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nd5aln_enrich

ID: 1499526238 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 516 (509)
Sequences: 5820 (2641.9)
Seq/Len: 11.434
Nf(neff/√len): 117.1

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: 11.434).

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
233_I288_I3.9811.00
84_L199_F3.7951.00
234_I275_S3.6601.00
213_G250_G3.2531.00
247_V344_T3.1931.00
37_M80_T2.9521.00
163_F215_I2.8781.00
285_E290_K2.7831.00
103_G113_A2.7371.00
302_T364_L2.7281.00
37_M76_L2.7091.00
30_D198_R2.6851.00
309_C355_S2.6601.00
77_I90_G2.5681.00
115_Q171_S2.4691.00
53_W379_N2.4441.00
288_I362_T2.4331.00
118_Y167_P2.4091.00
197_V258_F2.3811.00
445_F450_G2.3771.00
222_I450_G2.3611.00
279_I286_Q2.3541.00
84_L144_F2.3521.00
481_L484_T2.3451.00
81_A86_Q2.3031.00
306_I359_I2.2641.00
225_L353_I2.2091.00
277_S378_N2.1981.00
346_T350_L2.1611.00
356_T360_F2.1541.00
94_V188_M2.1441.00
228_N289_R2.1161.00
39_V265_A2.0761.00
260_H323_S2.0731.00
226_T446_S2.0251.00
304_A390_L2.0141.00
140_D143_I2.0121.00
295_F302_T2.0091.00
44_T72_L1.9381.00
249_I257_A1.9271.00
263_T319_T1.9241.00
301_T377_E1.9171.00
270_M308_G1.8981.00
107_R110_A1.8921.00
280_H284_N1.8911.00
310_L315_M1.8821.00
209_T250_G1.8661.00
328_I348_T1.8371.00
218_L347_A1.8181.00
90_G93_G1.8051.00
196_L203_M1.7961.00
288_I361_F1.7471.00
298_L301_T1.7411.00
193_I246_M1.7351.00
213_G243_G1.7311.00
60_Y63_Q1.7281.00
128_A151_G1.7241.00
40_S79_V1.7101.00
348_T424_M1.7051.00
328_I344_T1.6951.00
114_L117_L1.6881.00
305_L358_I1.6821.00
222_I350_L1.6711.00
241_Q351_T1.6701.00
39_V262_C1.6631.00
45_W49_E1.6491.00
138_T143_I1.6361.00
214_A340_A1.6351.00
325_D329_E1.6251.00
218_L343_L1.6171.00
281_N298_L1.6131.00
342_L346_T1.6061.00
421_A425_T1.6001.00
74_T93_G1.5981.00
355_S358_I1.5941.00
380_P384_N1.5751.00
125_G154_L1.5741.00
210_L247_V1.5651.00
158_G165_L1.5601.00
150_M154_L1.5581.00
132_W148_P1.5401.00
307_I390_L1.5251.00
282_L291_M1.5241.00
309_C359_I1.5141.00
274_C304_A1.5121.00
70_L97_M1.4961.00
53_W381_L1.4931.00
270_M386_I1.4841.00
32_F258_F1.4761.00
251_L331_A1.4741.00
28_K31_Y1.4521.00
85_F139_W1.4481.00
312_L355_S1.4461.00
391_I395_F1.4421.00
302_T359_I1.4291.00
415_L419_L1.4261.00
221_A347_A1.4081.00
300_F387_K1.4060.99
129_S155_A1.4040.99
215_I343_L1.4040.99
87_L195_L1.4000.99
196_L249_I1.3930.99
228_N287_D1.3900.99
30_D33_S1.3880.99
359_I364_L1.3750.99
149_L202_L1.3710.99
132_W135_N1.3680.99
41_L76_L1.3670.99
280_H376_N1.3640.99
126_L195_L1.3630.99
229_D286_Q1.3550.99
300_F383_I1.3510.99
52_M381_L1.3500.99
347_A350_L1.3430.99
196_L246_M1.3090.99
40_S44_T1.3070.99
149_L203_M1.2960.99
219_F450_G1.2890.99
157_A212_L1.2760.99
369_F375_I1.2720.99
74_T97_M1.2670.99
498_G503_Y1.2630.99
497_Q502_L1.2610.99
426_T430_I1.2560.99
197_V249_I1.2560.99
319_T396_A1.2560.99
49_E384_N1.2550.99
233_I361_F1.2550.99
53_W382_L1.2430.98
309_C313_T1.2370.98
150_M208_T1.2350.98
277_S301_T1.2330.98
16_V23_L1.2260.98
14_H24_T1.2260.98
163_F219_F1.2210.98
392_G396_A1.2210.98
430_I434_E1.2180.98
215_I339_W1.2160.98
14_H17_T1.2130.98
352_A425_T1.2110.98
383_I387_K1.2100.98
141_Q144_F1.2100.98
47_I273_L1.2090.98
153_V208_T1.1860.98
46_S269_A1.1830.98
304_A387_K1.1800.98
50_F284_N1.1750.98
14_H22_K1.1740.98
120_R123_D1.1730.98
210_L251_L1.1710.98
51_S64_F1.1660.97
329_E418_K1.1650.97
244_L348_T1.1600.97
42_F46_S1.1590.97
33_S194_F1.1560.97
483_K486_A1.1520.97
356_T429_F1.1520.97
390_L393_S1.1510.97
428_G432_A1.1410.97
157_A250_G1.1390.97
273_L386_I1.1350.97
387_K391_I1.1330.97
61_I65_F1.1300.97
303_T306_I1.1280.97
297_A375_I1.1260.97
355_S359_I1.1220.97
266_F396_A1.1210.97
248_T327_I1.1210.97
267_F320_G1.1200.96
127_L131_A1.1180.96
430_I433_F1.1140.96
448_L451_Y1.1090.96
316_P322_Y1.1050.96
29_M80_T1.1050.96
108_T174_E1.1030.96
217_T347_A1.1010.96
214_A343_L1.0990.96
156_A246_M1.0980.96
129_S133_F1.0980.96
385_P388_R1.0930.96
449_L453_P1.0910.96
449_L454_T1.0890.96
35_M258_F1.0870.96
153_V209_T1.0860.96
159_K231_K1.0860.96
130_M139_W1.0860.96
167_P456_M1.0860.96
81_A87_L1.0850.96
262_C400_L1.0850.96
133_F148_P1.0800.95
304_A386_I1.0790.95
50_F273_L1.0780.95
35_M262_C1.0750.95
280_H382_L1.0720.95
104_W107_R1.0720.95
288_I358_I1.0660.95
380_P387_K1.0650.95
260_H267_F1.0640.95
222_I446_S1.0640.95
174_E232_K1.0630.95
286_Q289_R1.0630.95
378_N383_I1.0620.95
351_T354_Y1.0620.95
106_G110_A1.0600.95
211_C215_I1.0570.95
306_I364_L1.0550.95
424_M428_G1.0540.95
166_H452_F1.0520.95
277_S377_E1.0510.94
48_M69_L1.0490.94
68_L179_V1.0480.94
282_L285_E1.0450.94
183_L190_V1.0440.94
384_N387_K1.0440.94
210_L340_A1.0410.94
26_S82_N1.0400.94
263_T323_S1.0340.94
240_S351_T1.0340.94
278_I305_L1.0310.94
473_D476_W1.0280.94
50_F280_H1.0280.94
293_G367_P1.0280.94
309_C312_L1.0260.94
306_I310_L1.0250.93
164_G239_S1.0230.93
234_I355_S1.0190.93
84_L133_F1.0180.93
71_F75_M1.0170.93
259_L263_T1.0130.93
427_L431_L1.0120.93
326_P329_E1.0120.93
464_L467_S1.0120.93
289_R361_F1.0110.93
33_S80_T1.0110.93
199_F203_M1.0070.93
332_T341_L1.0060.93
110_A174_E1.0050.93
259_L323_S1.0050.93
496_Q499_L1.0000.92
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  
3rkoL20.98841000.295Contact Map
4he8L20.98451000.297Contact Map
3rkoM20.80231000.476Contact Map
4he8M20.77521000.49Contact Map
3rkoN20.78491000.504Contact Map
4he8N20.75581000.515Contact Map
4he8K20.17257.60.981Contact Map
3rkoK20.18026.80.982Contact Map
1rklA10.06981.30.988Contact Map
2k3cA10.060110.989Contact 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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