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20170920B_a4

ID: 1505936639 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 301 (296)
Sequences: 3882 (2932.3)
Seq/Len: 13.115
Nf(neff/√len): 170.4

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: 13.115).

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
133_C147_C3.8491.00
49_D52_N3.4701.00
15_K77_Y3.2981.00
66_H120_R2.5381.00
90_I113_A2.3991.00
146_N210_V2.2871.00
12_L16_L2.2551.00
98_Y152_G2.2541.00
95_I163_L2.1641.00
252_S255_L2.0491.00
67_D70_L2.0311.00
131_S149_M1.9041.00
146_N208_A1.8801.00
66_H118_D1.8761.00
144_Q210_V1.8571.00
140_F143_D1.8541.00
74_P117_H1.8361.00
191_N204_D1.7921.00
153_S156_Y1.7281.00
141_P145_Q1.7181.00
162_D203_P1.7161.00
158_K203_P1.7061.00
64_E120_R1.6981.00
162_D190_Y1.6911.00
157_D160_K1.6791.00
35_L164_V1.6771.00
182_V212_R1.6711.00
143_D147_C1.6621.00
248_T252_S1.6171.00
8_A78_E1.5701.00
252_S256_S1.5591.00
116_F120_R1.5451.00
236_V250_C1.5431.00
17_F85_I1.5311.00
63_Q95_I1.5301.00
115_L121_V1.5271.00
8_A11_R1.5251.00
17_F20_Y1.5141.00
195_Y198_C1.5051.00
20_Y26_P1.4931.00
73_D76_D1.4901.00
144_Q212_R1.4781.00
184_V212_R1.4721.00
215_P219_T1.4511.00
182_V214_L1.4431.00
175_F181_W1.4431.00
254_L257_L1.4391.00
276_P279_G1.4181.00
178_S181_W1.4161.00
16_L20_Y1.4060.99
148_T208_A1.3970.99
65_W93_P1.3830.99
172_Q175_F1.3760.99
11_R15_K1.3640.99
143_D213_R1.3550.99
115_L119_G1.3490.99
277_L281_Y1.3380.99
48_V55_M1.3310.99
40_L59_V1.3310.99
67_D90_I1.3220.99
245_E248_T1.3180.99
290_T295_I1.2980.99
65_W91_W1.2960.99
48_V135_I1.2920.99
85_I115_L1.2890.99
281_Y286_M1.2800.99
91_W94_D1.2790.99
194_K201_I1.2670.99
35_L162_D1.2450.98
72_W77_Y1.2450.98
175_F178_S1.2380.98
251_I255_L1.2260.98
75_A81_T1.2240.98
218_Y222_L1.2230.98
135_I140_F1.2190.98
65_W70_L1.2110.98
191_N206_T1.2090.98
67_D91_W1.2080.98
57_T131_S1.2070.98
140_F145_Q1.2060.98
133_C143_D1.1830.98
49_D53_Q1.1830.98
21_N26_P1.1570.97
267_I270_S1.1500.97
29_N32_D1.1430.97
142_F145_Q1.1420.97
94_D153_S1.1370.97
213_R218_Y1.1330.97
234_V238_Y1.1230.97
70_L90_I1.1170.96
237_F244_G1.1130.96
135_I145_Q1.1110.96
56_T130_K1.1100.96
13_L21_N1.1080.96
90_I121_V1.1080.96
70_L91_W1.1040.96
21_N24_S1.0970.96
67_D93_P1.0880.96
269_P272_S1.0760.95
65_W72_W1.0740.95
158_K201_I1.0730.95
153_S161_I1.0720.95
282_L288_F1.0670.95
253_V257_L1.0670.95
47_D52_N1.0630.95
10_E14_K1.0600.95
67_D121_V1.0540.95
195_Y204_D1.0480.94
39_G62_K1.0480.94
66_H71_R1.0460.94
113_A121_V1.0430.94
70_L121_V1.0420.94
251_I254_L1.0410.94
32_D68_Y1.0370.94
140_F218_Y1.0360.94
230_S285_T1.0360.94
59_V127_A1.0350.94
297_V301_N1.0350.94
93_P99_N1.0330.94
103_G106_A1.0320.94
37_R164_V1.0310.94
213_R225_P1.0310.94
248_T255_L1.0290.94
59_V129_Y1.0270.94
292_S299_V1.0260.94
262_L266_E1.0260.94
141_P147_C1.0250.93
150_K206_T1.0200.93
227_L232_L1.0160.93
9_E13_L1.0120.93
67_D72_W1.0070.93
259_V263_L1.0060.93
14_K19_G1.0020.92
281_Y288_F1.0010.92
197_C200_E1.0000.92
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  
4aq5E10.98011000.033Contact Map
2bg9A20.98341000.034Contact Map
4aq5A20.98341000.037Contact Map
4aq5C10.97011000.043Contact Map
2bg9B10.97341000.045Contact Map
4aq5B10.97341000.047Contact Map
2bg9E10.98011000.053Contact Map
2bg9C10.97341000.061Contact Map
4pirA50.96681000.063Contact Map
4tnwA100.96681000.092Contact 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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