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HAHAHAHAH

ID: 1500978587 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 247 (243)
Sequences: 14024 (10177.4)
Seq/Len: 57.712
Nf(neff/√len): 652.9

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: 57.712).

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
136_C205_C4.3741.00
32_C48_C3.7101.00
41_W103_K3.0701.00
80_E103_K3.0111.00
41_W101_L2.9881.00
11_N157_M2.8901.00
34_G42_V2.7631.00
6_F156_K2.7201.00
49_F100_A2.6061.00
15_F139_T2.6041.00
35_S213_L2.5271.00
12_Q157_M2.5121.00
78_E105_R2.4801.00
17_A30_F2.4571.00
195_C223_C2.2871.00
40_C107_S2.2861.00
158_S192_T2.2831.00
43_A213_L2.2761.00
36_L108_T2.2741.00
97_N238_F2.2551.00
81_Q103_K2.2221.00
62_L108_T2.1861.00
16_A34_G2.1821.00
6_F154_N2.1821.00
40_C103_K2.1691.00
219_W231_V2.1261.00
12_Q139_T2.1251.00
47_H199_S2.0951.00
38_S41_W2.0791.00
168_C184_C2.0761.00
39_P107_S2.0531.00
138_I194_S2.0261.00
61_Y76_K2.0171.00
104_I108_T2.0131.00
16_A62_L2.0091.00
83_I245_H1.9541.00
99_I238_F1.9151.00
1_I4_G1.9071.00
86_E245_H1.8991.00
79_V102_L1.8791.00
181_K237_H1.8751.00
239_L243_Q1.8611.00
80_E105_R1.8531.00
77_F105_R1.8401.00
96_H181_K1.7691.00
77_F108_T1.7651.00
139_T204_I1.7481.00
136_C162_L1.7341.00
87_Y97_N1.6881.00
114_P120_T1.6671.00
16_A42_V1.6061.00
14_W204_I1.5541.00
233_T238_F1.5431.00
19_Y30_F1.5331.00
138_I158_S1.5281.00
194_S217_V1.4751.00
7_T12_Q1.4641.00
85_H97_N1.4331.00
66_K153_K1.4311.00
193_D230_G1.4311.00
121_I213_L1.4261.00
203_L232_Y1.4181.00
61_Y64_Q1.4181.00
59_V76_K1.4151.00
234_R237_H1.4081.00
205_C214_S1.4060.99
44_S49_F1.4030.99
10_E65_S1.3830.99
83_I103_K1.3800.99
144_E156_K1.3800.99
217_V220_G1.3750.99
135_D159_V1.3620.99
183_L203_L1.3550.99
9_V65_S1.3540.99
14_W122_A1.3490.99
137_E159_V1.3480.99
49_F84_L1.3470.99
15_F155_L1.3470.99
45_A216_I1.3470.99
35_S121_I1.3260.99
146_E225_E1.3150.99
99_I233_T1.3100.99
77_F106_T1.2940.99
84_L100_A1.2860.99
35_S216_I1.2830.99
47_H98_D1.2820.99
163_V229_P1.2600.99
82_L102_L1.2400.98
182_M219_W1.2400.98
15_F141_F1.2370.98
41_W245_H1.2340.98
15_F33_G1.2320.98
36_L62_L1.2310.98
68_S153_K1.2140.98
66_K154_N1.2070.98
121_I204_I1.2010.98
8_E11_N1.1960.98
138_I160_V1.1920.98
35_S43_A1.1910.98
14_W211_P1.1800.98
152_P156_K1.1720.98
18_I60_V1.1540.97
97_N181_K1.1510.97
200_G203_L1.1460.97
5_E157_M1.1420.97
221_R228_K1.1360.97
164_S167_Q1.1190.96
136_C203_L1.1120.96
36_L42_V1.1080.96
12_Q137_E1.1050.96
6_F65_S1.1030.96
42_V60_V1.0990.96
241_W245_H1.0940.96
64_Q74_E1.0730.95
85_H88_Y1.0560.95
7_T157_M1.0550.95
206_N211_P1.0530.95
12_Q211_P1.0510.94
204_I211_P1.0430.94
18_I102_L1.0400.94
49_F82_L1.0320.94
19_Y61_Y1.0280.94
10_E117_S1.0190.93
44_S100_A1.0000.92
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: (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  
2f83A10.8704100-0.022Contact Map
4nzqA10.95551000.005Contact Map
1rtfB10.97571000.007Contact Map
4durA20.91091000.008Contact Map
2vntA60.9961000.009Contact Map
4kkdA20.95951000.012Contact Map
2xxlA20.94331000.012Contact Map
3gylB10.95141000.012Contact Map
1fiwA10.97571000.015Contact Map
3nxpA10.94741000.015Contact 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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