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T0817

ID: 1402597570 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 525 (516)
Sequences: 618 (476.1)
Seq/Len: 1.198
Nf(neff/√len): 21.0

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: 1.198).

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
144_D147_H4.4401.00
291_Q348_K3.8041.00
466_A470_Q3.5171.00
143_V149_T3.4611.00
115_C148_I3.4451.00
303_A307_K3.2791.00
111_D114_A3.2211.00
141_E149_T2.8871.00
296_V394_I2.8721.00
195_I205_E2.8161.00
102_V189_T2.7931.00
296_V389_M2.7761.00
86_K97_T2.7731.00
110_F189_T2.7591.00
116_K142_V2.5941.00
193_V208_D2.5671.00
95_H147_H2.5141.00
341_A344_A2.5001.00
451_T485_N2.4881.00
470_Q473_P2.4660.99
102_V110_F2.4470.99
344_A348_K2.4400.99
84_D97_T2.2870.99
455_N458_P2.2540.99
85_W96_L2.2420.99
113_A142_V2.2270.99
455_N477_K2.1840.98
112_A142_V2.1790.98
100_E146_Y2.1490.98
292_V349_A2.1460.98
291_Q294_K2.1390.98
287_L366_L2.1290.98
290_P294_K2.0720.98
291_Q345_L2.0440.97
112_A143_V2.0200.97
298_I341_A2.0190.97
458_P462_A2.0010.97
305_I309_L2.0000.97
114_A118_N2.0000.97
463_A474_T1.9800.97
37_T219_R1.9750.97
116_K120_E1.9470.96
87_I94_L1.9300.96
38_L504_V1.9140.96
99_R102_V1.9080.96
150_V159_L1.9040.95
297_S486_D1.8970.95
69_V96_L1.8900.95
88_E92_K1.8820.95
83_T100_E1.8560.95
69_V85_W1.8450.94
116_K148_I1.7580.92
103_K109_K1.7350.92
88_E95_H1.7320.91
35_A218_E1.7220.91
173_S176_S1.6910.90
505_Q522_V1.6910.90
81_L102_V1.6900.90
36_G218_E1.6880.90
428_D471_I1.6850.90
283_R416_D1.6790.90
345_L348_K1.6480.89
284_A288_K1.6330.88
340_A343_S1.6330.88
72_G76_Q1.6070.87
93_T151_H1.5970.86
50_D121_R1.5960.86
453_P485_N1.5930.86
300_I389_M1.5880.86
99_R211_W1.5770.85
283_R286_P1.5760.85
299_G392_V1.5740.85
143_V147_H1.5550.84
97_T147_H1.5410.84
41_A240_I1.5370.83
216_T522_V1.5200.82
72_G78_E1.5080.82
196_S201_Q1.4990.81
95_H149_T1.4980.81
83_T99_R1.4830.80
114_A173_S1.4780.80
36_G522_V1.4740.80
35_A522_V1.4720.80
36_G216_T1.4710.79
111_D118_N1.4700.79
103_K209_G1.4520.78
192_W217_Y1.4500.78
193_V205_E1.4450.78
114_A174_P1.4280.77
341_A470_Q1.4200.76
287_L296_V1.4190.76
289_D349_A1.4150.76
323_A493_Y1.4130.76
81_L189_T1.3990.75
343_S347_E1.3980.74
351_W359_K1.3950.74
206_H218_E1.3710.72
340_A469_D1.3670.72
462_A466_A1.3630.72
236_R258_Q1.3570.71
235_L243_V1.3550.71
114_A117_W1.3430.70
97_T144_D1.3380.70
66_E189_T1.3350.70
390_K395_D1.3270.69
35_A216_T1.3240.69
341_A391_E1.3240.69
142_V148_I1.3220.68
279_F417_L1.3080.67
346_L394_I1.3030.67
120_E142_V1.2990.66
225_I240_I1.2960.66
292_V346_L1.2900.66
186_P194_Q1.2880.66
453_P481_W1.2870.65
119_L150_V1.2720.64
225_I234_A1.2710.64
306_S316_P1.2690.64
89_D348_K1.2670.64
206_H388_E1.2580.63
301_D304_A1.2560.63
366_L417_L1.2530.62
109_K146_Y1.2500.62
232_V236_R1.2490.62
339_A391_E1.2490.62
430_F475_I1.2460.62
347_E357_R1.2420.61
340_A348_K1.2380.61
36_G217_Y1.2370.61
142_V149_T1.2290.60
94_L152_F1.2290.60
385_I389_M1.2250.60
110_F194_Q1.2230.60
88_E93_T1.2210.59
409_D414_K1.2210.59
363_P395_D1.2170.59
451_T456_L1.2150.59
282_D450_V1.2100.58
235_L240_I1.2090.58
294_K345_L1.2080.58
157_L471_I1.2070.58
68_L82_A1.2010.58
88_E91_G1.2000.57
343_S357_R1.1970.57
104_F175_K1.1950.57
140_L148_I1.1900.56
504_V523_L1.1900.56
6_R9_L1.1870.56
103_K470_Q1.1810.56
347_E363_P1.1800.56
95_H143_V1.1740.55
386_Q398_I1.1710.55
459_L477_K1.1700.55
473_P476_Q1.1670.54
439_S457_D1.1650.54
105_Q189_T1.1650.54
466_A474_T1.1650.54
455_N481_W1.1610.54
203_V219_R1.1580.53
94_L160_M1.1580.53
365_T397_V1.1490.53
119_L163_L1.1480.52
66_E210_Y1.1470.52
463_A475_I1.1470.52
9_L12_A1.1470.52
321_F455_N1.1460.52
81_L98_L1.1400.52
353_G356_I1.1400.52
472_E476_Q1.1390.52
477_K480_D1.1300.51
94_L159_L1.1280.50
93_T149_T1.1260.50
38_L220_L1.1240.50
292_V350_G1.1220.50
389_M392_V1.1150.49
303_A316_P1.1140.49
456_L482_L1.1130.49
113_A145_D1.1120.49
217_Y503_R1.1090.49
456_L460_I1.1090.49
66_E191_P1.1050.48
66_E211_W1.0970.47
344_A347_E1.0970.47
309_L384_V1.0960.47
259_L264_F1.0920.47
454_V485_N1.0880.47
97_T146_Y1.0860.46
115_C171_F1.0850.46
140_L208_D1.0850.46
8_F12_A1.0840.46
85_W160_M1.0820.46
505_Q524_A1.0810.46
473_P477_K1.0740.45
206_H215_P1.0730.45
344_A469_D1.0730.45
265_N502_K1.0710.45
5_R17_G1.0680.45
112_A148_I1.0660.44
118_N171_F1.0620.44
103_K343_S1.0600.44
90_G95_H1.0580.44
317_A493_Y1.0570.44
91_G152_F1.0560.43
110_F118_N1.0560.43
150_V163_L1.0540.43
110_F115_C1.0520.43
64_M186_P1.0490.43
152_F159_L1.0450.42
422_T432_S1.0450.42
84_D147_H1.0400.42
101_G469_D1.0380.42
69_V98_L1.0370.42
245_G249_A1.0360.42
36_G192_W1.0330.41
439_S452_D1.0310.41
95_H144_D1.0190.40
208_D263_G1.0180.40
41_A340_A1.0170.40
5_R15_A1.0170.40
105_Q207_Y1.0150.40
158_A429_P1.0120.39
299_G389_M1.0120.39
69_V163_L1.0110.39
104_F121_R1.0110.39
104_F281_P1.0100.39
261_A365_T1.0090.39
105_Q188_G1.0060.39
39_R223_K1.0010.38
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  
1xocA10.91811000.252Contact Map
2nooA10.91051000.26Contact Map
3t66A10.89141000.262Contact Map
2wolA10.94861000.265Contact Map
3m8uA10.9011000.267Contact Map
4fajA10.88761000.267Contact Map
3tpaA10.8991000.269Contact Map
1dpeA10.9011000.27Contact Map
4gl8A20.89141000.275Contact Map
2grvA30.90671000.279Contact 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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