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ID: 1500207321 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 371 (371)
Sequences: 3179 (3152.8)
Seq/Len: 8.569
Nf(neff/√len): 163.7

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: 8.569).

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
295_V304_C4.0451.00
287_C345_L3.3311.00
202_S223_V3.1801.00
286_M289_K3.1691.00
302_K322_D3.1561.00
345_L364_M2.9431.00
198_I227_A2.8991.00
291_A362_L2.8001.00
288_L317_I2.6771.00
300_Q324_T2.6591.00
314_E365_A2.5591.00
206_R224_Q2.4981.00
303_T322_D2.4471.00
301_A322_D2.4031.00
320_S361_K2.3231.00
205_A220_L2.2811.00
277_S282_N2.2591.00
210_Y217_A2.2401.00
242_K343_E2.2161.00
291_A319_V2.2141.00
284_L315_V2.1801.00
291_A341_M2.0911.00
295_V299_S2.0271.00
318_T363_T2.0141.00
284_L317_I2.0021.00
321_D359_G2.0001.00
341_M352_L1.9881.00
278_L282_N1.9841.00
292_V304_C1.9731.00
199_G227_A1.9301.00
264_M267_Y1.9251.00
198_I223_V1.9181.00
248_K252_I1.9061.00
247_L251_L1.8611.00
251_L258_L1.8491.00
202_S220_L1.8371.00
318_T361_K1.8371.00
191_L234_V1.8351.00
345_L350_G1.8221.00
245_I249_D1.7801.00
250_E255_K1.7791.00
325_F356_T1.7711.00
263_I266_I1.7631.00
292_V296_V1.7601.00
249_D254_I1.7411.00
250_E257_I1.7391.00
276_I281_E1.7231.00
252_I259_E1.7231.00
265_F268_E1.7191.00
175_V179_E1.7011.00
206_R221_K1.6781.00
248_K253_N1.6681.00
354_I360_T1.6681.00
285_S289_K1.6641.00
316_V363_T1.6471.00
325_F360_T1.6451.00
203_D224_Q1.6421.00
351_S365_A1.6331.00
246_R250_E1.6321.00
345_L352_L1.6271.00
277_S281_E1.6221.00
249_D256_Q1.6101.00
276_I282_N1.6071.00
250_E254_I1.6061.00
251_L256_Q1.6011.00
212_D215_Q1.5991.00
252_I256_Q1.5781.00
246_R254_I1.5651.00
356_T360_T1.5631.00
249_D253_N1.5581.00
287_C364_M1.5501.00
338_L341_M1.5451.00
252_I257_I1.5411.00
352_L364_M1.5191.00
323_G359_G1.5051.00
205_A223_V1.4941.00
253_N257_I1.4891.00
266_I269_E1.4881.00
202_S227_A1.4851.00
246_R249_D1.4751.00
262_D265_F1.4741.00
203_D228_R1.4590.99
295_V301_A1.4430.99
251_L255_K1.4400.99
206_R220_L1.4370.99
276_I280_N1.4300.99
245_I253_N1.4210.99
192_G196_S1.4190.99
206_R217_A1.4010.99
308_I317_I1.4000.99
247_L252_I1.3990.99
293_T297_K1.3930.99
263_I267_Y1.3920.99
190_T233_E1.3840.99
261_A264_M1.3760.99
243_K247_L1.3680.99
316_V365_A1.3610.99
251_L254_I1.3580.99
199_G228_R1.3400.99
250_E253_N1.3330.99
249_D252_I1.3290.99
201_K219_E1.3230.99
279_L282_N1.3170.99
173_E176_K1.3150.99
306_V319_V1.3110.99
246_R251_L1.3110.99
277_S280_N1.3110.99
342_R346_E1.3040.99
307_D318_T1.3000.99
264_M269_E1.2930.98
243_K251_L1.2920.98
247_L250_E1.2870.98
224_Q228_R1.2730.98
287_C341_M1.2680.98
173_E177_L1.2660.98
244_G248_K1.2620.98
267_Y271_K1.2590.98
278_L281_E1.2540.98
247_L255_K1.2480.98
265_F270_E1.2450.98
264_M268_E1.2250.98
263_I268_E1.2240.98
248_K256_Q1.2190.97
244_G247_L1.2180.97
174_L178_E1.2090.97
194_K230_S1.2070.97
185_R343_E1.2070.97
284_L364_M1.2070.97
209_I216_A1.2050.97
249_D260_A1.1990.97
253_N260_A1.1830.97
248_K255_K1.1810.97
247_L253_N1.1790.97
248_K251_L1.1740.97
254_I258_L1.1720.97
288_L306_V1.1710.97
245_I251_L1.1700.97
284_L366_I1.1690.97
192_G234_V1.1660.96
243_K248_K1.1590.96
339_L343_E1.1560.96
201_K222_S1.1550.96
301_A324_T1.1510.96
241_M286_M1.1440.96
253_N258_L1.1400.96
245_I248_K1.1390.96
305_R320_S1.1360.96
290_E297_K1.1280.96
300_Q321_D1.1220.95
262_D266_I1.1210.95
234_V238_V1.1150.95
177_L181_Q1.1110.95
244_G252_I1.1080.95
244_G249_D1.0980.95
345_L348_A1.0970.95
242_K340_G1.0920.94
246_R252_I1.0910.94
192_G231_L1.0890.94
262_D267_Y1.0880.94
266_I270_E1.0850.94
265_F269_E1.0780.94
170_R174_L1.0740.94
266_I271_K1.0730.94
283_I348_A1.0660.93
244_G250_E1.0650.93
245_I258_L1.0640.93
179_E182_R1.0640.93
301_A321_D1.0620.93
259_E262_D1.0610.93
238_V336_H1.0610.93
244_G253_N1.0580.93
193_Q360_T1.0550.93
260_A263_I1.0500.93
253_N256_Q1.0450.92
252_I255_K1.0450.92
326_K356_T1.0450.92
168_N171_I1.0440.92
187_L237_I1.0430.92
234_V237_I1.0410.92
276_I279_L1.0410.92
212_D216_A1.0340.92
243_K249_D1.0180.91
247_L254_I1.0170.91
292_V295_V1.0170.91
255_K259_E1.0160.91
164_L168_N1.0140.91
242_K336_H1.0110.91
161_E165_E1.0090.91
186_D286_M1.0040.90
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  
3ehhA20.52831000.422Contact Map
4r39A40.512199.80.583Contact Map
4bixA20.549999.80.597Contact Map
4q20A20.547299.80.605Contact Map
2c2aA10.555399.80.623Contact Map
4ctiA40.606599.80.624Contact Map
3d36A20.53199.70.63Contact Map
4i5sA20.75299.70.632Contact Map
4gczA20.921899.70.635Contact Map
4fppA30.49699.70.644Contact 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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