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5pp1ag

ID: 1516100227 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 314 (295)
Sequences: 498 (383.4)
Seq/Len: 1.688
Nf(neff/√len): 22.3

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: 1.688).

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
149_R205_E3.1931.00
153_T159_V3.1171.00
214_V270_I2.6831.00
273_G279_R2.6771.00
217_I300_I2.4341.00
122_Y304_L2.2901.00
257_A268_M2.2630.99
20_Q35_V2.1890.99
146_P277_N2.1680.99
29_R306_D2.1150.99
142_D260_L2.0930.99
212_V278_Y2.0200.99
216_V221_V1.9980.98
151_L162_F1.9820.98
211_D271_K1.9460.98
293_E296_A1.9340.98
266_T283_L1.8570.97
182_K206_L1.7910.96
246_I278_Y1.7640.96
18_H290_R1.7500.96
212_V244_I1.7480.96
209_G271_K1.7360.95
293_E299_D1.7140.95
140_L280_V1.6960.95
217_I304_L1.6760.94
257_A283_L1.6720.94
274_A279_R1.6650.94
257_A261_V1.6430.93
234_F291_G1.6380.93
12_G18_H1.6360.93
300_I304_L1.6140.93
145_L254_C1.6130.92
211_D279_R1.6050.92
248_D251_K1.6050.92
247_S278_Y1.5930.92
301_C304_L1.5900.92
211_D274_A1.5770.91
266_T282_E1.5740.91
226_R242_E1.5720.91
214_V254_C1.5710.91
225_L298_V1.5620.91
12_G35_V1.5580.91
25_G302_G1.5550.91
288_M292_F1.5540.91
254_C270_I1.5110.89
214_V246_I1.5020.88
215_Y292_F1.4970.88
218_D307_A1.4830.88
273_G277_N1.4740.87
258_A266_T1.4700.87
140_L287_A1.4450.86
134_P152_W1.4420.86
18_H288_M1.4360.85
22_V305_C1.4340.85
122_Y307_A1.4200.84
234_F266_T1.4180.84
12_G287_A1.4150.84
163_H169_C1.4140.84
16_D72_R1.4050.84
210_D226_R1.4010.83
133_K233_D1.3900.83
270_I278_Y1.3730.82
69_V119_T1.3600.81
271_K281_L1.3590.81
22_V26_L1.3560.80
12_G20_Q1.3390.79
20_Q289_F1.3360.79
149_R166_V1.3240.78
246_I270_I1.3100.77
222_I303_P1.3090.77
208_T274_A1.2970.76
145_L253_Q1.2960.76
249_E253_Q1.2940.76
136_Q282_E1.2820.75
293_E301_C1.2790.75
293_E298_V1.2410.72
212_V224_A1.2270.70
170_I270_I1.2080.69
62_Q65_R1.2000.68
228_V242_E1.1820.66
266_T287_A1.1810.66
70_Y287_A1.1790.66
73_S288_M1.1790.66
225_L292_F1.1790.66
130_N287_A1.1730.65
263_L285_A1.1640.64
221_V255_V1.1540.63
182_K232_I1.1510.63
209_G287_A1.1500.63
14_P39_Q1.1440.62
120_A311_Q1.1430.62
170_I265_Y1.1400.62
211_D272_A1.1370.62
246_I251_K1.1320.61
210_D272_A1.1320.61
139_L260_L1.1290.61
85_A114_W1.1240.60
246_I254_C1.1230.60
268_M283_L1.1160.60
215_Y267_G1.1120.59
21_S290_R1.1110.59
143_A283_L1.1070.59
269_D284_N1.0950.57
209_G230_D1.0950.57
208_T273_G1.0940.57
216_V219_D1.0890.57
140_L267_G1.0890.57
241_I292_F1.0740.55
215_Y287_A1.0720.55
265_Y287_A1.0700.55
211_D273_G1.0690.55
217_I222_I1.0680.55
220_Q306_D1.0630.54
152_W303_P1.0550.53
35_V234_F1.0530.53
288_M291_G1.0380.51
217_I301_C1.0380.51
215_Y265_Y1.0370.51
153_T203_F1.0360.51
10_V289_F1.0350.51
70_Y290_R1.0340.51
265_Y286_S1.0320.51
287_A292_F1.0310.51
212_V272_A1.0300.51
296_A299_D1.0280.50
293_E297_N1.0260.50
74_L211_D1.0260.50
220_Q303_P1.0230.50
35_V291_G1.0220.50
194_E251_K1.0200.49
159_V183_L1.0200.49
109_A113_R1.0160.49
34_Y304_L1.0130.49
131_I285_A1.0070.48
216_V255_V1.0060.48
216_V258_A1.0050.48
123_N127_A1.0050.48
74_L288_M1.0030.48
255_V258_A1.0020.48
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  
3vpbA40.84711000.67Contact Map
4iwxA10.88851000.684Contact Map
1gsaA10.88221000.694Contact Map
3vpdA20.84391000.706Contact Map
2p0aA20.843999.90.733Contact Map
3r5xA40.850399.90.746Contact Map
4c5cA20.843999.90.746Contact Map
2q7dA20.856799.90.747Contact Map
1pk8A80.863199.90.747Contact Map
4eg0A20.831299.90.753Contact 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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