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4ryr

ID: 1501760867 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 151 (125)
Sequences: 789 (782.3)
Seq/Len: 6.312
Nf(neff/√len): 70.0

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 6.312).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 50% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
91_F104_D3.8391.00
99_F148_Y2.6521.00
112_T137_S2.3911.00
88_F144_S2.2591.00
109_A138_A2.1451.00
62_I123_S2.1301.00
43_M47_M2.0671.00
38_W142_Y2.0241.00
102_T145_W2.0011.00
115_L130_L1.9111.00
53_F85_N1.8651.00
60_V78_F1.8171.00
108_V133_Y1.7981.00
105_C137_S1.7841.00
85_N108_V1.6491.00
85_N133_Y1.6391.00
45_I140_A1.6241.00
84_F107_L1.5920.99
115_L119_S1.5840.99
81_N111_T1.5810.99
109_A141_T1.5590.99
78_F82_Y1.4850.99
102_T144_S1.4710.99
134_F138_A1.4250.99
84_F111_T1.3660.98
81_N133_Y1.3450.98
88_F92_Q1.3430.98
84_F104_D1.3250.98
114_L118_F1.3060.97
49_W52_L1.2970.97
52_L140_A1.2960.97
77_L114_L1.2860.97
44_T48_I1.2650.96
52_L139_F1.2430.96
47_M51_V1.2140.95
62_I65_N1.1990.95
45_I49_W1.1950.95
87_A90_Y1.1880.94
81_N85_N1.1740.94
109_A137_S1.1710.94
77_L111_T1.1580.93
58_L61_A1.1510.93
45_I88_F1.0800.90
29_W39_T1.0790.90
54_G58_L1.0770.90
101_A104_D1.0700.89
40_P139_F1.0600.89
29_W98_L1.0520.88
116_I127_A1.0480.88
42_G140_A1.0410.88
49_W136_W1.0340.87
46_G140_A1.0280.87
34_E150_I1.0250.86
29_W33_L1.0230.86
38_W68_G1.0050.85
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4ryoA101000.076Contact Map
4uc1A30.98011000.114Contact Map
2mgyA111000.148Contact Map
4i0uA100.377550.929Contact Map
4ev6A50.39074.90.93Contact Map
4qncA20.5432.50.939Contact Map
4n7wA20.33772.30.94Contact Map
4phzK30.77481.70.944Contact Map
4qndA10.62911.60.945Contact Map
1yewC30.62911.50.946Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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