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v1 25-240 5-210 15-206 -force run

ID: 1513228984 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 192 (191)
Sequences: 162 (54.9)
Seq/Len: 0.848
Nf(neff/√len): 4.0

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: 0.848).

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
88_G96_Q1.7860.88
127_T136_K1.6540.82
79_F122_R1.6480.81
95_G100_M1.6120.79
92_M121_M1.6070.79
155_H170_L1.5780.77
122_R127_T1.5720.77
121_M127_T1.4840.71
149_S152_T1.4330.67
87_Y96_Q1.3910.64
179_S182_V1.3740.62
105_P108_A1.3480.60
129_I134_G1.3480.60
129_I133_S1.3220.58
71_N74_N1.3110.57
87_Y113_D1.3090.57
151_V154_N1.3080.57
174_A177_H1.2970.56
185_T191_Y1.2940.56
121_M146_R1.2780.54
182_V185_T1.2690.53
60_K73_T1.2650.53
153_Y156_Q1.2650.53
19_E33_V1.2610.53
185_T192_F1.2600.53
174_A178_A1.2590.52
161_Y167_N1.2510.52
79_F101_F1.2460.51
172_Y177_H1.2330.50
129_I132_P1.2270.50
176_T184_A1.2250.49
180_N183_Y1.2230.49
57_F114_L1.2200.49
82_R85_R1.2180.49
22_D31_R1.2170.49
65_E68_K1.2120.48
129_I135_M1.2100.48
178_A184_A1.1980.47
79_F90_S1.1870.46
93_D96_Q1.1860.46
42_I114_L1.1830.46
13_C16_Q1.1810.46
128_V137_E1.1750.45
44_H48_K1.1690.44
9_C16_Q1.1600.44
169_L184_A1.1600.44
122_R146_R1.1580.43
87_Y90_S1.1520.43
184_A187_K1.1430.42
4_D10_E1.1390.42
122_R136_K1.1380.42
16_Q26_H1.1360.42
96_Q113_D1.1270.41
185_T189_R1.1240.41
22_D29_I1.1240.41
128_V138_Q1.1150.40
123_K127_T1.1150.40
174_A184_A1.1130.40
43_T48_K1.1040.39
20_Q31_R1.1040.39
151_V156_Q1.0980.38
154_N157_E1.0970.38
16_Q23_D1.0900.38
116_D119_Q1.0900.38
187_K191_Y1.0900.38
182_V192_F1.0830.37
175_C184_A1.0800.37
2_S5_V1.0750.36
1_R16_Q1.0730.36
9_C12_P1.0710.36
113_D155_H1.0640.36
108_A116_D1.0610.35
79_F114_L1.0600.35
100_M103_N1.0580.35
5_V30_V1.0560.35
93_D97_V1.0480.34
92_M96_Q1.0470.34
127_T146_R1.0460.34
182_V191_Y1.0430.34
153_Y157_E1.0410.34
6_P11_G1.0380.33
61_V73_T1.0370.33
84_R91_P1.0360.33
44_H49_R1.0320.33
1_R10_E1.0310.33
6_P9_C1.0300.33
9_C13_C1.0280.33
175_C178_A1.0230.32
111_K119_Q1.0190.32
1_R23_D1.0180.32
24_I29_I1.0140.32
13_C26_H1.0130.31
10_E17_S1.0120.31
22_D25_K1.0110.31
158_A165_T1.0100.31
80_L95_G1.0090.31
94_F98_F1.0090.31
112_N118_F1.0060.31
119_Q136_K1.0050.31
170_L177_H1.0010.31
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  
1jsdA10.281210.80.978Contact Map
3k7lA10.29697.20.979Contact Map
1e3pA10.27083.70.982Contact Map
2eroA20.31773.40.982Contact Map
2knpA10.16673.20.983Contact Map
1wqeA10.06773.10.983Contact Map
2h8eA10.31772.90.983Contact Map
2i15A30.2242.60.983Contact Map
1ansA10.07292.50.984Contact Map
2plxB10.13542.30.984Contact 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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