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Fused B 2

ID: 1501018469 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 216 (213)
Sequences: 222 (203.2)
Seq/Len: 1.042
Nf(neff/√len): 13.9

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: 1.042).

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
27_Y189_A2.4390.99
194_Q197_G2.3320.99
19_F28_F2.2230.98
194_Q212_P2.1470.98
180_F191_C2.1460.98
162_S201_N2.0750.97
194_Q215_V2.0390.96
145_F191_C1.9790.95
27_Y187_F1.8610.93
165_L200_L1.7580.90
153_P156_P1.7510.90
27_Y213_I1.7250.89
8_L60_V1.7150.89
142_S204_L1.7020.88
5_P8_L1.6350.85
149_R161_D1.6170.84
150_R178_L1.5320.80
145_F213_I1.5030.78
165_L169_L1.4510.74
70_P199_A1.4470.74
159_L213_I1.4330.73
18_V83_V1.3950.70
167_D191_C1.3810.69
21_D27_Y1.3650.68
202_D206_N1.3540.67
21_D187_F1.3480.66
104_L111_L1.3450.66
145_F165_L1.3220.64
7_R23_D1.3210.64
202_D207_L1.3130.63
20_L27_Y1.3060.63
191_C199_A1.3040.63
2_L52_L1.3020.63
101_A105_L1.2900.61
145_F200_L1.2870.61
145_F160_L1.2790.60
8_L28_F1.2750.60
11_V28_F1.2740.60
99_E168_F1.2680.59
110_L191_C1.2680.59
18_V77_P1.2680.59
10_Y19_F1.2680.59
106_R109_A1.2620.59
167_D180_F1.2610.59
157_V178_L1.2540.58
138_A178_L1.2520.58
144_A168_F1.2140.55
187_F213_I1.2130.54
25_D30_L1.2130.54
80_A84_D1.2070.54
182_V187_F1.2030.53
26_R182_V1.1960.53
183_I188_S1.1940.53
187_F202_D1.1810.51
188_S210_R1.1770.51
28_F38_F1.1730.51
166_L193_L1.1630.50
170_N175_D1.1580.49
156_P161_D1.1570.49
149_R200_L1.1550.49
161_D210_R1.1540.49
73_R122_L1.1480.48
174_L195_A1.1410.48
171_R194_Q1.1410.48
61_L201_N1.1380.47
38_F60_V1.1330.47
20_L189_A1.1270.46
179_V189_A1.1230.46
19_F38_F1.1220.46
194_Q210_R1.1180.46
152_V194_Q1.1080.45
11_V26_R1.1040.44
100_V106_R1.0980.44
16_A164_A1.0950.43
194_Q211_A1.0880.43
173_G176_A1.0880.43
182_V213_I1.0760.42
141_A162_S1.0750.42
161_D180_F1.0750.42
11_V213_I1.0710.41
27_Y182_V1.0650.41
183_I205_D1.0630.40
180_F189_A1.0620.40
15_D29_R1.0580.40
29_R210_R1.0550.40
21_D186_P1.0530.40
145_F189_A1.0530.40
163_V193_L1.0500.39
107_A112_R1.0420.39
99_E144_A1.0380.38
142_S165_L1.0370.38
199_A207_L1.0370.38
148_A155_R1.0370.38
199_A202_D1.0370.38
8_L24_N1.0340.38
189_A213_I1.0280.37
2_L5_P1.0260.37
150_R183_I1.0260.37
153_P183_I1.0210.37
96_T208_V1.0150.36
111_L114_G1.0130.36
153_P169_L1.0100.36
104_L148_A1.0060.35
15_D129_A1.0040.35
153_P174_L1.0020.35
154_I157_V1.0010.35
55_L59_G1.0010.35
169_L183_I1.0000.35
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  
2hlyA10.398167.80.914Contact Map
4fgqA20.569463.40.916Contact Map
4u65E20.555654.50.921Contact Map
2f4mA10.796342.80.926Contact Map
2q3zA10.907441.10.927Contact Map
1g0dA10.800939.30.927Contact Map
3isrA40.83834.50.93Contact Map
4ktyA20.814829.20.932Contact Map
1l9mA20.814823.30.935Contact Map
3g2bA10.379622.80.936Contact 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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