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Cph2

ID: 1502462218 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (383)
Sequences: 2287 (1535.9)
Seq/Len: 5.971
Nf(neff/√len): 78.5

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: 5.971).

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
36_R61_A4.5731.00
32_V46_I4.5141.00
368_H388_A3.4851.00
236_D361_K3.2391.00
50_A54_S3.0911.00
31_I182_V3.0751.00
134_L139_V2.7661.00
23_T26_E2.7541.00
239_V359_L2.7301.00
132_Q379_N2.6741.00
96_A126_V2.5991.00
330_P333_L2.5931.00
86_E89_G2.5751.00
88_L144_T2.4791.00
255_Q265_W2.4271.00
341_F357_I2.4051.00
145_V179_S2.3441.00
34_E37_I2.2651.00
134_L158_A2.2011.00
118_H121_G2.1961.00
28_L58_L2.1961.00
89_G148_M2.0751.00
400_N403_E2.0691.00
25_R29_Q2.0201.00
230_G235_A1.9741.00
24_L186_I1.9551.00
182_V186_I1.8931.00
342_L407_A1.8591.00
261_D264_N1.8401.00
98_D140_L1.8121.00
131_I135_L1.7841.00
90_N120_N1.7701.00
100_A135_L1.7661.00
100_A140_L1.7601.00
101_H125_T1.7271.00
255_Q259_R1.7011.00
319_E322_Q1.6651.00
29_Q33_E1.6551.00
73_L367_K1.6301.00
48_K56_E1.5980.99
56_E74_H1.5920.99
132_Q384_L1.5730.99
382_P386_F1.5300.99
88_L146_P1.5080.99
238_A256_W1.5010.99
82_P86_E1.4970.99
382_P385_S1.4940.99
368_H390_E1.4940.99
217_D220_E1.4760.99
45_K137_M1.4620.99
237_G359_L1.4490.99
316_T404_R1.4460.99
45_K158_A1.4380.99
86_E90_N1.4360.99
383_R386_F1.4310.99
237_G259_R1.4090.98
53_G152_Q1.4080.98
47_Y55_G1.3990.98
63_N66_A1.3930.98
29_Q59_A1.3810.98
67_L162_S1.3800.98
198_Q405_K1.3580.98
234_E403_E1.3550.98
239_V357_I1.3510.98
106_S118_H1.3480.98
260_F359_L1.3480.98
372_K375_I1.3420.97
35_A145_V1.3400.97
371_G386_F1.3370.97
157_M179_S1.3270.97
83_Q127_D1.3270.97
339_Q361_K1.3240.97
386_F391_E1.3230.97
240_L356_L1.3180.97
50_A53_G1.3180.97
99_V134_L1.3130.97
237_G260_F1.3130.97
129_C375_I1.2870.97
79_D133_Y1.2860.97
379_N384_L1.2830.96
411_S415_Y1.2780.96
185_A188_Q1.2780.96
33_E61_A1.2720.96
149_Q190_Q1.2710.96
363_K397_P1.2700.96
168_T171_E1.2590.96
401_R405_K1.2510.96
265_W359_L1.2470.96
88_L126_V1.2400.95
228_T231_Q1.2400.95
89_G92_R1.2380.95
139_V160_H1.2300.95
92_R183_S1.2270.95
50_A56_E1.2170.95
139_V158_A1.1990.94
234_E397_P1.1970.94
273_E276_R1.1930.94
80_I84_A1.1860.94
235_A403_E1.1850.94
386_F389_W1.1680.93
99_V135_L1.1650.93
372_K376_D1.1650.93
81_P133_Y1.1650.93
212_V221_T1.1630.93
339_Q396_V1.1570.93
47_Y130_H1.1490.92
62_V66_A1.1420.92
88_L156_I1.1400.92
79_D130_H1.1340.92
238_A356_L1.1340.92
70_L158_A1.1340.92
364_S390_E1.1300.92
89_G152_Q1.1260.91
49_F153_L1.1210.91
99_V131_I1.1170.91
35_A157_M1.1130.91
140_L164_P1.1080.91
17_K34_E1.1050.90
130_H133_Y1.0970.90
136_A383_R1.0950.90
206_Q409_V1.0950.90
32_V44_V1.0920.90
83_Q88_L1.0910.90
136_A385_S1.0900.90
88_L129_C1.0900.90
366_V390_E1.0860.89
55_G385_S1.0830.89
237_G257_N1.0820.89
96_A137_M1.0810.89
70_L137_M1.0800.89
47_Y79_D1.0770.89
344_V411_S1.0730.89
142_S160_H1.0720.88
321_E395_L1.0710.88
108_E111_G1.0710.88
48_K190_Q1.0660.88
130_H134_L1.0630.88
130_H142_S1.0630.88
200_V203_A1.0600.88
318_G398_T1.0590.88
150_D394_K1.0570.88
28_L46_I1.0570.88
49_F88_L1.0490.87
230_G256_W1.0470.87
378_R384_L1.0450.87
169_E173_E1.0450.87
315_Y323_R1.0440.87
114_S393_Q1.0420.87
119_S377_R1.0400.86
411_S416_M1.0380.86
209_E212_V1.0360.86
145_V175_M1.0350.86
85_R153_L1.0270.85
381_L387_E1.0270.85
107_H113_I1.0260.85
88_L143_L1.0210.85
115_P119_S1.0210.85
83_Q146_P1.0150.85
320_L330_P1.0140.84
215_Y224_Y1.0120.84
101_H126_V1.0120.84
54_S74_H1.0110.84
144_T158_A1.0090.84
338_F361_K1.0080.84
133_Y136_A1.0080.84
239_V255_Q1.0070.84
141_S161_H1.0060.84
55_G60_E1.0060.84
32_V59_A1.0050.84
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  
4ourA10.75941000.226Contact Map
4q0jA10.85381000.245Contact Map
4bwiA20.90331000.262Contact Map
3nhqA80.84911000.276Contact Map
3zq5A10.87741000.287Contact Map
4r70A201000.339Contact Map
4s21A201000.339Contact Map
4gw9A40.88211000.344Contact Map
4cqhA10.42451000.549Contact Map
2oolA20.45051000.569Contact 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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