YRC Public Data Repository - Protein Structure Prediction

Protein:	APN1
Organism:	Saccharomyces cerevisiae
Length:	367 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 APN1.

Description	E-value	Query Range	Subject Range
gi\|171068 - gi\|171068\|gb\|AAA34429.1\| apurinic endonuclease (APN1)	0.0	[1..367]	[1..367]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-70	[17..330]	[2..311]
gi\|214000084 - gi\|214000084\|ref\|ZP_03410819.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213979778 - gi\|213979778\|ref\|ZP_03407037.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213855420 - gi\|213855420\|ref\|ZP_03383660.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213417706 - gi\|213417706\|ref\|ZP_03350830.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|200387407, gi... - gi\|200387407\|ref\|ZP_03214019.1\| endonuclease 4 [Salmonella enterica subsp. enterica serovar Virchow ... gi\|213649962 - gi\|213649962\|ref\|ZP_03380015.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213611243 - gi\|213611243\|ref\|ZP_03370069.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213583239 - gi\|213583239\|ref\|ZP_03365065.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... gi\|213424240 - gi\|213424240\|ref\|ZP_03357099.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi s... END4_SALTI - Probable endonuclease 4 OS=Salmonella typhi GN=nfo PE=3 SV=1 gi\|29141162, gi\|... - gi\|29141162\|ref\|NP_804504.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi str.... gi\|16761144 - gi\|16761144\|ref\|NP_456761.1\| endonuclease IV [Salmonella enterica subsp. enterica serovar Typhi str.... END4_SALTI - Probable endonuclease 4 OS=Salmonella typhi GN=nfo PE=3 SV=1	1.0E-66	[16..302]	[3..284]
END4_SALTY - Probable endonuclease 4 OS=Salmonella typhimurium GN=nfo PE=3 SV=1 END4_SALPB - Probable endonuclease 4 OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=nfo PE=3 SV=1 gi\|205330602, gi... - gi\|205330602\|gb\|EDZ17366.1\| endonuclease 4 [Salmonella enterica subsp. enterica serovar 4,[5],12:i:-... END4_SALTY - Probable endonuclease 4 OS=Salmonella typhimurium GN=nfo PE=3 SV=1 gi\|168466107, gi... - gi\|195631363\|gb\|EDX49923.1\| endonuclease 4 [Salmonella enterica subsp. enterica serovar Newport str.... lcl\|NC_016856.1_... - [gene=nfo] [protein=endonuclease IV] [protein_id=YP_005238259.1] [location=2354212..2355069] END4_SALPB - Probable endonuclease 4 OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=nfo PE=3 SV=1 END4_SALTY - Probable endonuclease 4 OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=nfo PE=3 ... gi\|167551168, gi... - gi\|205324051\|gb\|EDZ11890.1\| endonuclease 4 [Salmonella enterica subsp. enterica serovar Saintpaul st...	2.0E-66	[16..302]	[3..284]
gi\|168788974, gi... - gi\|189371374\|gb\|EDU89790.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC869], gi\|168788974\|ref\|Z... gi\|189002169, gi... - gi\|189002169\|gb\|EDU71155.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4076], gi\|168780008\|ref\|... gi\|187771296, gi... - gi\|187771296\|gb\|EDU35140.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4196], gi\|168773124\|ref\|... gi\|168767778, gi... - gi\|189362945\|gb\|EDU81364.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4486], gi\|168767778\|ref\|... gi\|208725960, gi... - gi\|208806159\|ref\|ZP_03248496.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4206], gi\|208725960\|... gi\|195935538 - gi\|195935538\|ref\|ZP_03080920.1\| endonuclease IV [Escherichia coli O157:H7 str. EC4024] END4_ECODH - Probable endonuclease 4 OS=Escherichia coli (strain K12 / DH10B) GN=nfo PE=3 SV=1 gi\|168801146, gi... - gi\|189376626\|gb\|EDU95042.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC508], gi\|168801146\|ref\|Z... END4_ECOLI - Endonuclease 4 (EC 3.1.21.2) (Endonuclease IV) (Endodeoxyribonuclease IV) - Escherichia coli gi\|189366099, gi... - gi\|189366099\|gb\|EDU84515.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4501], gi\|168763821\|ref\|... gi\|189355386, gi... - gi\|189355386\|gb\|EDU73805.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4401], gi\|168757747\|ref\|... gi\|168750545, gi... - gi\|188015349\|gb\|EDU53471.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4113], gi\|168750545\|ref\|... END4_ECOBW - Probable endonuclease 4 OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=nfo PE=3 SV=1 gi\|13362520, gi\|... - gi\|15832305\|ref\|NP_311078.1\| endonuclease IV [Escherichia coli O157:H7 str. Sakai], gi\|13362520\|dbj\|... gi\|254794058, gi... - gi\|254794058\|ref\|YP_003078895.1\| endonuclease IV with intrinsic 3'-5' exonuclease activity [Escheric... END4_SHIDS - Probable endonuclease 4 OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=nfo PE=3 SV=1 gi\|89108976, gi\|... - gi\|89108976\|ref\|AP_002756.1\| endonuclease IV with intrinsic 3'-5' exonuclease activity [Escherichia ... gi\|217319290, gi... - gi\|217326923\|ref\|ZP_03443006.1\| endonuclease 4 [Escherichia coli O157:H7 str. TW14588], gi\|217319290... END4_ECO5E - Probable endonuclease 4 OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=nfo PE=3 SV=1 gi\|208819989, gi... - gi\|208819989\|ref\|ZP_03260309.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4042], gi\|208740112\|... gi\|208735775, gi... - gi\|208814498\|ref\|ZP_03255827.1\| endonuclease 4 [Escherichia coli O157:H7 str. EC4045], gi\|208735775\|... END4_ECO57 - Endonuclease 4 OS=Escherichia coli O157:H7 GN=nfo PE=3 SV=1 EG10651 - endonuclease IV with intrinsic 3'-5' exonuclease activity / AP endodeoxyribonuclease IV; member of s... EG10651 - endonuclease IV with intrinsic 3'-5' exonuclease activity / AP endodeoxyribonuclease IV; member of s...	7.0E-64	[16..298]	[3..280]
gi\|6573704 - gi\|6573704\|pdb\|1QTW\|A Chain A, High-Resolution Crystal Structure Of The Escherichia Coli Dna Repair ...	8.0E-64	[16..298]	[3..280]

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Predicted Domain #1

Region A:
Residues: [1-367]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPSTPSFVRS AVSKYKFGAH MSGAGGISNS VTNAFNTGCN SFAMFLKSPR KWVSPQYTQE  60
   61 EIDKFKKNCA TYNYNPLTDV LPHGQYFINL ANPDREKAEK SYESFMDDLN RCEQLGIGLY 120
  121 NLHPGSTLKG DHQLQLKQLA SYLNKAIKET KFVKIVLENM AGTGNLVGSS LVDLKEVIGM 180
  181 IEDKSRIGVC IDTCHTFAAG YDISTTETFN NFWKEFNDVI GFKYLSAVHL NDSKAPLGAN 240
  241 RDLHERLGQG YLGIDVFRMI AHSEYLQGIP IVLETPYEND EGYGNEIKLM EWLESKSESE 300
  301 LLEDKEYKEK NDTLQKLGAK SRKEQLDKFE VKQKKRAGGT KRKKATAEPS DNDILSQMTK 360
  361 KRKTKKE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	688.67837
Match:	1qtwA_
Description:	Endonuclease IV
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
deoxyribonuclease activity	1.46354552309786	bayes_pls_golite062009
catalytic activity	1.28975577984201	bayes_pls_golite062009
binding	1.21937946213086	bayes_pls_golite062009
endodeoxyribonuclease activity	0.960974549724719	bayes_pls_golite062009
DNA-(apurinic or apyrimidinic site) lyase activity	0.952482439706792	bayes_pls_golite062009
nuclease activity	0.476817046894313	bayes_pls_golite062009
endodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.250454213851443	bayes_pls_golite062009
double-stranded DNA specific exodeoxyribonuclease activity	0.17972995021274	bayes_pls_golite062009
protein binding	0.0986812836806968	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: