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hCHIP

ID: 1501600643 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 303 (283)
Sequences: 313 (225.5)
Seq/Len: 1.106
Nf(neff/√len): 13.4

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: 1.106).

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
294_I300_V3.3501.00
30_K34_N2.7191.00
66_R82_D2.3580.99
33_G45_A1.9990.96
34_N37_F1.9690.96
87_L259_E1.9540.96
101_G117_L1.9150.95
45_A49_Y1.8080.93
264_V267_F1.8010.92
85_R88_E1.7920.92
89_L123_L1.7530.91
236_S256_D1.7410.91
293_F297_N1.7370.90
268_D272_R1.7270.90
165_L211_M1.7090.89
251_T286_M1.7030.89
33_G49_Y1.6810.88
40_R157_Q1.6400.87
34_N49_Y1.6390.87
227_I239_L1.6340.86
84_R104_Q1.6240.86
79_A99_F1.6150.86
29_L34_N1.5800.84
97_H116_N1.5770.84
45_A52_A1.5590.83
34_N45_A1.5530.82
33_G37_F1.5490.82
34_N65_N1.5420.82
233_G237_F1.5300.81
240_M290_I1.5120.80
140_R233_G1.5020.79
37_F45_A1.4950.79
79_A103_C1.4680.77
242_E254_R1.4290.75
135_I161_L1.4030.73
41_K44_E1.3980.72
37_F49_Y1.3970.72
257_I280_L1.3800.71
63_Y211_M1.3680.70
94_V251_T1.3640.70
104_Q116_N1.3570.69
275_L279_Q1.3490.68
243_P249_G1.3410.68
100_L230_Y1.3190.66
98_F253_D1.3140.65
65_N95_K1.3040.65
141_I145_K1.3030.64
30_K45_A1.2990.64
87_L97_H1.2850.63
80_L100_L1.2850.63
261_L274_P1.2830.63
67_A83_C1.2780.62
49_Y52_A1.2730.62
269_P272_R1.2700.61
147_W298_G1.2540.60
240_M263_R1.2450.59
30_K33_G1.2390.59
254_R268_D1.2350.58
237_F257_I1.2310.58
101_G138_A1.2300.58
215_F287_K1.2290.58
263_R271_T1.2240.57
55_R162_H1.2190.57
93_S97_H1.2130.56
230_Y292_A1.2130.56
297_N300_V1.1780.53
72_K147_W1.1770.53
151_E297_N1.1660.52
247_P250_I1.1640.52
167_R171_A1.1520.50
292_A296_E1.1500.50
69_C101_G1.1500.50
83_C275_L1.1470.50
225_R297_N1.1440.50
71_L102_Q1.1400.49
297_N302_D1.1360.49
229_D260_H1.1350.49
121_Y233_G1.1340.49
117_L139_L1.1340.49
282_P294_I1.1330.49
259_E263_R1.1320.49
247_P267_F1.1300.48
280_L283_N1.1180.47
251_T265_G1.1160.47
81_A97_H1.1150.47
205_D209_A1.1140.47
189_D195_A1.1100.46
151_E225_R1.1080.46
68_L86_A1.0980.45
294_I299_W1.0950.45
247_P279_Q1.0940.45
197_Q201_E1.0930.45
30_K150_I1.0920.45
141_I242_E1.0910.45
107_M293_F1.0800.44
172_E176_E1.0730.43
117_L251_T1.0700.43
238_E271_T1.0680.42
179_E182_R1.0670.42
148_N279_Q1.0630.42
39_G97_H1.0620.42
179_E204_H1.0620.42
113_A124_A1.0590.42
244_C269_P1.0570.41
171_A175_R1.0560.41
59_V247_P1.0560.41
117_L292_A1.0520.41
146_R150_I1.0490.41
50_G73_M1.0480.41
121_Y136_P1.0470.41
161_L215_F1.0460.40
27_Q31_E1.0430.40
202_A206_K1.0390.40
114_I139_L1.0370.40
254_R272_R1.0370.40
27_Q38_V1.0350.39
151_E302_D1.0340.39
293_F302_D1.0340.39
76_H238_E1.0320.39
268_D271_T1.0310.39
269_P283_N1.0270.39
232_C267_F1.0260.39
253_D289_V1.0260.39
162_H166_S1.0240.38
46_A239_L1.0240.38
54_T146_R1.0230.38
56_N238_E1.0210.38
89_L211_M1.0190.38
83_C122_S1.0130.37
102_Q143_K1.0090.37
260_H268_D1.0090.37
234_K250_I1.0080.37
286_M289_V1.0030.37
97_H123_L1.0020.36
51_R109_S1.0010.36
249_G271_T1.0010.36
268_D283_N1.0010.36
30_K49_Y1.0010.36
160_E236_S1.0000.36
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  
2c2lA40.92741000.531Contact Map
2f42A10.45541000.684Contact Map
3rkvA10.425799.90.798Contact Map
3m62A10.775699.80.806Contact Map
2fbnA20.455499.80.811Contact Map
4wz0A10.320199.80.819Contact Map
3q49B10.435699.80.821Contact Map
4apoA20.448899.70.825Contact Map
3upvA10.409299.70.827Contact Map
4wz3B10.339999.70.828Contact 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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