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T0808 40-330 -force run

ID: 1405184637 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 291 (290)
Sequences: 84 (72.7)
Seq/Len: 0.290
Nf(neff/√len): 4.3

Jackhmmer Results: (2014_04_16)
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: 0.290).

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
22_F78_I2.2750.84
135_W251_Y2.0690.76
176_L219_Q2.0470.75
151_S206_V1.9150.67
181_S216_S1.9100.67
200_L266_F1.8570.64
134_E237_Q1.8470.63
187_N190_E1.8260.62
222_L263_I1.8010.60
135_W277_R1.7770.59
238_I275_Y1.7670.58
236_M250_A1.7070.54
136_F278_P1.6810.53
213_N262_L1.5490.44
230_N254_A1.5250.42
209_G213_N1.5230.42
80_L261_K1.4820.40
28_T100_N1.4210.36
181_S188_P1.4180.36
251_Y278_P1.4000.34
19_S79_D1.3680.33
181_S191_I1.3460.31
126_Y138_N1.3430.31
160_E273_T1.3410.31
23_Y93_I1.3280.30
115_W197_I1.3200.30
66_G264_A1.3170.30
43_K50_G1.3150.30
199_L255_T1.3070.29
70_I165_M1.3020.29
107_Y279_H1.2900.28
147_E150_H1.2880.28
8_V279_H1.2820.28
27_P107_Y1.2720.27
118_R268_R1.2690.27
119_G268_R1.2620.27
150_H153_Y1.2590.27
210_E248_Y1.2590.27
167_Y275_Y1.2570.26
208_I276_K1.2570.26
275_Y278_P1.2550.26
155_A234_F1.2460.26
251_Y277_R1.2440.26
108_V116_G1.2380.25
150_H186_Q1.2380.25
7_G136_F1.2280.25
110_D113_D1.2260.25
147_E167_Y1.2240.25
136_F251_Y1.2220.25
222_L287_P1.2190.24
68_I113_D1.2170.24
238_I245_N1.2140.24
13_N21_Y1.2070.24
19_S77_R1.2020.24
45_S104_K1.2020.24
22_F98_A1.1980.23
82_G90_F1.1930.23
120_P143_P1.1920.23
114_Y271_T1.1910.23
141_T231_T1.1900.23
236_M275_Y1.1870.23
55_L146_G1.1810.23
120_P219_Q1.1810.23
165_M175_I1.1760.22
181_S185_T1.1700.22
116_G266_F1.1690.22
53_V221_Y1.1670.22
87_G92_E1.1570.22
124_L155_A1.1560.22
119_G182_P1.1550.21
96_L267_L1.1530.21
116_G181_S1.1510.21
39_H140_I1.1490.21
179_V263_I1.1440.21
8_V59_D1.1360.21
42_I175_I1.1340.21
200_L277_R1.1320.20
36_A55_L1.1300.20
34_L55_L1.1280.20
12_T25_H1.1250.20
165_M263_I1.1210.20
135_W278_P1.1190.20
51_F68_I1.1160.20
14_P170_P1.1150.20
19_S81_Q1.1130.20
24_L78_I1.1110.20
137_Y233_K1.1070.19
172_E269_P1.1070.19
5_Q253_Y1.1060.19
9_T55_L1.1030.19
165_M193_D1.1030.19
134_E239_R1.1000.19
172_E284_N1.0990.19
188_P216_S1.0980.19
171_T227_K1.0970.19
17_I81_Q1.0950.19
191_I216_S1.0930.19
183_F216_S1.0890.19
167_Y202_Q1.0870.19
19_S244_G1.0840.18
116_G191_I1.0770.18
154_M219_Q1.0770.18
70_I73_A1.0760.18
107_Y276_K1.0730.18
121_S139_E1.0690.18
154_M269_P1.0680.18
182_P268_R1.0680.18
176_L221_Y1.0670.18
174_R265_S1.0660.18
19_S22_F1.0630.18
145_E167_Y1.0630.18
80_L183_F1.0600.18
182_P218_G1.0580.17
118_R182_P1.0570.17
160_E183_F1.0550.17
150_H236_M1.0500.17
3_I18_V1.0490.17
245_N267_L1.0480.17
6_R89_G1.0480.17
235_L260_W1.0460.17
192_P213_N1.0450.17
186_Q276_K1.0430.17
124_L163_F1.0400.17
249_T266_F1.0380.17
83_V149_M1.0380.17
232_Y271_T1.0380.17
76_V96_L1.0380.17
222_L282_L1.0360.17
143_P250_A1.0350.17
15_K140_I1.0350.17
120_P176_L1.0340.17
125_G175_I1.0340.17
24_L175_I1.0330.16
30_A100_N1.0310.16
169_S173_R1.0310.16
137_Y260_W1.0290.16
200_L249_T1.0290.16
104_K140_I1.0290.16
181_S262_L1.0290.16
200_L209_G1.0270.16
78_I113_D1.0220.16
163_F173_R1.0200.16
52_K128_L1.0170.16
122_V282_L1.0150.16
124_L213_N1.0150.16
115_W129_P1.0110.16
33_S247_T1.0100.16
120_P282_L1.0080.16
145_E231_T1.0060.16
36_A251_Y1.0050.15
55_L170_P1.0050.15
216_S262_L1.0030.15
133_T238_I1.0010.15
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: (05Jul14)
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  
2bgoA10.343693.30.953Contact Map
2vzsA20910.956Contact Map
4kmqA10.333389.60.958Contact Map
2vzpA20.32384.80.961Contact Map
2w87A20.360883.30.962Contact Map
2w47A10.350577.30.964Contact Map
2w3jA10.360873.40.965Contact Map
2wz8A10.333373.20.965Contact Map
2y8kA10.326569.90.966Contact Map
2xwxA20.336862.10.967Contact 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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