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190

ID: 1500057776 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 190 (183)
Sequences: 443 (306.9)
Seq/Len: 2.421
Nf(neff/√len): 22.7

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: 2.421).

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 > 50% 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
66_R69_L1.9390.99
28_E32_Y1.8380.99
124_F127_N1.8070.98
145_V149_L1.7540.98
140_A144_L1.7500.98
187_E190_D1.6500.97
139_S144_L1.6340.96
98_Q101_M1.6190.96
59_P62_S1.6170.96
20_Q26_D1.6090.96
22_Y46_S1.5750.95
100_E105_L1.5460.95
127_N130_I1.5310.94
19_V22_Y1.5210.94
58_T62_S1.5060.94
49_I52_K1.4910.93
96_A101_M1.4770.93
30_N33_Q1.4260.91
31_F36_Q1.4170.91
162_P165_A1.4040.90
50_W53_F1.3960.90
103_T106_L1.3760.89
97_D101_M1.3710.89
146_S149_L1.3650.89
59_P63_P1.3210.86
30_N36_Q1.3200.86
45_P52_K1.3180.86
30_N35_Q1.3170.86
61_L64_S1.3020.85
23_F55_L1.3000.85
115_F118_D1.2960.85
29_E32_Y1.2930.85
98_Q102_V1.2750.83
52_K55_L1.2690.83
48_D53_F1.2630.83
145_V148_K1.2530.82
169_S175_S1.2460.81
138_F144_L1.2420.81
114_S117_C1.2400.81
159_S162_P1.2400.81
58_T65_R1.2370.81
98_Q103_T1.2290.80
29_E34_Q1.2260.80
106_L130_I1.2230.80
181_L185_A1.2110.79
21_P56_L1.2060.78
24_Y137_G1.1950.78
50_W55_L1.1890.77
143_K149_L1.1750.76
48_D55_L1.1690.75
31_F35_Q1.1690.75
22_Y44_A1.1630.75
30_N34_Q1.1610.75
107_G115_F1.1600.75
113_Q117_C1.1600.75
32_Y36_Q1.1580.74
101_M104_E1.1510.74
31_F34_Q1.1460.73
12_Y16_Y1.1450.73
31_F38_S1.1440.73
59_P65_R1.1430.73
45_P48_D1.1430.73
19_V25_C1.1360.72
99_L106_L1.1330.72
180_D183_A1.1230.71
145_V150_A1.1080.70
97_D100_E1.1080.70
46_S49_I1.1020.69
146_S150_A1.0980.69
94_S98_Q1.0980.69
47_E52_K1.0950.68
18_S24_Y1.0880.68
171_C174_S1.0700.66
76_A79_P1.0670.65
148_K152_Y1.0630.65
33_Q38_S1.0580.65
109_D114_S1.0580.65
165_A173_T1.0530.64
47_E51_K1.0530.64
119_P122_E1.0520.64
61_L66_R1.0500.64
24_Y54_E1.0480.63
153_Q156_R1.0460.63
174_S179_Q1.0370.62
35_Q46_S1.0370.62
161_S169_S1.0370.62
48_D52_K1.0370.62
102_V105_L1.0370.62
161_S167_G1.0260.61
33_Q36_Q1.0250.61
186_S190_D1.0250.61
60_P63_P1.0230.61
164_P168_H1.0220.61
98_Q105_L1.0210.60
110_M113_Q1.0170.60
76_A81_S1.0140.60
161_S164_P1.0140.60
103_T108_G1.0090.59
95_T98_Q1.0080.59
152_Y156_R1.0020.58
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  
2yuhA10.378920.971Contact Map
2xl1A10.07891.70.972Contact Map
1h5oA10.22111.40.973Contact Map
4qhwA10.31581.20.974Contact Map
1n0uA10.31581.10.975Contact Map
3suiB10.07891.10.975Contact Map
4w22410.315810.976Contact Map
4bjoA20.13160.90.976Contact Map
1x9uA20.22630.70.977Contact Map
2eqpA10.16320.70.978Contact 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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