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laobp

ID: 1501766726 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 238 (232)
Sequences: 23810 (15893.4)
Seq/Len: 102.629
Nf(neff/√len): 1043.5

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: 102.629).

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
115_G155_L4.4211.00
9_G64_I3.8371.00
5_T46_T3.3181.00
40_R216_E2.9251.00
140_Y149_D2.6641.00
73_I78_Q2.6481.00
36_E222_T2.4061.00
7_R46_T2.3351.00
58_S64_I2.2551.00
38_C45_C2.2381.00
85_D215_T2.2361.00
146_I158_A2.2151.00
60_K80_E2.2111.00
32_D229_K2.1311.00
36_E39_K2.1261.00
58_S63_K2.1141.00
207_K211_D2.0421.00
160_Q165_A2.0391.00
142_N145_L2.0371.00
40_R213_A2.0221.00
82_A207_K2.0161.00
21_D27_I2.0031.00
7_R48_V1.9961.00
222_T225_K1.9721.00
224_D228_K1.9661.00
81_I198_G1.9601.00
5_T44_K1.9441.00
85_D211_D1.9201.00
84_S211_D1.9171.00
199_L207_K1.8821.00
149_D154_R1.8751.00
97_A153_G1.8231.00
95_I165_A1.8221.00
75_D78_Q1.7921.00
73_I196_G1.7911.00
215_T219_Q1.7771.00
199_L210_F1.7591.00
123_E127_N1.7571.00
36_E217_L1.7081.00
32_D230_Y1.6851.00
105_T108_S1.6721.00
8_I34_G1.6591.00
123_E139_A1.6531.00
37_M213_A1.6371.00
36_E40_R1.6351.00
50_S58_S1.6181.00
113_H138_V1.6101.00
41_M213_A1.5991.00
93_R162_E1.5931.00
114_V157_A1.5861.00
19_S27_I1.5771.00
213_A217_L1.5631.00
113_H156_D1.5551.00
31_I35_N1.5371.00
8_I66_A1.5361.00
40_R220_D1.5311.00
57_P61_A1.5231.00
112_K156_D1.5211.00
96_A157_A1.5191.00
213_A216_E1.5121.00
200_R203_D1.4861.00
94_L157_A1.4821.00
118_Q141_A1.4771.00
82_A204_T1.4721.00
140_Y146_I1.4661.00
115_G146_I1.4631.00
208_A212_K1.4531.00
148_S152_A1.4521.00
113_H136_D1.4471.00
68_I197_V1.4371.00
149_D155_L1.4321.00
209_A212_K1.4201.00
204_T208_A1.4010.99
55_L67_I1.3880.99
148_S151_T1.3830.99
97_A100_S1.3760.99
150_L158_A1.3760.99
91_D162_E1.3630.99
35_N47_W1.3570.99
89_A194_G1.3560.99
57_P60_K1.3460.99
222_T226_M1.3110.99
209_A213_A1.2740.99
30_D87_L1.2640.99
71_L198_G1.2570.99
21_D25_E1.2420.98
40_R222_T1.2410.98
218_R223_Y1.2300.98
20_K49_A1.2220.98
51_D54_A1.2120.98
83_F198_G1.2100.98
66_A199_L1.2030.98
216_E220_D1.2020.98
162_E166_S1.2000.98
115_G140_Y1.1730.98
212_K216_E1.1720.98
104_P108_S1.1610.97
74_T77_R1.1590.97
118_Q139_A1.1430.97
150_L178_Y1.1310.97
96_A181_A1.1170.96
82_A202_D1.1150.96
146_I149_D1.1090.96
151_T177_E1.1070.96
141_A145_L1.1020.96
116_V123_E1.1000.96
4_Q43_V1.1000.96
34_G68_I1.0970.96
211_D215_T1.0930.96
92_S122_Q1.0880.96
54_A58_S1.0840.96
27_I32_D1.0830.96
29_F227_A1.0780.95
98_K179_A1.0760.95
33_L223_Y1.0520.95
56_I81_I1.0480.94
29_F226_M1.0420.94
145_L148_S1.0410.94
138_V149_D1.0380.94
125_Y129_N1.0320.94
82_A201_K1.0300.94
217_L222_T1.0240.93
98_K177_E1.0230.93
9_G55_L1.0210.93
59_L81_I1.0120.93
35_N39_K1.0120.93
99_G179_A1.0090.93
67_I71_L1.0030.93
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  
1lstA10.99581000.032Contact Map
4powA20.96641000.048Contact Map
3tqlA10.94121000.056Contact Map
3i6vA10.9161000.057Contact Map
3k4uA60.96641000.061Contact Map
4ohnA10.97481000.066Contact Map
4kqpA10.95381000.068Contact Map
3kzgA40.93281000.07Contact Map
4g4pA10.94121000.072Contact Map
3hv1A20.97481000.074Contact 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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