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PIMA

ID: 1517946348 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 390 (366)
Sequences: 39665 (31114.5)
Seq/Len: 108.374
Nf(neff/√len): 1626.4

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: 108.374).

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
196_L267_A4.2191.00
96_H364_Y3.5121.00
226_E250_R3.2901.00
235_E239_R2.9801.00
6_R38_E2.9571.00
147_G168_V2.9411.00
270_Y287_A2.8091.00
213_A241_Q2.7331.00
40_S92_F2.5731.00
194_T228_L2.5061.00
347_R350_R2.4221.00
217_K324_A2.4071.00
192_G226_E2.3901.00
228_L252_L2.3531.00
215_L227_I2.3111.00
298_D303_R2.2141.00
306_L312_G2.2121.00
156_R160_M2.1281.00
96_H120_T2.1061.00
197_F208_M2.0971.00
193_R331_L2.0651.00
230_V263_A2.0501.00
217_K321_D2.0271.00
298_D316_P2.0191.00
219_V248_H1.9761.00
195_V269_V1.9601.00
8_G92_F1.9481.00
8_G42_L1.9311.00
5_M37_H1.9101.00
194_T226_E1.8961.00
355_V359_Q1.8821.00
193_R268_D1.8751.00
221_R328_I1.8451.00
37_H361_M1.8351.00
333_D336_L1.8191.00
153_D156_R1.8191.00
194_T266_S1.8081.00
316_P322_G1.8061.00
40_S90_G1.8021.00
228_L250_R1.7911.00
270_Y292_T1.7831.00
207_G210_V1.7771.00
173_G353_W1.7761.00
211_L227_I1.7701.00
213_A320_A1.7681.00
147_G363_V1.7581.00
329_G336_L1.7521.00
153_D304_R1.7511.00
307_A310_D1.7311.00
35_A358_A1.7221.00
211_L271_C1.7201.00
195_V327_L1.7021.00
329_G333_D1.6981.00
232_R235_E1.6981.00
326_A329_G1.6981.00
311_A347_R1.6941.00
296_A314_L1.6911.00
346_E349_H1.6791.00
119_A145_I1.6711.00
337_R341_V1.6621.00
291_G345_S1.6591.00
242_A251_F1.6561.00
313_R326_A1.6501.00
194_T268_D1.6181.00
322_G326_A1.6081.00
218_L328_I1.5861.00
156_R169_E1.5731.00
198_L260_K1.5701.00
168_V366_T1.5621.00
200_R203_E1.5581.00
153_D157_R1.5511.00
195_V271_C1.5351.00
150_A167_A1.5221.00
319_D322_G1.5131.00
207_G275_L1.4921.00
156_R167_A1.4921.00
336_L339_G1.4881.00
31_V34_D1.4721.00
256_D259_T1.4701.00
26_L30_E1.4481.00
307_A311_A1.4451.00
274_H278_E1.4431.00
9_M98_H1.4401.00
307_A347_R1.4341.00
35_A361_M1.4281.00
230_V252_L1.4221.00
7_I37_H1.4191.00
267_A292_T1.4111.00
320_A324_A1.3990.99
242_A245_L1.3900.99
328_I332_E1.3890.99
361_M365_E1.3830.99
153_D169_E1.3810.99
6_R40_S1.3690.99
243_G246_A1.3680.99
31_V357_S1.3620.99
259_T262_S1.3610.99
215_L225_V1.3560.99
149_I363_V1.3540.99
196_L230_V1.3530.99
201_Y229_I1.3470.99
209_A275_L1.3440.99
179_F290_A1.3400.99
31_V354_S1.3330.99
310_D343_R1.3280.99
313_R329_G1.3240.99
260_K264_M1.3200.99
339_G343_R1.3180.99
230_V255_V1.3170.99
214_A323_M1.3170.99
255_V259_T1.3090.99
98_H122_H1.2960.99
338_A342_A1.2940.99
315_V326_A1.2720.99
296_A302_F1.2680.99
208_M229_I1.2660.99
122_H282_I1.2620.99
255_V263_A1.2510.99
343_R346_E1.2490.99
359_Q362_R1.2470.99
341_V344_A1.2460.98
9_M32_L1.2430.98
149_I360_I1.2410.98
296_A306_L1.2350.98
97_I117_I1.2300.98
297_S315_V1.2290.98
198_L230_V1.2170.98
270_Y283_V1.2090.98
355_V358_A1.1990.98
278_E281_G1.1950.98
228_L263_A1.1890.98
334_D337_R1.1850.98
9_M29_A1.1790.98
280_F285_V1.1780.98
200_R205_R1.1720.98
196_L263_A1.1660.97
151_V172_N1.1620.97
197_F211_L1.1610.97
147_G366_T1.1580.97
352_D355_V1.1540.97
264_M290_A1.1400.97
206_K278_E1.1360.97
150_A159_Q1.1320.97
205_R276_G1.1300.97
272_A283_V1.1260.97
157_R160_M1.1260.97
257_D260_K1.1220.97
33_R36_G1.1150.96
198_L264_M1.1100.96
210_V275_L1.1080.96
265_R290_A1.1040.96
284_L302_F1.1030.96
358_A362_R1.1010.96
261_A290_A1.0980.96
151_V279_S1.0970.96
209_A241_Q1.0900.96
193_R269_V1.0870.96
218_L225_V1.0830.96
316_P319_D1.0830.96
217_K320_A1.0810.95
322_G325_A1.0790.95
193_R225_V1.0690.95
194_T267_A1.0690.95
150_A156_R1.0640.95
228_L267_A1.0540.95
196_L264_M1.0510.94
19_G22_Q1.0490.94
193_R224_D1.0480.94
287_A292_T1.0450.94
281_G302_F1.0450.94
218_L327_L1.0450.94
24_H282_I1.0440.94
210_V318_D1.0430.94
27_Q30_E1.0420.94
217_K220_A1.0420.94
157_R161_E1.0380.94
170_I363_V1.0370.94
206_K283_V1.0370.94
295_V315_V1.0350.94
292_T341_V1.0340.94
232_R254_Q1.0330.94
195_V215_L1.0330.94
149_I170_I1.0320.94
288_M294_V1.0280.94
117_I145_I1.0270.94
300_D303_R1.0220.93
29_A33_R1.0170.93
209_A213_A1.0150.93
252_L255_V1.0130.93
342_A346_E1.0130.93
29_A41_V1.0100.93
168_V359_Q1.0050.93
252_L263_A1.0000.92
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  
4n9wA10.92311000.064Contact Map
2r60A10.93331000.202Contact Map
3c48A20.95131000.211Contact Map
3froA30.94361000.212Contact Map
1rzuA20.92311000.213Contact Map
2qzsA10.91541000.228Contact Map
3okpA10.91000.234Contact Map
2x0dA20.87691000.241Contact Map
2x6qA20.89741000.246Contact Map
2jjmA120.87441000.256Contact 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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