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pfam_02261_new

ID: 1507635925 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 97 (97)
Sequences: 7077 (4917.5)
Seq/Len: 72.959
Nf(neff/√len): 499.3

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: 72.959).

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
4_E25_Y3.3971.00
76_V89_A3.1361.00
8_K81_F3.1221.00
40_P48_Y2.5021.00
25_Y49_L2.1601.00
26_R30_V1.9681.00
52_L71_L1.8501.00
4_E50_E1.8281.00
86_G90_R1.7151.00
28_S82_R1.6881.00
71_L96_L1.6871.00
83_D87_R1.6651.00
4_E46_P1.6501.00
56_L96_L1.6111.00
45_I78_I1.6041.00
3_T6_D1.5951.00
6_D95_L1.5731.00
55_W70_W1.5641.00
56_L71_L1.5281.00
9_E13_I1.5261.00
9_E12_R1.5221.00
4_E53_F1.5021.00
10_I88_T1.4551.00
48_Y51_E1.4441.00
70_W74_E1.4211.00
79_H86_G1.4010.99
50_E54_D1.3800.99
44_E47_A1.3770.99
29_N42_P1.3680.99
72_H89_A1.3210.99
4_E8_K1.3150.99
68_A93_M1.3010.99
21_W82_R1.2320.98
7_L53_F1.2300.98
72_H76_V1.2250.98
29_N41_P1.2180.98
44_E48_Y1.2070.98
67_K96_L1.1940.98
8_K24_E1.1620.97
4_E49_L1.1400.97
46_P50_E1.1380.97
75_F89_A1.1320.97
24_E27_T1.0980.96
26_R45_I1.0870.96
89_A93_M1.0860.96
32_I35_G1.0830.96
59_N67_K1.0730.95
11_H23_G1.0500.94
51_E54_D1.0310.94
12_R16_R1.0270.94
48_Y78_I1.0200.93
8_K11_H1.0190.93
37_Y77_Y1.0180.93
52_L78_I1.0170.93
84_G87_R1.0050.93
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  
4rglA10.989799.9-0.003Contact Map
4npsA10.969199.9-0.001Contact Map
3n3uA10.927899.9-0.001Contact Map
4u04A20.979499.90.004Contact Map
2jk8A2199.80.011Contact Map
4n67A1199.80.011Contact Map
4py3A10099.80.013Contact Map
4m16A1199.80.016Contact Map
3cucA2199.80.018Contact Map
3shgA10.979499.80.033Contact 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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