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YOHK_ECOLI

ID: 1425766848 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 231 (225)
Sequences: 1920 (1360.6)
Seq/Len: 8.533
Nf(neff/√len): 90.7

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: 8.533).

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
132_I212_G4.6811.00
133_A151_V4.1001.00
135_A138_G3.4601.00
137_G147_S3.1271.00
125_P137_G2.7071.00
174_K197_D2.6701.00
181_M193_C2.6331.00
162_G181_M2.6251.00
12_T55_Y2.5451.00
158_G185_S2.4111.00
15_V40_V2.3361.00
128_V136_V2.1811.00
190_T204_S2.1751.00
167_N177_R2.0741.00
162_G166_L1.9811.00
192_R195_E1.9441.00
110_A115_A1.9371.00
19_A36_V1.7921.00
110_A120_A1.7821.00
166_L181_M1.7421.00
15_V37_A1.7201.00
177_R200_E1.6791.00
197_D200_E1.6771.00
121_A140_I1.6661.00
21_K25_R1.6511.00
36_V40_V1.6351.00
97_I101_V1.6191.00
122_S143_I1.6151.00
99_S211_C1.5831.00
19_A37_A1.5801.00
122_S142_G1.5711.00
56_F63_N1.5611.00
18_A22_L1.5391.00
15_V41_I1.5001.00
15_V44_F1.5001.00
110_A123_I1.4921.00
127_S154_V1.4791.00
43_P46_M1.4741.00
43_P47_L1.4741.00
8_S50_I1.4741.00
206_L212_G1.4620.99
179_L183_T1.4550.99
87_R90_S1.4520.99
82_H86_A1.4390.99
106_G154_V1.4380.99
15_V19_A1.4080.99
117_P121_A1.3840.99
129_T132_I1.3730.99
96_F214_I1.3590.99
164_T168_A1.3570.99
108_S112_L1.3520.99
107_T124_L1.3520.99
44_F48_T1.3110.99
18_A40_V1.3080.99
56_F59_S1.3020.99
179_L207_A1.2770.98
57_K60_E1.2740.98
131_P135_A1.2640.98
99_S103_M1.2550.98
39_V43_P1.2520.98
179_L203_F1.2510.98
70_V75_Y1.2450.98
125_P147_S1.2390.98
21_K26_Y1.2350.98
185_S204_S1.2340.98
128_V132_I1.2340.98
14_I18_A1.2290.98
134_M148_A1.2280.98
81_L85_R1.2250.98
88_W92_I1.2250.98
45_L52_Y1.2120.97
87_R203_F1.2080.97
103_M219_A1.2070.97
144_P148_A1.2020.97
126_K154_V1.1910.97
56_F60_E1.1890.97
152_I156_I1.1810.97
130_T152_I1.1660.96
104_V108_S1.1610.96
67_Q131_P1.1520.96
136_V215_T1.1470.96
11_L41_I1.1420.96
146_I150_C1.1220.95
23_A31_L1.1180.95
70_V154_V1.1180.95
116_S119_I1.1080.95
108_S111_L1.1000.95
18_A21_K1.0830.94
193_C197_D1.0600.93
42_I46_M1.0590.93
48_T51_S1.0490.93
28_F31_L1.0470.93
174_K200_E1.0400.92
26_Y31_L1.0390.92
119_I122_S1.0380.92
20_R24_A1.0360.92
166_L171_I1.0340.92
154_V185_S1.0330.92
8_S58_G1.0330.92
76_P205_S1.0320.92
103_M124_L1.0250.91
21_K24_A1.0180.91
66_L187_A1.0140.91
22_L36_V1.0030.90
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  
3zuxA10.744694.10.918Contact Map
4n7wA20.722991.90.924Contact Map
2zy9A20.727349.60.949Contact Map
4cz8A20.943744.30.95Contact Map
4bwzA10.913437.60.952Contact Map
4czbA30.948123.80.957Contact Map
4u9nA20.714315.10.961Contact Map
2a65A10.376614.60.961Contact Map
3b9wA10.800914.20.961Contact Map
3nd0A20.904812.80.962Contact 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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