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3uwsC

ID: 1501409581 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 107 (107)
Sequences: 533 (459.2)
Seq/Len: 4.981
Nf(neff/√len): 44.4

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: 4.981).

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
21_N24_S4.3691.00
18_A99_W3.3201.00
11_N41_A3.1201.00
1_T92_D2.9841.00
39_Y49_L2.6811.00
6_V25_M2.4631.00
5_L82_I2.4121.00
5_L85_V2.3401.00
3_T35_N2.2171.00
35_N51_R2.0111.00
26_I61_K1.9951.00
41_A69_K1.9391.00
24_S99_W1.9051.00
22_I38_V1.8831.00
41_A72_S1.8611.00
2_R93_S1.6400.99
91_A94_Y1.6070.99
2_R95_G1.5890.99
6_V99_W1.5830.99
3_T94_Y1.5120.99
5_L94_Y1.4530.98
8_M99_W1.4330.98
15_N42_P1.3610.97
3_T90_P1.3260.96
78_M96_L1.2790.95
80_S84_E1.2690.95
21_N99_W1.2500.94
39_Y67_Y1.2260.93
35_N91_A1.2230.93
4_I97_V1.2040.92
35_N89_Y1.1690.91
49_L84_E1.1640.91
9_M72_S1.1540.90
39_Y84_E1.1200.88
70_Q77_V1.0760.85
67_Y84_E1.0720.85
65_K84_E1.0700.85
19_S40_Y1.0640.84
5_L81_V1.0630.84
26_I36_L1.0530.84
30_T36_L1.0400.83
100_S107_P1.0360.82
74_D77_V1.0330.82
84_E88_Q1.0320.82
23_E26_I1.0320.82
82_I85_V1.0270.81
21_N25_M1.0220.81
79_R88_Q1.0120.80
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  
3uwsA211000.014Contact Map
3bjrA10.3645490.883Contact Map
3hxkA40.336426.10.899Contact Map
1ycgA40.906518.80.906Contact Map
4tkxL10.766418.20.906Contact Map
1e5dA20.906515.10.909Contact Map
2ohhA40.9065150.91Contact Map
4q3kA20.448614.20.911Contact Map
3g5cA20.9439140.911Contact Map
3j60Q10.523413.90.911Contact 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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