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CobBSIRT2

ID: 1506350732 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 279 (242)
Sequences: 4410 (2807.3)
Seq/Len: 18.223
Nf(neff/√len): 180.5

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: 18.223).

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
54_E259_S3.2561.00
55_S107_N3.1781.00
136_E145_H2.7021.00
125_L203_A2.6951.00
152_K186_H2.5351.00
115_K118_D2.4731.00
213_I258_A2.4341.00
155_C158_S2.4311.00
108_A263_P2.3721.00
256_G261_V2.2701.00
71_R74_D2.2691.00
257_P260_Q2.2521.00
155_C177_C2.2511.00
51_I109_A2.2431.00
114_A118_D2.1761.00
174_C177_C2.1261.00
113_L126_L2.1191.00
109_A262_V2.1051.00
112_A266_V2.0931.00
42_R206_M2.0621.00
161_V186_H2.0561.00
256_G260_Q2.0351.00
220_Y224_G2.0311.00
45_V113_L2.0281.00
115_K119_A1.9831.00
241_L257_P1.9351.00
117_Q142_N1.9041.00
162_L183_L1.8321.00
45_V211_I1.8091.00
54_E257_P1.8021.00
112_A263_P1.8001.00
77_T80_G1.7421.00
149_E152_K1.7401.00
105_Q137_R1.7041.00
59_T62_A1.6791.00
230_K251_A1.6771.00
79_E191_G1.6701.00
53_A59_T1.6591.00
264_E267_E1.6571.00
220_Y223_A1.6361.00
158_S177_C1.6311.00
42_R124_F1.6201.00
133_N137_R1.6111.00
229_A234_A1.6021.00
209_I237_V1.6011.00
239_L261_V1.5931.00
44_L207_A1.5901.00
160_Q175_H1.5711.00
78_P82_D1.5651.00
117_Q140_N1.5591.00
154_R186_H1.5571.00
109_A258_A1.5541.00
125_L144_I1.5511.00
144_I199_E1.5451.00
47_T135_H1.5431.00
108_A111_L1.5271.00
201_Y228_E1.5221.00
155_C174_C1.5131.00
145_H149_E1.4811.00
90_A94_A1.4611.00
235_H252_E1.4241.00
209_I235_H1.4171.00
41_P208_D1.3910.99
99_L104_I1.3700.99
82_D156_S1.3600.99
47_T126_L1.3500.99
86_E90_A1.3340.99
47_T51_I1.3100.99
81_F156_S1.2990.99
243_P255_Y1.2980.99
242_E255_Y1.2890.99
264_E268_K1.2880.99
158_S174_C1.2830.99
42_R208_D1.2770.99
213_I239_L1.2580.99
154_R161_V1.2530.99
202_M206_M1.2440.98
235_H251_A1.2430.98
112_A115_K1.2340.98
112_A262_V1.2330.98
256_G264_E1.2240.98
160_Q176_C1.2240.98
115_K266_V1.2090.98
117_Q141_T1.2080.98
58_R69_E1.1960.98
133_N145_H1.1920.98
105_Q111_L1.1870.98
108_A112_A1.1840.98
99_L150_L1.1810.98
196_G199_E1.1700.97
213_I262_V1.1680.97
162_L175_H1.1660.97
211_I237_V1.1590.97
81_F184_R1.1530.97
62_A68_E1.1270.97
205_S228_E1.1270.97
44_L210_F1.1240.97
133_N149_E1.1230.97
254_Y261_V1.1220.97
92_Y95_R1.1200.96
47_T113_L1.1120.96
136_E143_V1.1100.96
108_A259_S1.1040.96
260_Q264_E1.0980.96
254_Y268_K1.0950.96
33_V237_V1.0920.96
238_E247_G1.0900.96
152_K161_V1.0820.96
156_S182_P1.0710.95
49_A52_S1.0700.95
42_R203_A1.0680.95
146_M222_A1.0680.95
88_V92_Y1.0670.95
111_L115_K1.0590.95
70_H87_L1.0590.95
89_Q172_D1.0530.95
74_D83_R1.0490.94
116_L266_V1.0440.94
76_A189_W1.0370.94
74_D87_L1.0370.94
57_I104_I1.0350.94
67_W76_A1.0320.94
238_E250_F1.0170.93
114_A138_A1.0160.93
133_N151_L1.0120.93
199_E202_M1.0100.93
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  
1m2kA10.87811000.214Contact Map
1yc5A10.81361000.222Contact Map
4twjA10.81721000.228Contact Map
3riyA20.8711000.228Contact Map
3u31A10.89611000.228Contact Map
1s5pA10.80651000.232Contact Map
5btrA301000.249Contact Map
4iaoA20.9571000.253Contact Map
4kxqA10.90321000.255Contact Map
2hjhA20.94271000.258Contact 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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