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nd4

ID: 1499526956 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 392 (392)
Sequences: 730 (207.4)
Seq/Len: 1.862
Nf(neff/√len): 10.5

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: 1.862).

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
35_P267_T3.0641.00
73_L92_A2.9891.00
197_M255_I2.7781.00
128_L156_A2.5431.00
265_G334_F2.5161.00
319_T326_S2.0490.99
37_L79_T2.0190.99
84_I133_I1.9810.99
269_L331_G1.9170.98
166_L363_Y1.8920.98
317_S364_M1.8110.97
32_L198_L1.7800.97
253_A339_A1.7660.97
84_I88_I1.7480.96
254_A262_S1.7260.96
128_L144_F1.7080.96
40_T368_T1.7010.96
250_L336_V1.6330.94
11_N189_L1.6320.94
198_L268_A1.6310.94
309_M383_S1.6210.94
231_L359_L1.6070.94
226_T229_I1.6010.93
236_L269_L1.5820.93
3_P7_L1.5810.93
156_A189_L1.5620.92
11_N141_S1.5570.92
306_L383_S1.5470.92
1_I72_V1.4570.88
231_L252_I1.4550.88
130_V198_L1.4480.88
358_A362_L1.4440.88
292_H361_S1.4300.87
240_I284_A1.4010.85
216_L305_F1.3920.85
231_L272_A1.3730.84
161_M269_L1.3680.83
236_L336_V1.3570.83
37_L59_R1.3410.82
53_S58_P1.3320.81
128_L189_L1.3200.80
36_L373_H1.3110.80
48_L64_I1.3050.79
132_L153_C1.3050.79
225_M368_T1.3040.79
132_L203_M1.2940.79
131_A152_A1.2900.78
111_L280_L1.2860.78
361_S364_M1.2810.78
67_L218_L1.2750.77
249_A252_I1.2750.77
189_L201_T1.2650.76
292_H368_T1.2640.76
36_L156_A1.2610.76
129_L156_A1.2560.76
11_N128_L1.2530.75
234_T272_A1.2510.75
161_M204_L1.2470.75
287_N375_H1.2460.75
117_F204_L1.2400.74
263_Y284_A1.2400.74
65_T72_V1.2280.73
348_L392_A1.2220.73
6_M9_P1.2190.72
94_L358_A1.2190.72
267_T271_I1.2180.72
198_L263_Y1.2170.72
64_I336_V1.2140.72
24_S380_I1.2120.72
189_L298_L1.2110.72
197_M296_M1.2110.72
150_W221_W1.2100.72
179_I246_S1.2100.72
144_F343_S1.2090.72
223_M353_N1.2020.71
297_I342_W1.1980.71
44_L367_M1.1970.70
36_L128_L1.1970.70
246_S357_T1.1950.70
140_G364_M1.1910.70
309_M342_W1.1890.70
9_P286_S1.1880.70
151_L374_T1.1880.70
305_F346_T1.1840.69
35_P225_M1.1830.69
168_L362_L1.1830.69
262_S389_A1.1810.69
265_G343_S1.1800.69
50_A390_L1.1780.69
129_L148_F1.1770.69
4_T7_L1.1710.68
64_I209_E1.1710.68
65_T336_V1.1700.68
35_P271_I1.1570.67
271_I344_N1.1550.67
306_L309_M1.1550.67
25_L321_L1.1530.66
45_P340_F1.1490.66
66_M158_L1.1470.66
16_L63_Y1.1450.66
215_F256_L1.1450.66
117_F299_A1.1410.65
57_E141_S1.1290.64
84_I336_V1.1270.64
88_I164_Y1.1250.64
129_L189_L1.1230.63
27_F55_L1.1210.63
61_K115_L1.1180.63
52_Q265_G1.1170.63
156_A161_M1.1130.62
89_M327_I1.1060.62
154_M200_I1.1040.61
135_L341_S1.1040.61
276_T279_M1.1040.61
123_V198_L1.1010.61
92_A130_V1.1010.61
266_A336_V1.1000.61
23_Y215_F1.1000.61
31_P141_S1.0980.61
189_L380_I1.0920.60
102_T250_L1.0890.60
296_M367_M1.0890.60
76_M79_T1.0870.60
1_I27_F1.0870.60
67_L361_S1.0850.59
7_L57_E1.0840.59
57_E60_K1.0840.59
124_G299_A1.0820.59
151_L304_I1.0820.59
152_A256_L1.0820.59
148_F305_F1.0820.59
23_Y130_V1.0820.59
118_L142_L1.0780.59
223_M249_A1.0750.58
305_F381_T1.0740.58
251_V269_L1.0710.58
27_F76_M1.0700.58
330_I347_I1.0700.58
180_A266_A1.0690.58
161_M179_I1.0670.57
128_L269_L1.0660.57
9_P117_F1.0660.57
200_I215_F1.0660.57
336_V343_S1.0650.57
129_L269_L1.0630.57
388_H391_M1.0620.57
317_S361_S1.0610.57
133_I299_A1.0560.56
140_G207_L1.0560.56
297_I361_S1.0560.56
36_L229_I1.0540.56
189_L269_L1.0530.56
268_A272_A1.0520.56
123_V130_V1.0520.56
232_R261_W1.0510.56
236_L250_L1.0500.56
102_T111_L1.0470.55
151_L352_T1.0460.55
92_A148_F1.0450.55
23_Y61_K1.0440.55
152_A197_M1.0440.55
251_V331_G1.0430.55
1_I12_S1.0420.55
131_A382_P1.0390.54
84_I189_L1.0350.54
156_A198_L1.0350.54
7_L309_M1.0320.54
73_L158_L1.0300.53
184_V297_I1.0300.53
224_I266_A1.0290.53
345_P352_T1.0260.53
155_M310_A1.0240.53
250_L353_N1.0240.53
201_T211_M1.0230.53
131_A303_Q1.0220.53
267_T344_N1.0220.53
15_L268_A1.0200.52
164_Y339_A1.0180.52
18_L48_L1.0170.52
15_L111_L1.0160.52
261_W362_L1.0150.52
63_Y100_I1.0140.52
95_I240_I1.0130.52
102_T189_L1.0130.52
94_L282_C1.0110.51
215_F298_L1.0100.51
214_P343_S1.0080.51
9_P32_L1.0080.51
80_A228_S1.0080.51
75_I284_A1.0030.51
117_F124_G1.0000.50
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  
3rkoM20.99741000.648Contact Map
4he8M20.96681000.672Contact Map
3rkoN20.98471000.71Contact Map
4he8N20.94131000.717Contact Map
3rkoL20.97961000.717Contact Map
4he8L20.98211000.728Contact Map
2l0nA10.07653.20.989Contact Map
1hznA10.056130.989Contact Map
2jo4A40.0511.40.991Contact Map
5bxvB201.10.991Contact 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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