [Shigella dysenteriae Sd19...	226.0	[0..1]	[216..1]
gi\|192958431, gi... - gi\|75238008\|ref\|ZP_00722013.1\| COG3145: Alkylated DNA repair protein [Escherichia coli E110019], gi\|...	226.0	[0..1]	[216..1]
gi\|110806186, gi... - gi\|110806186\|ref\|YP_689706.1\| alkylated DNA repair protein [Shigella flexneri 5 str. 8401], gi\|11061... gi\|82544554, gi\|... - gi\|82544554\|ref\|YP_408501.1\| AlkB [Shigella boydii Sb227], gi\|81245965\|gb\|ABB66673.1\| AlkB [Shigella... gi\|24113597, gi\|... - gi\|24113597\|ref\|NP_708107.1\| alkylated DNA repair protein [Shigella flexneri 2a str. 301], gi\|240526... gi\|30063651, gi\|... - gi\|30063651\|ref\|NP_837822.1\| alkylated DNA repair protein [Shigella flexneri 2a str. 2457T], gi\|3004...	226.0	[0..1]	[216..1]
gi\|218427939, gi... - gi\|218690375\|ref\|YP_002398587.1\| oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA ... gi\|26248599, gi\|... - gi\|26248599\|ref\|NP_754639.1\| alkylated DNA repair protein AlkB [Escherichia coli CFT073], gi\|2610900... gi\|227887270, gi... - gi\|227887270\|ref\|ZP_04005075.1\| alkylated DNA repair protein AlkB [Escherichia coli 83972], gi\|22783...	226.0	[0..1]	[216..1]
gi\|75196254, gi\|... - gi\|75196254\|ref\|ZP_00706324.1\| COG3145: Alkylated DNA repair protein [Escherichia coli HS], gi\|15716...	226.0	[0..1]	[216..1]

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Predicted Domain #1

Region A:
Residues: [1-216]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLDLFADAEP WQEPLAAGAV ILRRFAFNAA EQLIRDINDV ASQSPFRQMV TPGGYTMSVA  60
   61 MTNCGHLGWT THRQGYLYSP IDPQTNKPWP AMPQSFHNLC QRAATAAGYP DFQPDACLIN 120
  121 RYAPGAKLSL HQDKDEPDLR APIVSVSLGL PAIFQFGGLK RNDPLKRLLL EHGDVVVWGG 180
  181 ESRLFYHGIQ PLKAGFHPLT IDCRYNLTFR QAGKKE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	54.0
Match:	2fd8A
Description:	Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.29176034651701	bayes_pls_golite062009
damaged DNA binding	0.93829227106437	bayes_pls_golite062009
binding	0.0486041256295213	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: