YRC Public Data Repository - Protein Structure Prediction

Protein:	SDN2_ARATH
Organism:	Arabidopsis thaliana
Length:	466 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 SDN2_ARATH.

Description	E-value	Query Range	Subject Range
DPO3_BACSU - DNA polymerase III polC-type OS=Bacillus subtilis GN=polC PE=1 SV=2 gi\|221318783 - gi\|221318783\|ref\|ZP_03600077.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. JH64... gi\|221313860 - gi\|221313860\|ref\|ZP_03595665.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. NCIB... gi\|221323055 - gi\|221323055\|ref\|ZP_03604349.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. SMY] DPO3_BACSU - DNA polymerase III PolC-type OS=Bacillus subtilis (strain 168) GN=polC PE=1 SV=2	305.0	[0..15]	[462..296]
gi\|143342 - gi\|143342\|gb\|AAA22666.1\| polymerase III	301.0	[0..15]	[462..296]
gi\|152976184, gi... - gi\|89203212\|ref\|ZP_01181903.1\| DNA polymerase III, epsilon subunit:DNA polymerase III, alpha subunit...	300.0	[0..15]	[462..293]
gi\|228660107, gi... - gi\|229123331\|ref\|ZP_04252535.1\| DNA polymerase III polC-type [Bacillus cereus 95/8201], gi\|228660107... gi\|21401801, gi\|... - gi\|65321145\|ref\|ZP_00394104.1\| COG2176: DNA polymerase III, alpha subunit (gram-positive type) [Baci... gi\|228947537, gi... - gi\|228947537\|ref\|ZP_04109827.1\| DNA polymerase III polC-type [Bacillus thuringiensis serovar monterr... gi\|227813274, gi... - gi\|227813274\|ref\|YP_002813283.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus ant... gi\|165872624, gi... - gi\|165872624\|ref\|ZP_02217255.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|170687849, gi... - gi\|170687849\|ref\|ZP_02879063.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|170128318, gi... - gi\|170706900\|ref\|ZP_02897358.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|49180595, gi\|... - gi\|49186668\|ref\|YP_029920.1\| DNA polymerase III PolC [Bacillus anthracis str. Sterne], gi\|49180595\|g... gi\|52141670, gi\|... - gi\|52141670\|ref\|YP_085159.1\| DNA polymerase III PolC [Bacillus cereus E33L], gi\|51975139\|gb\|AAU16689... gi\|30258465, gi\|... - gi\|30263821\|ref\|NP_846198.1\| DNA polymerase III PolC [Bacillus anthracis str. Ames], gi\|30258465\|gb\|... gi\|47504393, gi\|... - gi\|47529245\|ref\|YP_020594.1\| DNA polymerase III PolC [Bacillus anthracis str. 'Ames Ancestor'], gi\|4... gi\|190568456, gi... - gi\|190568456\|ref\|ZP_03021363.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|196042171, gi... - gi\|196042171\|ref\|ZP_03109454.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus cere... gi\|218904946, gi... - gi\|218904946\|ref\|YP_002452780.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus cer... gi\|254759330 - gi\|254759330\|ref\|ZP_05211355.1\| DNA polymerase III PolC [Bacillus anthracis str. Australia 94] gi\|254756009 - gi\|254756009\|ref\|ZP_05208040.1\| DNA polymerase III PolC [Bacillus anthracis str. Vollum] gi\|254721996 - gi\|254721996\|ref\|ZP_05183785.1\| DNA polymerase III PolC [Bacillus anthracis str. A1055] gi\|254683475 - gi\|254683475\|ref\|ZP_05147335.1\| DNA polymerase III PolC [Bacillus anthracis str. CNEVA-9066] gi\|229601637, gi... - gi\|229601637\|ref\|YP_002868056.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus ant...	297.0	[0..15]	[462..293]
gi\|49478392, gi\|... - gi\|49478392\|ref\|YP_037879.1\| DNA polymerase III PolC [Bacillus thuringiensis serovar konkukian str. ...	297.0	[0..15]	[462..293]
gi\|89098599, gi\|... - gi\|89098599\|ref\|ZP_01171481.1\| DNA polymerase III subunit alpha [Bacillus sp. NRRL B-14911], gi\|8908...	296.0	[0..3]	[462..282]
DPO3_BACCR - DNA polymerase III PolC-type OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 ... gi\|229146389, gi... - gi\|229146389\|ref\|ZP_04274760.1\| DNA polymerase III polC-type [Bacillus cereus BDRD-ST24], gi\|2286370...	296.0	[0..15]	[462..295]
gi\|163863752, gi... - gi\|89208601\|ref\|ZP_01187099.1\| DNA polymerase III, epsilon subunit:DNA polymerase III, alpha subunit...	295.0	[0..15]	[462..293]
gi\|75760862, gi\|... - gi\|75760862\|ref\|ZP_00740876.1\| DNA polymerase III alpha subunit [Bacillus thuringiensis serovar isra...	295.0	[0..15]	[462..295]
gi\|47569095, gi\|... - gi\|47569095\|ref\|ZP_00239784.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus cereu...	295.0	[0..15]	[462..293]

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Predicted Domain #1

Region A:
Residues: [1-135]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEDVLATAEG VVLVKLVKVA QKLGLKGENG TWKEFLDFYD KQLGSSSLSD PSKRRKDDLV  60
   61 AFLTTLKKKE DLQLLAKSLK LDNDVFEKFK KKSLDETAEQ RLVRMTLTHD EYPLDYLFPS 120
  121 NAEDWVRTGL GKKKM

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [136-326]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPTKIEMIAI DCEMVLCEDG SEAVVRVAAV DRDLKVILDE FVKPNQPVVD YRTFITGLTA  60
   61 QDLEKATISV VDIQEKLLMF ISEDTILVGQ SLNHDLKVLK VDHARVIDTS LVFKYNYDGT 120
  121 RRPLRLKRPS LNYLCKCILG YEVQKEGVPH NCVHDAEAAM KLVLAILDNG AETSVPLSKE 180
  181 MLEAEKSKLY L

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.0
Match:	1wljA
Description:	human ISG20
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [327-466]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HRIPCNVPYE ELNGVVSRDI PHEVKPSKKQ DRHYYSAIVV FKSPEEANQA FENIAGDFGK  60
   61 DSRGLSQKQI FLEPSSSEPR LYVLVRKMVE DDLVGEVIAE ENNASSKKRK RENHSKGTRD 120
  121 RRRCKPLSRR KQRSNVKRRR

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	0.967
Match:	1fnxH
Description:	Hu antigen C (Huc)
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