GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
PilE

ID: 1513726180 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 129 (118)
Sequences: 1843 (1237.2)
Seq/Len: 15.619
Nf(neff/√len): 113.9

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: 15.619).

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 > 75% 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
50_D91_Q3.4631.00
62_A85_D3.4201.00
67_D83_Y3.0881.00
89_T97_G2.6821.00
42_L46_K2.4571.00
119_T123_V2.2521.00
99_V112_S2.2251.00
64_Y70_D2.0151.00
94_K117_G2.0151.00
49_A53_T1.8951.00
104_T109_V1.8901.00
25_A28_G1.8461.00
73_V77_K1.8151.00
99_V111_V1.7951.00
100_I108_V1.7491.00
41_T44_Q1.7201.00
76_T80_Q1.6431.00
55_Q59_E1.5231.00
91_Q98_F1.5131.00
99_V114_G1.5011.00
61_A110_N1.4881.00
53_T98_F1.4871.00
99_V113_I1.4611.00
60_A84_L1.4081.00
37_R40_G1.3990.99
54_A110_N1.3310.99
105_T109_V1.2820.99
58_A85_D1.2760.99
43_N47_V1.2610.99
15_F30_L1.2480.99
102_V108_V1.2300.98
55_Q58_A1.2150.98
32_A36_P1.2090.98
74_T77_K1.2030.98
42_L45_A1.1980.98
58_A62_A1.1980.98
53_T57_I1.1840.98
72_N90_P1.1670.97
52_A56_T1.1490.97
50_D92_S1.1430.97
50_D54_A1.1300.97
19_E23_V1.0880.96
31_A35_V1.0790.95
16_T22_V1.0590.95
48_N51_K1.0570.95
57_I111_V1.0530.95
20_L24_I1.0500.94
61_A71_T1.0480.94
43_N46_K1.0460.94
47_V113_I1.0320.94
33_I45_A1.0080.93
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  
3g20A20.728799.70.49Contact Map
3sokA20.87699.60.515Contact Map
2hi2A10.868299.60.527Contact Map
1t92A20.666799.60.542Contact Map
3gn9A30.682299.50.552Contact Map
2kepA10.689999.50.56Contact Map
2m7gA10.472999.30.597Contact Map
1oqwA20.87699.20.615Contact Map
4noaA10.620270.30.88Contact Map
4d40A2054.70.891Contact 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.

Page generated in 0.0201 seconds.