P01112 EVcouplings Configuration PLM

Protein := P01112
In Membrane? := no
Coupling Scoring := PLM
Compute Structures? := no
Known Structure := 121p
Your Job Name := eas_PLM
Your Email := julia.gerke@t-online.de
Domain/Family Name := 
(Generate Alignment) Tool For Generating Alignment := hhblits
(Generate Alignment) Start offset in Sequence := 1
(Generate Alignment) End offset in Sequence := 
(Generate Alignment) E-Value := -3
(Generate Alignment) Match Column Gap Pct Limit := 50
(Upload Alignment) Alignment File := 
(Lookup Alignment) PFAM Accession := PF00071
PFAM Member Selector := RASH_HUMAN
Alignment Member Gap Pct Limit := 70
Contact Map EC Counts := 
Residue Contact Proximity Threshold := 5
Residue Contact Proximity Measure := nearest_atom
False Positive Plot EC Count := 300
(Secondary Structure) Flanking Upstream Residues := 7
(Secondary Structure) Flanking Downstream Residues := 7
Membrane Helix Topology Override := 
Psipred Helix Override := 
Psipred Strand Override := 
High Conservation Filter Threshold := 100
High Conservation Filter Excludes Gaps? := no
Constraint Minimum Residue Offset Distance := 5
Allowable Mismatch Offset List := 
Gap Count Limit := 3
Identical Dist := 0
Correct Ambiguous Dist := 1
Ambiguous Ambiguous Dist := 2
Other Ambiguous Dist := 4
Mismatch Dist := 34
Unaligned Residue Dist := 10
Internal Gap Open Dist := 3
Peripheral Gap Open Dist := 1
Maximum Distance Cutoff Sequence Length Denominator := 16
Maximum Distance Cutoff Absolute Minimum := 4
Substantial Coverage After Gap := 4
Suggestion Gap Count := 2
MSA Member Weighting Distance Threshold := 0.1
EC Pseudocount Adjustment := 0.5
EC Method To Resolve Ambiguous Residues := suppress_member
Maximum Domain Width := 500
Minimum Domain Width := 30
Minimum Alignment Member Count := 300
Minimum Alignment Match Col Pct := 30
PLM Field Coefficient := 0.01
PLM Coupling Coefficient := 0.01