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ECOLI_YQFA

ID: 1505325490 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 219 (213)
Sequences: 3858 (2503.4)
Seq/Len: 18.113
Nf(neff/√len): 171.5

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: 18.113).

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
65_F205_S3.7301.00
177_V207_C3.2251.00
26_G202_L2.6971.00
60_S97_G2.6781.00
150_W179_S2.6321.00
146_L179_S2.6261.00
102_F211_A2.5641.00
34_L58_G2.5021.00
177_V203_G2.4671.00
27_L62_I2.4341.00
27_L66_L2.3981.00
177_V204_G2.2971.00
117_I121_S2.2461.00
16_E19_N2.1731.00
48_A52_T2.0901.00
55_S59_G2.0751.00
20_S73_A2.0741.00
113_R117_I1.9761.00
199_G203_G1.9281.00
146_L182_V1.8701.00
100_T120_W1.8651.00
169_T173_V1.8211.00
110_P114_G1.7521.00
165_A169_T1.7351.00
130_K141_S1.7311.00
190_I193_N1.7291.00
187_C190_I1.7081.00
22_S199_G1.6951.00
206_V210_L1.6681.00
71_Y84_K1.6671.00
93_L127_I1.6551.00
114_G118_V1.6221.00
60_S93_L1.6121.00
82_W86_F1.5961.00
19_N22_S1.5901.00
35_V39_V1.5881.00
170_L210_L1.5801.00
18_A195_A1.5661.00
113_R116_M1.5461.00
12_S15_E1.5381.00
185_Y188_K1.5321.00
61_M205_S1.5201.00
67_A86_F1.4961.00
194_H198_H1.4801.00
155_V158_E1.4791.00
170_L207_C1.4691.00
51_I55_S1.4571.00
182_V197_W1.4171.00
14_A192_Y1.4010.99
13_L17_I1.3960.99
168_V172_A1.3920.99
61_M94_L1.3710.99
96_A123_A1.3690.99
14_A17_I1.3580.99
173_V177_V1.3490.99
167_S215_Y1.3410.99
105_V216_I1.3350.99
96_A120_W1.3290.99
114_G117_I1.3080.99
66_L70_L1.2870.99
34_L62_I1.2690.99
24_G69_T1.2650.99
122_L148_M1.2530.99
33_G209_F1.2450.98
108_D112_A1.2430.98
22_S195_A1.2420.98
60_S94_L1.2380.98
203_G207_C1.2320.98
50_A105_V1.2310.98
173_V207_C1.1990.98
157_Y161_V1.1950.98
62_I66_L1.1800.98
172_A176_V1.1750.98
67_A90_A1.1740.98
209_F213_Y1.1700.97
178_Y205_S1.1660.97
103_L107_L1.1510.97
40_Q213_Y1.1380.97
92_Y126_G1.1370.97
111_L158_E1.1330.97
33_G37_L1.1320.97
109_S112_A1.1290.97
119_I148_M1.1280.97
52_T55_S1.1190.96
16_E22_S1.1190.96
30_G61_M1.1130.96
17_I21_V1.1100.96
115_L155_V1.1000.96
57_Y61_M1.0970.96
128_L132_T1.0910.96
138_K188_K1.0820.96
49_T108_D1.0800.95
38_L55_S1.0780.95
21_V24_G1.0710.95
53_S104_L1.0700.95
95_I178_Y1.0470.94
64_L94_L1.0410.94
18_A22_S1.0390.94
149_G175_G1.0340.94
111_L114_G1.0200.93
205_S208_H1.0180.93
14_A18_A1.0070.93
126_G144_T1.0030.93
103_L115_L1.0020.92
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  
3wxwA10.98171000.188Contact Map
4fbzA10.2741.50.965Contact Map
2auvA10.13241.20.967Contact Map
2lifA10.12330.90.97Contact Map
2ls2A10.11420.90.97Contact Map
3pjzA20.40180.80.971Contact Map
2losA10.49770.80.971Contact Map
2nlkA10.09130.80.972Contact Map
3dwlE20.11420.80.972Contact Map
2mmuA10.21460.70.972Contact 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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