GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
BMSP

ID: 1515265724 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 574 (548)
Sequences: 5552 (3788.7)
Seq/Len: 10.131
Nf(neff/√len): 161.8

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: 10.131).

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
321_M524_S4.7061.00
16_N167_D4.6751.00
114_G125_I4.2941.00
263_Q339_K3.9111.00
105_R112_E3.8981.00
113_I130_L3.8801.00
209_T254_S3.6851.00
20_N56_R3.6821.00
92_R126_E3.6401.00
308_A339_K3.6401.00
82_H135_E3.4041.00
109_N136_N3.3841.00
97_F140_I3.2541.00
239_E247_K3.2241.00
100_V164_I3.1661.00
211_S254_S3.0811.00
212_I264_I3.0681.00
91_K172_T2.9861.00
108_L113_I2.9491.00
213_P252_I2.8881.00
108_L138_I2.8481.00
239_E245_N2.8281.00
304_E332_Y2.8231.00
384_Y445_V2.7551.00
100_V104_C2.6331.00
374_K411_L2.6051.00
80_A137_F2.5341.00
254_S259_R2.5221.00
242_S245_N2.5091.00
93_Q131_L2.4311.00
373_I408_G2.4311.00
242_S281_K2.4151.00
210_V253_V2.3971.00
91_K174_P2.3561.00
211_S252_I2.3531.00
100_V142_V2.3101.00
243_S343_I2.2731.00
182_F377_Q2.2661.00
312_N316_A2.2601.00
215_L247_K2.2471.00
18_K56_R2.2221.00
97_F100_V2.2171.00
308_A312_N2.1991.00
235_I266_F2.1981.00
405_L409_K2.1851.00
370_S407_T2.1801.00
187_K240_R2.1791.00
122_P375_R2.1471.00
366_Q403_S2.1211.00
93_Q172_T2.1191.00
322_I342_F2.1141.00
178_L197_V2.0951.00
407_T411_L2.0851.00
409_K417_Y2.0811.00
271_V416_L2.0561.00
285_M383_G2.0491.00
250_E263_Q2.0341.00
108_L127_V2.0331.00
369_L408_G2.0321.00
105_R115_S2.0181.00
250_E261_E1.9821.00
61_G66_Q1.9821.00
95_L106_V1.9561.00
15_L83_F1.9561.00
412_D415_R1.9451.00
252_I259_R1.9361.00
251_V264_I1.9351.00
94_F126_E1.9351.00
317_L560_A1.9291.00
374_K377_Q1.9251.00
311_L342_F1.9231.00
278_L343_I1.9131.00
402_T406_E1.9131.00
278_L283_T1.8951.00
111_A130_L1.8911.00
272_K277_Y1.8811.00
210_V251_V1.8671.00
92_R175_Q1.8601.00
338_E379_R1.8481.00
20_N80_A1.8461.00
105_R141_E1.8221.00
84_D135_E1.8181.00
465_A517_I1.7991.00
296_Q534_P1.7931.00
80_A139_A1.7841.00
252_I261_E1.7811.00
98_G169_L1.7761.00
337_A344_L1.7601.00
186_D268_N1.7541.00
276_I383_G1.7531.00
235_I238_L1.7491.00
78_W141_E1.7451.00
12_I169_L1.7431.00
82_H137_F1.7321.00
181_Y253_V1.7271.00
310_L555_G1.7161.00
311_L340_M1.7041.00
95_L127_V1.6771.00
85_A131_L1.6701.00
14_S167_D1.6361.00
366_Q407_T1.6361.00
51_F80_A1.6301.00
269_I276_I1.6281.00
63_W77_V1.6191.00
76_T141_E1.6191.00
94_F173_T1.6151.00
322_I333_T1.6041.00
186_D194_I1.6001.00
194_I232_V1.5881.00
55_L66_Q1.5771.00
406_E410_Q1.5631.00
294_I306_D1.5431.00
213_P221_M1.5381.00
346_Q372_M1.5371.00
244_E315_K1.5371.00
298_M303_S1.5361.00
370_S411_L1.5301.00
196_K230_E1.5281.00
346_Q376_D1.5161.00
527_I531_F1.5141.00
176_T205_G1.5091.00
309_M312_N1.5061.00
112_E115_S1.5051.00
244_E281_K1.4981.00
212_I251_V1.4951.00
405_L417_Y1.4801.00
268_N280_G1.4701.00
270_T277_Y1.4671.00
243_S283_T1.4661.00
183_I262_E1.4641.00
96_Y124_Q1.4591.00
303_S306_D1.4571.00
180_D377_Q1.4551.00
369_L404_L1.4521.00
179_E200_S1.4511.00
33_K36_R1.4451.00
193_M264_I1.4441.00
215_L219_I1.4441.00
298_M301_A1.4441.00
407_T410_Q1.4411.00
343_I383_G1.4391.00
508_R512_R1.4331.00
92_R177_Y1.4321.00
78_W139_A1.4291.00
263_Q335_R1.4231.00
116_H123_F1.4191.00
94_F124_Q1.4081.00
312_N340_M1.4070.99
183_I251_V1.4040.99
92_R129_D1.3920.99
113_I125_I1.3840.99
57_L66_Q1.3770.99
179_E198_A1.3760.99
64_N162_G1.3720.99
20_N51_F1.3670.99
556_I560_A1.3630.99
96_Y169_L1.3630.99
21_A77_V1.3600.99
288_I319_V1.3590.99
329_Q334_V1.3580.99
367_R371_E1.3580.99
238_L266_F1.3570.99
338_E381_A1.3540.99
184_Q196_K1.3470.99
178_L255_S1.3410.99
191_N266_F1.3400.99
244_E283_T1.3310.99
314_A342_F1.3300.99
274_T277_Y1.3290.99
96_Y171_V1.3250.99
117_E364_K1.3130.99
108_L130_L1.3110.99
317_L561_W1.3080.99
176_T201_D1.3040.99
304_E308_A1.3040.99
563_L567_Y1.3030.99
15_L81_R1.3000.99
183_I264_I1.2930.99
178_L253_V1.2870.99
94_F177_Y1.2850.99
116_H371_E1.2750.99
211_S221_M1.2700.99
336_L340_M1.2680.99
83_F138_I1.2640.99
210_V231_T1.2630.99
90_H175_Q1.2610.99
529_F555_G1.2510.99
92_R128_T1.2470.99
103_R117_E1.2440.98
221_M224_D1.2420.98
311_L337_A1.2340.98
277_Y282_P1.2310.98
298_M306_D1.2270.98
214_E220_D1.2220.98
333_T337_A1.2170.98
185_L191_N1.2170.98
107_Y112_E1.2170.98
58_N61_G1.2160.98
213_P250_E1.2090.98
290_F329_Q1.2080.98
344_L381_A1.2070.98
121_T371_E1.1990.98
86_K172_T1.1970.98
305_A308_A1.1950.98
223_T233_F1.1940.98
104_C116_H1.1910.98
18_K58_N1.1840.98
409_K444_D1.1830.98
184_Q194_I1.1820.98
527_I548_K1.1720.98
314_A319_V1.1690.97
214_E247_K1.1620.97
399_E402_T1.1620.97
58_N66_Q1.1580.97
248_L263_Q1.1550.97
13_R172_T1.1530.97
294_I303_S1.1470.97
182_F196_K1.1450.97
185_L266_F1.1430.97
140_I164_I1.1380.97
370_S410_Q1.1320.97
366_Q370_S1.1310.97
214_E239_E1.1310.97
208_I253_V1.1300.97
183_I195_A1.1280.97
324_L329_Q1.1280.97
76_T143_N1.1270.97
106_V140_I1.1130.96
10_R258_D1.1100.96
197_V231_T1.1030.96
83_F136_N1.1020.96
561_W564_M1.1000.96
334_V344_L1.1000.96
215_L239_E1.0990.96
127_V131_L1.0970.96
315_K340_M1.0920.96
190_P240_R1.0890.96
305_A312_N1.0880.96
283_T343_I1.0870.96
336_L339_K1.0870.96
468_E519_N1.0850.96
302_F307_A1.0830.96
307_A333_T1.0780.95
92_R173_T1.0740.95
116_H121_T1.0730.95
373_I411_L1.0720.95
290_F310_L1.0680.95
24_D78_W1.0680.95
362_R403_S1.0670.95
476_I521_R1.0660.95
253_V262_E1.0660.95
270_T280_G1.0650.95
356_F365_A1.0650.95
348_I372_M1.0630.95
194_I230_E1.0630.95
308_A340_M1.0570.95
195_A210_V1.0560.95
193_M266_F1.0560.95
531_F548_K1.0530.95
387_I408_G1.0510.94
308_A336_L1.0480.94
86_K93_Q1.0460.94
243_S278_L1.0450.94
314_A551_V1.0450.94
370_S374_K1.0420.94
314_A528_L1.0420.94
311_L333_T1.0330.94
565_R568_Y1.0310.94
418_V447_A1.0300.94
525_P563_L1.0300.94
489_S501_E1.0210.93
275_D282_P1.0200.93
372_M382_V1.0190.93
104_C140_I1.0180.93
77_V162_G1.0170.93
13_R86_K1.0170.93
334_V376_D1.0150.93
304_E336_L1.0150.93
103_R115_S1.0150.93
173_T258_D1.0120.93
345_W384_Y1.0070.93
14_S169_L1.0030.93
192_R232_V1.0010.92
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  
1jz7A40.90421000.254Contact Map
1yq2A60.90591000.264Contact Map
3fn9A40.93381000.269Contact Map
3bgaA20.89371000.269Contact Map
3cmgA10.91641000.271Contact Map
3obaA40.89721000.273Contact Map
3gm8A10.89021000.275Contact Map
4ypjA201000.278Contact Map
4cu7A10.93551000.3Contact Map
3hn3A40.94951000.3Contact 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 0.026 seconds.