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V2EDE2

ID: 1514007283 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 219 (77.2)
Seq/Len: 2.517
Nf(neff/√len): 8.3

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: 2.517).

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
28_V31_A2.7311.00
46_A81_V1.7960.98
12_Y18_G1.6430.97
3_A7_L1.6360.97
74_A79_Q1.6290.97
42_N45_H1.5640.95
9_V17_L1.5400.95
21_L44_F1.5230.95
73_Q76_V1.4860.94
27_S31_A1.4850.94
72_D77_E1.4290.92
42_N71_M1.4260.92
9_V85_Q1.4190.91
55_L63_C1.3840.90
59_I62_C1.3510.89
4_V8_Q1.3330.88
43_H49_E1.3020.86
63_C66_C1.3010.86
66_C69_H1.2940.85
24_D68_R1.2720.84
15_D19_Y1.2670.84
27_S81_V1.2130.80
13_S19_Y1.1950.79
45_H48_L1.1870.78
16_T24_D1.1580.76
51_T54_E1.1520.75
40_R47_R1.1250.72
11_T15_D1.1240.72
5_K84_V1.1190.72
4_V76_V1.1060.71
57_Q67_P1.0980.70
61_C64_P1.0920.69
65_H68_R1.0830.68
78_A86_K1.0730.67
42_N81_V1.0680.67
63_C69_H1.0480.65
39_R42_N1.0310.63
36_E60_P1.0300.63
4_V39_R1.0220.62
11_T51_T1.0180.61
31_A39_R1.0160.61
33_N54_E1.0120.61
42_N76_V1.0050.60
76_V87_P1.0040.60
33_N39_R1.0020.59
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  
4wwsA50.735613.90.942Contact Map
2wnfA10.321811.30.944Contact Map
1vdhA50.735610.10.945Contact Map
1t0tV50.73567.40.949Contact Map
3nsjA116.30.95Contact Map
4rbnA404.80.953Contact Map
3ibyA40.58624.70.953Contact Map
2xocA20.19544.20.954Contact Map
1m45B10.26444.10.954Contact Map
4q9aA20.36784.10.954Contact 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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