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testMSA_representSequence

ID: 1506153679 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 103 (103)
Sequences: 1496 (684.9)
Seq/Len: 14.524
Nf(neff/√len): 67.5

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: 14.524).

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
46_E100_K2.6461.00
11_E14_K2.0561.00
73_Q76_T2.0231.00
12_E54_V1.9971.00
34_D37_G1.9601.00
10_Q14_K1.9451.00
71_V75_R1.9161.00
69_M73_Q1.8311.00
90_E93_N1.7181.00
15_R47_E1.7151.00
53_R90_E1.7131.00
37_G40_M1.7031.00
74_L78_L1.6851.00
20_Y24_M1.6621.00
66_Q69_M1.6571.00
22_Q44_T1.5521.00
72_E75_R1.5481.00
35_R39_K1.5421.00
72_E76_T1.4801.00
88_M92_M1.4791.00
68_K72_E1.3730.99
53_R93_N1.3670.99
16_L48_L1.3610.99
47_E51_R1.3580.99
92_M96_L1.3570.99
35_R38_K1.3510.99
98_R101_S1.3360.99
77_Q80_Q1.3290.99
42_I103_L1.3170.99
12_E15_R1.3140.99
90_E94_Q1.3130.99
94_Q98_R1.3090.99
50_E53_R1.3020.99
68_K71_V1.2530.99
71_V74_L1.2140.98
50_E54_V1.2000.98
97_S101_S1.1940.98
11_E15_R1.1850.98
69_M72_E1.1620.97
29_E32_K1.1540.97
6_S61_L1.1520.97
8_I12_E1.1270.97
67_A70_T1.1040.96
88_M95_T1.1000.96
25_Q37_G1.0960.96
91_Q94_Q1.0910.96
96_L99_M1.0870.96
95_T98_R1.0700.95
75_R79_G1.0640.95
11_E18_N1.0550.95
9_V55_F1.0310.94
48_L52_Y1.0050.93
16_L59_F1.0040.93
33_F41_F1.0000.92
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  
3onjA10.7864410.896Contact Map
1vcsA10.776725.10.907Contact Map
2qywA10.786421.50.91Contact Map
1v2zA10.69917.70.913Contact Map
3zg1A40.524317.50.913Contact Map
2o8xA30.592216.20.915Contact Map
1r5qA10.582515.30.916Contact Map
1l9zH10.922312.80.919Contact Map
2a6hF20.902912.80.919Contact Map
2xxaA20.786410.50.922Contact 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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