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T0817

ID: 1402604606 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 525 (485)
Sequences: 8971 (6820.8)
Seq/Len: 18.497
Nf(neff/√len): 309.7

HHblits Results: (2013_03)
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: 18.497).

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
195_I205_E4.2711.00
291_Q348_K4.0821.00
144_D147_H4.0271.00
303_A307_K3.9371.00
143_V149_T3.6071.00
141_E149_T3.5821.00
341_A344_A3.5791.00
466_A470_Q3.5011.00
451_T485_N3.4901.00
100_E146_Y3.1721.00
193_V205_E3.1651.00
116_K120_E3.1251.00
116_K142_V3.1141.00
301_D304_A3.0951.00
296_V389_M3.0721.00
458_P462_A3.0551.00
113_A142_V2.9271.00
84_D97_T2.8221.00
298_I341_A2.7891.00
110_F189_T2.7711.00
86_K97_T2.7011.00
455_N458_P2.6931.00
72_G76_Q2.6771.00
284_A288_K2.6591.00
344_A348_K2.6591.00
69_V85_W2.6071.00
291_Q345_L2.5831.00
453_P481_W2.5201.00
453_P485_N2.5161.00
290_P294_K2.4711.00
102_V110_F2.4601.00
88_E92_K2.4581.00
291_Q294_K2.4571.00
470_Q473_P2.4101.00
390_K395_D2.3961.00
111_D114_A2.3511.00
455_N477_K2.3421.00
115_C148_I2.3291.00
119_L150_V2.3081.00
193_V208_D2.3001.00
105_Q207_Y2.2851.00
50_D121_R2.2621.00
93_T151_H2.2401.00
439_S452_D2.2381.00
192_W217_Y2.2361.00
439_S457_D2.2261.00
83_T100_E2.1961.00
103_K109_K2.1541.00
93_T149_T2.1261.00
87_I94_L2.1191.00
365_T397_V2.1121.00
141_E151_H2.0901.00
72_G78_E2.0771.00
97_T147_H2.0761.00
462_A474_T2.0351.00
95_H149_T2.0231.00
279_F489_A1.9881.00
363_P395_D1.9861.00
294_K341_A1.9851.00
138_Q153_K1.9761.00
37_T219_R1.9651.00
283_R416_D1.9571.00
473_P477_K1.9291.00
456_L478_V1.9251.00
37_T221_E1.9231.00
103_K209_G1.9211.00
279_F417_L1.9211.00
203_V219_R1.9071.00
365_T395_D1.9031.00
66_E80_C1.9001.00
317_A493_Y1.8841.00
101_G109_K1.8791.00
85_W96_L1.8691.00
234_A239_E1.8641.00
463_A474_T1.8591.00
463_A475_I1.8501.00
102_V189_T1.8331.00
459_L477_K1.8301.00
113_A116_K1.8151.00
480_D484_D1.8081.00
113_A145_D1.7941.00
386_Q390_K1.7941.00
41_A240_I1.7851.00
296_V394_I1.7621.00
338_D341_A1.7371.00
69_V96_L1.7361.00
428_D471_I1.7301.00
287_L296_V1.7301.00
477_K480_D1.6941.00
347_E357_R1.6821.00
196_S201_Q1.6811.00
297_S486_D1.6811.00
292_V349_A1.6751.00
196_S203_V1.6711.00
83_T97_T1.6681.00
343_S347_E1.6681.00
300_I385_I1.6661.00
462_A470_Q1.6631.00
206_H218_E1.6321.00
225_I234_A1.6251.00
88_E95_H1.6181.00
236_R258_Q1.6101.00
195_I219_R1.6091.00
474_T477_K1.6061.00
292_V346_L1.6061.00
112_A142_V1.6031.00
283_R286_P1.5901.00
367_E399_R1.5841.00
106_D173_S1.5681.00
459_L474_T1.5661.00
290_P485_N1.5621.00
205_E219_R1.5601.00
105_Q193_V1.5571.00
39_R221_E1.5521.00
452_D457_D1.5451.00
114_A174_P1.5401.00
345_L348_K1.5341.00
88_E93_T1.5041.00
409_D414_K1.4931.00
113_A174_P1.4691.00
83_T99_R1.4641.00
299_G392_V1.4621.00
340_A343_S1.4501.00
470_Q474_T1.4491.00
109_K146_Y1.4421.00
108_T175_K1.4381.00
111_D145_D1.4351.00
66_E189_T1.4281.00
505_Q522_V1.4281.00
36_G218_E1.4271.00
173_S176_S1.4161.00
143_V147_H1.4081.00
150_V159_L1.4081.00
454_V458_P1.4070.99
112_A143_V1.4070.99
81_L189_T1.4060.99
105_Q194_Q1.4000.99
95_H147_H1.3960.99
455_N481_W1.3950.99
139_S151_H1.3860.99
206_H215_P1.3850.99
466_A474_T1.3830.99
99_R102_V1.3810.99
306_S316_P1.3800.99
402_D405_S1.3740.99
35_A218_E1.3720.99
481_W485_N1.3710.99
473_P476_Q1.3710.99
94_L159_L1.3660.99
257_K260_E1.3490.99
282_D450_V1.3420.99
367_E397_V1.3360.99
103_K207_Y1.3340.99
66_E211_W1.3330.99
97_T146_Y1.3310.99
303_A316_P1.3290.99
216_T522_V1.3270.99
265_N502_K1.3210.99
201_Q221_E1.3200.99
287_L366_L1.3130.99
294_K345_L1.3110.99
294_K486_D1.3110.99
230_S234_A1.3070.99
142_V145_D1.3020.99
290_P484_D1.2930.99
234_A240_I1.2860.99
472_E476_Q1.2820.99
451_T456_L1.2760.99
408_T412_E1.2740.99
241_D501_S1.2680.99
505_Q524_A1.2640.99
108_T173_S1.2580.99
459_L481_W1.2570.99
39_R223_K1.2550.99
104_F114_A1.2520.99
310_Y314_A1.2510.99
388_E391_E1.2380.98
351_W359_K1.2360.98
379_R383_E1.2280.98
97_T100_E1.2250.98
235_L499_A1.2230.98
204_F222_A1.2180.98
371_S398_I1.2170.98
205_E208_D1.2100.98
298_I335_P1.2090.98
299_G389_M1.2020.98
203_V221_E1.1910.98
45_P197_A1.1880.98
279_F296_V1.1820.98
97_T144_D1.1760.98
323_A493_Y1.1750.98
105_Q209_G1.1740.98
116_K140_L1.1730.98
114_A118_N1.1720.98
384_V388_E1.1670.97
320_M490_P1.1660.97
344_A347_E1.1630.97
38_L504_V1.1620.97
41_A231_R1.1620.97
399_R409_D1.1610.97
241_D503_R1.1550.97
283_R288_K1.1460.97
306_S314_A1.1390.97
455_N459_L1.1370.97
339_A392_V1.1330.97
79_P85_W1.1280.97
174_P178_D1.1280.97
265_N500_H1.1220.97
88_E91_G1.1210.97
413_Q450_V1.1160.96
297_S302_R1.1120.96
83_T146_Y1.1100.96
403_H407_H1.0950.96
462_A477_K1.0950.96
116_K148_I1.0950.96
140_L148_I1.0860.96
86_K95_H1.0860.96
115_C171_F1.0770.95
67_P80_C1.0760.95
138_Q151_H1.0710.95
99_R211_W1.0710.95
114_A117_W1.0710.95
389_M396_L1.0680.95
305_I381_I1.0590.95
459_L462_A1.0560.95
39_R241_D1.0560.95
95_H143_V1.0510.94
386_Q398_I1.0470.94
462_A466_A1.0470.94
291_Q349_A1.0470.94
438_L461_N1.0430.94
195_I203_V1.0380.94
96_L150_V1.0320.94
264_F499_A1.0310.94
304_A388_E1.0270.94
70_K78_E1.0250.93
120_E142_V1.0240.93
154_E465_A1.0210.93
152_F159_L1.0210.93
438_L457_D1.0200.93
206_H214_K1.0180.93
225_I240_I1.0030.93
451_T487_A1.0010.92
96_L160_M1.0010.92
109_K145_D1.0010.92
278_A418_G1.0000.92
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: (07Jun14)
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  
1xocA10.91811000.191Contact Map
4fajA10.89141000.194Contact Map
3t66A10.89141000.202Contact Map
2wolA10.94861000.206Contact Map
2nooA10.91051000.206Contact Map
3m8uA10.8991000.212Contact Map
3tpaA10.89711000.213Contact Map
4gl8A20.88951000.214Contact Map
1dpeA10.9011000.215Contact Map
2grvA30.90481000.218Contact 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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