YRC Public Data Repository - Protein Structure Prediction

Protein:	exo-3
Organism:	Caenorhabditis elegans
Length:	288 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 exo-3.

Description	E-value	Query Range	Subject Range
gi\|157748305 - gi\|157748305\|ref\|XP_001669247.1\| Hypothetical protein CBG18693 [Caenorhabditis briggsae AF16] gi\|187024770, gi... - gi\|39580209\|emb\|CAE71716.1\| Hypothetical protein CBG18693 [Caenorhabditis briggsae], gi\|187024770\|em...	249.0	[0..1]	[288..1]
gi\|109082628, gi... - gi\|109082640\|ref\|XP_001090240.1\| PREDICTED: APEX nuclease isoform 8 [Macaca mulatta], gi\|109082638\|r... gi\|90078218 - gi\|90078218\|dbj\|BAE88789.1\| unnamed protein product [Macaca fascicularis]	247.0	[0..2]	[286..32]
gi\|16800960 - gi\|16800960\|ref\|NP_471228.1\| hypothetical protein lin1894 [Listeria innocua Clip11262] gi\|25289128, gi\|... - pir\|\|AD1669 3'-exo-deoxyribonuclease exoA homolog lin1894 [imported] - Listeria innocua (strain Clip...	246.0	[0..34]	[287..1]
gi\|82723280, gi\|... - gi\|82748860\|ref\|ZP_00911335.1\| AP endonuclease, family 1:Exodeoxyribonuclease III xth [Clostridium b...	245.0	[0..35]	[287..5]
gi\|46908012, gi\|... - gi\|46908012\|ref\|YP_014401.1\| exodeoxyribonuclease [Listeria monocytogenes str. 4b F2365], gi\|4688128... gi\|47017476, gi\|... - gi\|47094151\|ref\|ZP_00231871.1\| exodeoxyribonuclease [Listeria monocytogenes str. 4b H7858], gi\|47017... gi\|133726867, gi... - gi\|153167588\|ref\|ZP_01927728.1\| exodeoxyribonuclease [Listeria monocytogenes FSL N1-017], gi\|1337268... gi\|133735073, gi... - gi\|254933631\|ref\|ZP_05266990.1\| 3'-exo-deoxyribonuclease exoA [Listeria monocytogenes HPB2262], gi\|1... gi\|225876847, gi... - gi\|226224385\|ref\|YP_002758492.1\| 3'-exo-deoxyribonuclease exoA [Listeria monocytogenes Clip81459], g... gi\|254880606 - gi\|254880606\|ref\|ZP_05253316.1\| 3'-exo-deoxyribonuclease exoA [Listeria monocytogenes FSL J2-071] gi\|254826392 - gi\|254826392\|ref\|ZP_05231393.1\| 3'-exo-deoxyribonuclease exoA [Listeria monocytogenes FSL J1-194] gi\|255521086 - gi\|255521086\|ref\|ZP_05388323.1\| 3'-exo-deoxyribonuclease exoA [Listeria monocytogenes FSL J1-175] gi\|217964070, gi... - gi\|217964070\|ref\|YP_002349748.1\| exodeoxyribonuclease III [Listeria monocytogenes HCC23], gi\|2173333...	245.0	[0..34]	[287..1]
APEX1_RAT - DNA-(apurinic or apyrimidinic site) lyase OS=Rattus norvegicus GN=Apex1 PE=1 SV=2	245.0	[0..2]	[286..31]
gi\|157830335, gi... - gi\|5542121\|pdb\|1BIX\| Chain , The Crystal Structure Of The Human Dna Repair Endonuclease Hap1 Sugge...	245.0	[0..2]	[286..1]
gi\|60652565 - gi\|60652565\|gb\|AAX28977.1\| APEX nuclease 1 [synthetic construct]	244.0	[0..5]	[286..35]

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Predicted Domain #1

Region A:
Residues: [1-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKRKAEEAP APKLASIFTK KVKPAEEDNN QKSWKFVCWN VAGLRACVKK SDFKEVLAEE  60
   61 PDLVFLGETK CKEWPPEMEE TFKNYTKTLV VSTEKNGGYA GVGLLSKCAP MKVHKGIGDP 120
  121 EFDTAGRLII AEFSKFYFIG AYVPNSGAKL VNLEKRGRWE KLLTEKMKEM DEKKPVIYGG 180
  181 DLNVAHNEID LKNPESNRNK TAGFTDQERG WFSEMLELGF TDTFRAMHPD EKKYSFWSYL 240
  241 ANSRQKDVGW RLDYYVVSNR IMNKVKRSDI MSSVMGSDHA PVVMQIDF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	65.0
Match:	1bixA
Description:	THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
exonuclease activity	2.70644978530491	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	2.57658637220545	bayes_pls_golite062009
deoxyribonuclease activity	2.54419310609558	bayes_pls_golite062009
hydrolase activity	2.50832753420463	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.36841783202726	bayes_pls_golite062009
exodeoxyribonuclease activity	1.8139951607534	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	1.7967853371745	bayes_pls_golite062009
nuclease activity	1.78432551160775	bayes_pls_golite062009
catalytic activity	1.76511376991978	bayes_pls_golite062009
binding	1.74593496417303	bayes_pls_golite062009
DNA binding	0.961734136090079	bayes_pls_golite062009
nucleic acid binding	0.947430734766989	bayes_pls_golite062009
transcription regulator activity	0.597390739522692	bayes_pls_golite062009
transcription coactivator activity	0.58571720340663	bayes_pls_golite062009
transcription factor binding	0.55477888309075	bayes_pls_golite062009
protein binding	0.476649214025345	bayes_pls_golite062009
inositol or phosphatidylinositol phosphatase activity	0.228910502815798	bayes_pls_golite062009
phosphoric ester hydrolase activity	0.100365481550461	bayes_pls_golite062009
phosphatase activity	0.00559251346312178	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: