GREMLIN Database
Protein RarDLast updated: 1453711237
Organism: ECOLI    
Function: known
Type: MEM
Uniprot: P27844
Ecogene: EG11466
Pfam: PF00892 EamA (2 hits)
Co-evolution data: 1419809959



Notes:
  • Structural similarity to EmrE (see below, we model this structure as a control)
  • One of the reviewers pointed out the regions 32-69 and 173-208 appear to be in a "knot". If you restrict the helices from flipping within the membrane they do indeed appear tangled up. To test if this is a modeling error, we deleted these regions and rebuilt in them in 33,664 independent trajactory. The top 10 models converge on the same placement of the helices.
 Contact map:
EMRE - Multidrug transporter EmrE
Uniprot: P23895
Ecogene: EG10629
Pfam: PF00893 Multi_Drug_Res
Co-evolution data: 
  • paralogs of EMRE include: MDTI/MDTJ (hetero-dimer) SUGE (homo-dimer), we'd expect the homo-dimer contacts to be averaged out if MDTI/MDTJ sequences are included in the alignment. To test for this we include different number of iterations for alignment generation.
    iter 1: 1424800711
    iter 2: 1424727933
    iter 4: 1424718769
    iter 8: 1422922927
    We have to go to 1 iteration before the homo-dimer signal is above average!

The difference from native maybe in part due to the fact that we model in symmetry (while the native structure is asymmetric).
Models
Name DB Rc Date Action
Model P27844_ECOLI 0.911 19Jan2015 View - Download
Model P27844_ECOLI 0.909 19Jan2015 View - Download
Model P27844_ECOLI 0.897 19Jan2015 View - Download
Model P27844_ECOLI 0.874 19Jan2015 View - Download
Model P27844_ECOLI 0.872 19Jan2015 View - Download
Files
File
RARD_models.png
RARD_19Jan2015.zip
RARD_contacts-fs8.png
EMRE_models.png
EMRE_26Feb2015.zip
EMRE_iter1_contacts-fs8.png
EMRE_3B5D_fullatom.pdb
RARD_rebuild_knot_top10.zip
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