GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
v2

ID: 1513314175 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 108 (90)
Sequences: 245 (91)
Seq/Len: 2.722
Nf(neff/√len): 9.6

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: 2.722).

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
48_I51_S2.2421.00
29_S48_I1.9220.99
41_L64_F1.8180.99
101_A107_Q1.7480.98
27_L30_Q1.6230.97
96_G103_E1.6220.97
32_Y38_G1.5250.95
27_L37_L1.4960.95
62_R97_M1.4870.94
99_K105_E1.4450.93
80_I85_C1.4450.93
89_C92_H1.4340.93
62_R65_N1.4230.93
35_D71_T1.3860.91
86_C89_C1.3690.91
36_T44_D1.3210.88
63_H69_E1.3150.88
76_L86_C1.3030.87
22_V26_Q1.2810.86
31_D35_D1.2500.84
98_D105_E1.2420.84
78_Q90_P1.2350.83
47_C51_S1.2320.83
44_D91_R1.2220.83
94_T103_E1.1990.81
33_S39_Y1.1750.79
28_L31_D1.1610.78
88_H91_R1.1560.77
29_S42_I1.1500.77
26_Q97_M1.1450.76
35_D39_Y1.1430.76
81_H98_D1.1130.74
82_Q93_K1.1110.73
68_V106_A1.1090.73
86_C92_H1.1070.73
84_C87_P1.0990.72
25_L29_S1.0990.72
60_R67_R1.0900.71
31_D71_T1.0870.71
71_T75_E1.0710.69
100_Q103_E1.0700.69
53_N75_E1.0690.69
51_S59_C1.0580.68
59_C62_R1.0490.67
36_T40_D1.0460.67
44_D88_H1.0240.64
68_V94_T1.0210.64
72_S96_G1.0080.63
21_S25_L1.0010.62
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  
3qkyA10.94446.40.961Contact Map
4oe9A20.351960.961Contact Map
4w8yA20.62044.80.963Contact Map
3x1lA104.50.964Contact Map
4mbeH40.12044.30.964Contact Map
2wnfA10.20374.10.964Contact Map
1dl0A10.25933.80.965Contact Map
2ashA40.92593.50.966Contact Map
4p0gA10.57413.40.966Contact Map
3pdeA40.50933.20.966Contact 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 0.0319 seconds.