GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
trial1

ID: 1518135843 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 543 (511)
Sequences: 2672 (1309.9)
Seq/Len: 5.229
Nf(neff/√len): 57.9

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: 5.229).

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
130_K133_E4.2921.00
341_G358_E4.1071.00
290_I305_A3.4111.00
482_D485_E3.3631.00
151_T172_E3.3511.00
408_E495_K3.3201.00
147_K176_E3.2131.00
206_T369_I3.1381.00
226_K342_L3.0841.00
404_G483_M3.0831.00
135_L492_L2.9871.00
128_A499_I2.9381.00
103_L124_Y2.8151.00
106_K435_D2.7921.00
340_A356_V2.7551.00
102_E105_R2.7051.00
277_K303_I2.6191.00
147_K179_S2.6171.00
234_L323_A2.6071.00
107_A124_Y2.4891.00
274_A278_A2.4751.00
317_L356_V2.4461.00
174_I384_V2.4221.00
134_L414_K2.3921.00
128_A503_A2.3511.00
172_E176_E2.3391.00
233_A332_L2.3391.00
267_K271_D2.2781.00
32_A101_G2.2551.00
139_A492_L2.2451.00
285_F356_V2.2061.00
136_K496_T2.2021.00
474_N477_T2.1951.00
201_A205_D2.1641.00
95_T498_A2.1561.00
227_V230_A2.1401.00
422_I430_V2.1031.00
270_K274_A2.0841.00
437_L499_I2.0331.00
433_F503_A2.0301.00
369_I377_I1.9831.00
135_L496_T1.9541.00
155_M168_E1.9161.00
59_N64_I1.9121.00
400_I489_V1.9121.00
439_V443_T1.9051.00
135_L407_T1.8981.00
415_L430_V1.8461.00
173_I206_T1.8031.00
231_K339_D1.7941.00
106_K109_E1.7841.00
240_E289_G1.7831.00
124_Y433_F1.7811.00
263_E267_K1.7741.00
231_K280_G1.7631.00
318_A325_V1.7381.00
103_L433_F1.7361.00
402_S406_S1.7271.00
285_F309_V1.7201.00
197_K378_E1.7061.00
410_E463_H1.6921.00
474_N481_E1.6901.00
176_E210_K1.6891.00
130_K430_V1.6861.00
298_L305_A1.6861.00
407_T411_L1.6861.00
131_A411_L1.6821.00
306_A354_I1.6821.00
124_Y503_A1.6360.99
228_T342_L1.6350.99
233_A337_L1.6290.99
102_E439_V1.6230.99
126_A426_E1.5920.99
277_K301_E1.5920.99
130_K134_L1.5880.99
462_A471_A1.5780.99
234_L318_A1.5700.99
385_D389_G1.5690.99
32_A36_R1.5530.99
470_C482_D1.5430.99
438_E460_R1.5420.99
39_L98_V1.5330.99
130_K418_Y1.5330.99
379_E382_R1.5330.99
203_I380_V1.5300.99
458_K479_A1.5290.99
418_Y430_V1.5250.99
134_L137_T1.5020.99
174_I387_A1.4910.99
132_Q136_K1.4890.99
450_L475_V1.4860.99
60_D386_D1.4650.98
259_M263_E1.4600.98
180_A210_K1.4580.98
94_T386_D1.4560.98
431_R435_D1.4510.98
276_I284_L1.4510.98
130_K414_K1.4450.98
346_R357_E1.4190.98
320_A359_C1.3890.97
122_K426_E1.3690.97
93_T386_D1.3640.97
226_K344_E1.3630.97
494_V498_A1.3630.97
37_S46_K1.3530.97
441_P459_V1.3510.97
450_L455_I1.3510.97
140_C484_C1.3460.97
124_Y127_A1.3440.97
123_G127_A1.3400.97
260_E263_E1.3330.97
416_R438_E1.3290.96
284_L298_L1.3250.96
61_G94_T1.3220.96
218_R304_V1.3210.96
417_E420_E1.3210.96
289_G307_R1.3160.96
234_L317_L1.3100.96
134_L410_E1.3050.96
81_V96_A1.2950.96
276_I281_A1.2920.96
369_I380_V1.2810.95
14_R514_D1.2790.95
153_I400_I1.2730.95
59_N382_R1.2680.95
154_A391_V1.2660.95
86_E386_D1.2650.95
289_G308_R1.2590.95
232_I340_A1.2580.95
28_G104_L1.2510.95
322_G338_G1.2400.94
474_N486_N1.2400.94
218_R354_I1.2380.94
413_M417_E1.2290.94
110_L429_A1.2270.94
176_E179_S1.2270.94
154_A175_V1.2240.94
227_V283_V1.2220.94
250_I261_F1.2170.93
239_I276_I1.2110.93
210_K358_E1.2060.93
273_V294_A1.2020.93
411_L437_L1.2010.93
345_E352_S1.1950.93
207_E368_L1.1920.92
151_T155_M1.1880.92
384_V388_V1.1830.92
95_T440_I1.1810.92
288_K308_R1.1810.92
367_M384_V1.1790.92
283_V356_V1.1760.92
125_Q507_E1.1760.92
134_L411_L1.1720.92
257_K260_E1.1720.92
218_R345_E1.1720.92
311_K315_E1.1700.92
490_E495_K1.1690.91
29_R105_R1.1690.91
404_G488_V1.1640.91
178_V193_I1.1640.91
359_C362_P1.1540.91
160_G383_A1.1530.91
355_F368_L1.1490.91
147_K172_E1.1490.91
314_M317_L1.1480.91
123_G429_A1.1450.90
111_L119_I1.1350.90
230_A283_V1.1310.90
298_L303_I1.1280.89
275_E278_A1.1260.89
132_Q496_T1.1240.89
197_K381_A1.1220.89
106_K436_A1.1210.89
133_E136_K1.1200.89
86_E93_T1.1200.89
234_L325_V1.1180.89
254_D257_K1.1180.89
127_A430_V1.1160.89
491_P494_V1.1160.89
296_H300_K1.1120.89
177_A208_L1.1120.89
234_L314_M1.1110.89
415_L434_A1.1040.88
401_V492_L1.1020.88
14_R17_G1.0980.88
339_D360_K1.0920.87
240_E291_D1.0890.87
412_S416_R1.0830.87
445_A450_L1.0820.87
36_R446_E1.0810.87
304_V354_I1.0800.87
269_L293_L1.0800.87
219_V295_Q1.0790.86
138_I407_T1.0750.86
401_V407_T1.0750.86
416_R431_R1.0740.86
220_S307_R1.0740.86
40_G43_G1.0730.86
229_D341_G1.0640.85
76_K79_I1.0610.85
225_K345_E1.0560.85
150_L154_A1.0560.85
27_A72_H1.0550.85
59_N386_D1.0500.84
44_M117_P1.0490.84
444_L475_V1.0450.84
147_K151_T1.0430.84
99_V502_A1.0410.84
439_V442_R1.0400.84
100_A502_A1.0390.84
61_G386_D1.0390.84
229_D502_A1.0390.84
173_I367_M1.0380.83
283_V343_V1.0370.83
32_A35_V1.0320.83
341_G359_C1.0320.83
128_A132_Q1.0310.83
467_G471_A1.0310.83
134_L138_I1.0260.82
130_K411_L1.0230.82
124_Y429_A1.0220.82
227_V282_N1.0190.82
45_D59_N1.0190.82
492_L496_T1.0130.81
397_D493_R1.0130.81
264_Q267_K1.0110.81
61_G93_T1.0090.81
114_N117_P1.0080.81
281_A337_L1.0070.81
168_E172_E1.0060.81
39_L95_T1.0060.81
410_E414_K1.0050.81
61_G90_G1.0020.80
160_G164_E1.0000.80
177_A181_V1.0000.80
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  
3ruvA40.95031000.021Contact Map
3j1bA160.93191000.039Contact Map
1q3qA40.94661000.045Contact Map
1a6dA10.92081000.066Contact Map
3p9dG20.93191000.091Contact Map
3ko1A90.92451000.093Contact Map
1a6dB10.9191000.104Contact Map
3p9dA20.96321000.111Contact Map
3p9dD20.94291000.114Contact Map
3iygA10.94111000.12Contact 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.

Page generated in 0.0228 seconds.