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mak3

ID: 1514406875 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 176 (153)
Sequences: 28269 (20559)
Seq/Len: 184.765
Nf(neff/√len): 1662.1

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: 184.765).

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
6_K51_V3.2931.00
97_K133_M2.8191.00
104_I156_L2.8071.00
114_E155_I2.6171.00
104_I135_F2.5471.00
6_K15_Q2.5021.00
25_A87_E2.3871.00
65_I103_A2.3131.00
138_M155_I2.2831.00
127_L131_E2.0931.00
97_K132_G2.0451.00
67_C103_A2.0261.00
50_A95_I1.9691.00
62_I90_Y1.9411.00
101_E133_M1.9271.00
102_I105_D1.9061.00
117_L130_Y1.8971.00
137_R152_F1.8921.00
131_E137_R1.8491.00
48_Y102_I1.8211.00
137_R140_R1.7691.00
63_G86_V1.7461.00
49_I61_P1.7361.00
102_I106_K1.7331.00
90_Y93_H1.7211.00
106_K109_R1.6721.00
97_K101_E1.6011.00
104_I115_I1.5571.00
52_D62_I1.5421.00
128_N131_E1.5201.00
18_S61_P1.5171.00
47_T66_V1.5071.00
121_V150_D1.5031.00
51_V61_P1.5021.00
18_S21_K1.4881.00
127_L137_R1.4841.00
100_V133_M1.4441.00
126_A130_Y1.3690.99
106_K110_E1.3650.99
78_R114_E1.3340.99
140_R150_D1.3150.99
52_D90_Y1.3000.99
79_G112_C1.2930.99
108_Q158_L1.2700.99
137_R154_L1.2680.99
8_L49_I1.2650.99
60_I87_E1.2650.99
119_T123_N1.2650.99
8_L19_I1.2640.99
48_Y106_K1.2610.99
127_L154_L1.2490.99
7_P106_K1.2420.98
21_K25_A1.2400.98
50_A99_L1.1980.98
98_K102_I1.1930.98
65_I99_L1.1860.98
114_E157_P1.1830.98
17_A33_I1.1800.98
86_V95_I1.1790.98
60_I89_T1.1790.98
33_I37_R1.1790.98
87_E90_Y1.1720.98
115_I135_F1.1440.97
140_R152_F1.1440.97
124_S128_N1.1380.97
98_K101_E1.1380.97
123_N126_A1.1330.97
25_A88_S1.1270.97
60_I90_Y1.0890.96
121_V140_R1.0870.96
52_D93_H1.0870.96
20_K24_D1.0670.95
4_V51_V1.0630.95
121_V152_F1.0580.95
124_S127_L1.0550.95
79_G107_M1.0510.94
51_V59_N1.0450.94
18_S60_I1.0430.94
107_M115_I1.0360.94
94_G97_K1.0290.94
67_C107_M1.0280.94
127_L152_F1.0180.93
15_Q51_V1.0060.93
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  
4pv6C160.85899.90.324Contact Map
4kvxA20.846699.90.326Contact Map
2ob0A30.926199.90.333Contact Map
4r3lA10.846699.90.34Contact Map
2j8mA20.886499.90.342Contact Map
2reeA20.869399.90.343Contact Map
3dr6A30.897799.80.348Contact Map
3kkwA10.835299.80.358Contact Map
2cntA40.840999.80.358Contact Map
2r7hA20.840999.80.359Contact 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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