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OPENSEQ.org

HET-S -force run

ID: 1428409374 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 289 (283)
Sequences: 229 (201)
Seq/Len: 0.809
Nf(neff/√len): 11.9

Jackhmmer Results: (2015_01_07)
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: 0.809).

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
13_G16_G1.9550.92
37_D153_G1.9350.92
25_F167_V1.9310.92
80_A174_F1.9010.91
47_I83_I1.7620.86
51_R168_D1.7250.84
27_Y136_R1.7240.84
48_A80_A1.6200.79
278_G282_G1.6030.78
51_R171_E1.5890.77
3_E10_G1.5140.72
240_Q244_V1.4750.69
54_R208_D1.4720.69
105_A129_L1.3940.63
3_E6_E1.3860.62
17_L52_L1.3750.61
63_D160_V1.3620.60
27_Y98_S1.3500.59
5_F10_G1.3480.59
263_S266_T1.3420.58
187_E208_D1.3310.57
11_A219_I1.3290.57
4_P8_V1.3200.56
145_K160_V1.3190.56
25_F45_L1.3110.56
23_A91_F1.3070.55
247_A252_G1.3050.55
37_D149_A1.3040.55
239_V243_N1.2990.55
101_Y152_D1.2930.54
44_R175_P1.2930.54
261_T265_E1.2880.54
51_R91_F1.2860.53
90_L166_F1.2770.53
25_F163_V1.2620.51
191_V201_K1.2590.51
23_A185_E1.2420.50
26_E32_R1.2380.49
138_K144_K1.2370.49
30_L48_A1.2340.49
31_G68_H1.2210.48
35_G137_Q1.2190.48
80_A84_V1.2110.47
18_F28_V1.2090.47
9_A156_L1.2000.46
246_T249_A1.1950.45
235_K238_R1.1860.45
268_V280_E1.1840.44
42_Q61_I1.1820.44
263_S272_E1.1660.43
5_F9_A1.1590.42
56_G157_E1.1580.42
9_A25_F1.1510.42
259_Q264_V1.1500.42
136_R174_F1.1450.41
98_S103_L1.1430.41
18_F27_Y1.1430.41
48_A83_I1.1420.41
266_T276_L1.1420.41
122_G126_H1.1390.41
271_G276_L1.1390.41
263_S270_K1.1360.40
244_V252_G1.1340.40
279_N283_G1.1330.40
273_S278_G1.1300.40
279_N282_G1.1260.40
58_A219_I1.1250.39
268_V281_Y1.1230.39
132_L136_R1.1220.39
257_S261_T1.1210.39
97_T101_Y1.1200.39
21_C52_L1.1140.39
272_E276_L1.1050.38
269_G276_L1.1040.38
88_L132_L1.1030.38
34_F194_E1.1010.37
166_F173_A1.1000.37
253_E266_T1.0990.37
271_G280_E1.0990.37
133_V136_R1.0980.37
272_E280_E1.0970.37
265_E275_V1.0970.37
258_D261_T1.0930.37
245_V264_V1.0910.37
7_I218_K1.0870.36
41_C48_A1.0840.36
7_I130_K1.0820.36
266_T272_E1.0810.36
240_Q243_N1.0780.36
15_A141_S1.0750.35
2_S6_E1.0750.35
153_G162_Q1.0750.35
261_T266_T1.0740.35
100_R181_H1.0730.35
29_Q32_R1.0720.35
8_V168_D1.0720.35
240_Q246_T1.0720.35
69_S72_P1.0710.35
52_L63_D1.0700.35
54_R151_Y1.0690.35
18_F56_G1.0690.35
251_H256_I1.0670.35
33_H145_K1.0630.34
271_G275_V1.0620.34
268_V274_K1.0570.34
203_A218_K1.0560.34
141_S145_K1.0520.34
156_L159_I1.0490.33
163_V167_V1.0470.33
264_V274_K1.0430.33
16_G28_V1.0410.33
19_N23_A1.0410.33
261_T264_V1.0410.33
21_C167_V1.0400.33
21_C101_Y1.0400.33
254_I259_Q1.0380.32
21_C152_D1.0380.32
21_C50_V1.0370.32
34_F97_T1.0350.32
96_K172_K1.0340.32
260_T266_T1.0340.32
106_D131_D1.0330.32
265_E274_K1.0320.32
246_T254_I1.0310.32
278_G281_Y1.0290.32
246_T250_L1.0280.32
261_T272_E1.0280.32
147_A212_S1.0260.32
218_K222_I1.0240.31
13_G210_A1.0240.31
93_S201_K1.0220.31
258_D266_T1.0220.31
266_T270_K1.0220.31
12_L22_V1.0210.31
43_L87_I1.0200.31
234_E239_V1.0190.31
12_L20_N1.0170.31
50_V187_E1.0130.31
101_Y163_V1.0130.31
22_V159_I1.0120.30
69_S163_V1.0110.30
276_L280_E1.0090.30
125_L128_R1.0090.30
238_R244_V1.0070.30
266_T274_K1.0050.30
15_A193_D1.0050.30
249_A253_E1.0030.30
240_Q245_V1.0020.30
52_L159_I1.0010.30
90_L159_I1.0010.30
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: (31Jan15)
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  
2wvqA20.7371000.399Contact Map
2kj3A30.252699.60.778Contact Map
4ogqG10.114212.80.964Contact Map
5rubA20.207612.70.964Contact Map
3he4A40.1557120.964Contact Map
1q90G10.0911.50.964Contact Map
1w3iA40.332210.90.965Contact Map
2q58A20.41528.10.967Contact Map
4btfA10.59527.70.967Contact Map
3cf6E10.3467.50.967Contact 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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