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2M3K

ID: 1515674516 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 119 (100)
Sequences: 190 (166.2)
Seq/Len: 1.900
Nf(neff/√len): 16.6

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: 1.900).

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
77_D80_P3.5341.00
86_N90_V2.2121.00
69_L85_M2.1981.00
18_E22_F1.9070.98
9_I80_P1.8330.98
20_A67_F1.7790.97
25_K83_I1.7740.97
16_L71_A1.6490.95
9_I77_D1.5980.94
10_N62_A1.5940.93
9_I51_F1.5930.93
54_R72_V1.4460.88
9_I23_M1.4310.87
16_L100_S1.3670.84
11_A48_A1.3000.79
33_F91_T1.2700.77
52_C74_I1.2590.76
23_M33_F1.2580.76
5_E79_N1.2560.76
12_V81_F1.2080.72
51_F73_A1.1860.70
69_L88_N1.1800.70
3_E30_N1.1710.69
7_A29_Q1.1580.67
10_N39_K1.1580.67
58_I66_K1.1410.66
36_T67_F1.1380.65
7_A79_N1.1370.65
41_P44_P1.1280.64
26_F29_Q1.1180.63
64_D69_L1.1120.63
62_A69_L1.0910.61
26_F30_N1.0840.60
55_L87_E1.0750.59
11_A53_I1.0630.58
39_K61_G1.0570.57
6_K83_I1.0480.56
19_N90_V1.0280.54
21_H45_I1.0280.54
51_F75_D1.0270.54
36_T74_I1.0200.53
7_A31_G1.0150.52
25_K29_Q1.0140.52
30_N56_N1.0140.52
3_E78_K1.0040.51
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  
2m3kA10.991699.90.281Contact Map
4d40A2099.60.516Contact Map
4noaA10.857199.50.551Contact Map
2opeA40.9328990.644Contact Map
1x6zA10.873995.80.814Contact Map
3g20A20.857195.70.815Contact Map
2hi2A10.974893.90.832Contact Map
3sokA20.91693.70.833Contact Map
3jyzA10.949689.90.85Contact Map
1oqwA20.890888.90.853Contact 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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