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T-TE HHblits

ID: 1507661485 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (400)
Sequences: 1404 (1115)
Seq/Len: 3.510
Nf(neff/√len): 55.8

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: 3.510).

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
12_D90_R4.6041.00
189_M220_V3.6011.00
197_Q223_A3.5581.00
37_F42_A3.5261.00
216_M358_M3.2891.00
182_D214_R3.1841.00
193_H220_V3.0921.00
36_S39_E2.9751.00
133_H184_Y2.8601.00
18_L54_L2.8291.00
132_F211_V2.7941.00
205_G230_I2.7481.00
32_G35_Q2.7431.00
131_V199_I2.7391.00
43_D46_I2.6741.00
203_L207_I2.6691.00
129_R199_I2.6631.00
139_M159_G2.6141.00
210_E214_R2.5891.00
189_M218_R2.4911.00
142_F201_Y2.4891.00
11_L33_R2.4211.00
191_T196_L2.3951.00
185_A211_V2.3281.00
128_L156_S2.3121.00
34_S83_A2.2931.00
23_A30_S2.2901.00
14_L90_R2.2681.00
189_M196_L2.2231.00
196_L220_V2.2001.00
22_W82_V2.1661.00
155_G197_Q2.1521.00
188_L211_V2.1261.00
399_G403_S2.0701.00
134_A141_I2.0001.00
163_A183_D1.9981.00
210_E213_R1.9921.00
134_A142_F1.9821.00
124_Q156_S1.9541.00
24_E53_R1.9421.00
22_W37_F1.8751.00
12_D16_S1.8490.99
134_A201_Y1.8400.99
129_R157_I1.8240.99
11_L83_A1.8080.99
36_S80_P1.7870.99
8_E33_R1.7670.99
191_T194_S1.7450.99
22_W42_A1.7440.99
38_Y42_A1.7400.99
131_V157_I1.7170.99
10_K15_E1.6920.99
8_E34_S1.6850.99
192_G196_L1.6820.99
361_I388_C1.6570.99
19_A33_R1.6530.99
133_H142_F1.6360.98
181_A214_R1.6270.98
13_E16_S1.6260.98
133_H201_Y1.6190.98
176_L179_T1.5970.98
79_Y88_F1.5740.98
130_V196_L1.5670.98
21_L54_L1.5500.98
360_D390_G1.5410.97
185_A214_R1.5370.97
128_L158_V1.5350.97
130_V158_V1.5340.97
134_A137_G1.5270.97
226_V364_L1.5200.97
126_G155_G1.5040.97
150_K418_E1.5000.97
127_L197_Q1.4930.97
38_Y47_M1.4860.97
55_R61_D1.4800.96
10_K33_R1.4750.96
345_Q349_A1.4590.96
12_D33_R1.4580.96
365_L396_T1.4550.96
15_E33_R1.4400.96
130_V194_S1.4380.96
133_H137_G1.4360.96
163_A180_V1.4340.96
191_T220_V1.4330.96
26_L37_F1.4250.95
18_L86_A1.4200.95
124_Q128_L1.4120.95
18_L50_V1.4120.95
130_V191_T1.4050.95
360_D391_E1.4030.95
203_L346_S1.4020.95
160_V188_L1.4000.95
400_N403_S1.3950.95
41_G44_S1.3930.95
31_I40_H1.3880.94
185_A189_M1.3850.94
202_S229_D1.3720.94
33_R82_V1.3670.94
133_H180_V1.3670.94
342_V346_S1.3670.94
121_G150_K1.3600.94
14_L17_I1.3470.93
19_A31_I1.3440.93
199_I226_V1.3440.93
128_L155_G1.3390.93
210_E352_Y1.3300.93
130_V188_L1.3250.92
43_D47_M1.3230.92
132_F207_I1.3170.92
141_I201_Y1.3160.92
127_L223_A1.3030.92
388_C391_E1.2990.91
14_L58_L1.2980.91
139_M146_L1.2960.91
207_I211_V1.2900.91
361_I392_L1.2880.91
23_A29_V1.2870.91
19_A82_V1.2810.91
15_E86_A1.2670.90
185_A188_L1.2660.90
75_Q88_F1.2600.90
72_L75_Q1.2590.90
224_D417_L1.2590.90
164_D342_V1.2580.90
26_L42_A1.2430.89
191_T195_E1.2380.89
18_L21_L1.2360.89
132_F160_V1.2220.88
228_I404_C1.2190.88
17_I57_K1.2150.87
198_L215_L1.2010.87
9_E32_G1.1980.86
178_E352_Y1.1890.86
132_F184_Y1.1800.85
51_A76_M1.1720.85
227_L361_I1.1690.84
200_G204_G1.1650.84
189_M194_S1.1620.84
23_A28_L1.1590.84
148_H414_A1.1500.83
398_E412_R1.1420.83
205_G384_W1.1300.82
217_E355_L1.1220.81
360_D393_G1.1100.80
130_V195_E1.1010.79
42_A47_M1.1010.79
134_A184_Y1.0920.78
25_A50_V1.0880.78
26_L41_G1.0850.78
395_I416_L1.0830.78
213_R357_Y1.0820.78
202_S401_H1.0790.77
209_V352_Y1.0770.77
17_I58_L1.0740.77
79_Y84_D1.0710.77
22_W36_S1.0710.77
10_K32_G1.0660.76
177_I181_A1.0650.76
192_G195_E1.0630.76
28_L31_I1.0610.76
8_E22_W1.0600.76
25_A46_I1.0590.75
49_Q53_R1.0580.75
47_M77_L1.0540.75
19_A23_A1.0530.75
216_M357_Y1.0450.74
117_L160_V1.0440.74
74_R140_D1.0420.74
226_V362_R1.0360.73
150_K155_G1.0330.73
203_L350_A1.0310.73
338_G342_V1.0300.73
11_L15_E1.0260.72
383_F399_G1.0250.72
137_G204_G1.0240.72
214_R218_R1.0230.72
116_V187_C1.0180.71
125_E154_I1.0090.70
132_F198_L1.0080.70
362_R420_P1.0070.70
36_S42_A1.0060.70
8_E11_L1.0060.70
145_L417_L1.0040.70
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  
2vz8A20.00711000.413Contact Map
3tejA20.751000.501Contact Map
2vsqA10.6911000.526Contact Map
2px6A20.601499.90.703Contact Map
2cb9A10.492999.90.715Contact Map
1jmkC20.535499.90.717Contact Map
1kezA30.622699.90.747Contact Map
4r0mB20.19199.90.748Contact Map
3ilsA10.577899.80.757Contact Map
2k2qB10.551999.80.76Contact 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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