GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
test-gremling-vh4

ID: 1502208222 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 107 (105)
Sequences: 6681 (3724.5)
Seq/Len: 63.629
Nf(neff/√len): 363.5

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: 63.629).

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
12_V85_V2.9331.00
13_K16_E2.6541.00
98_G101_T2.2471.00
67_V82_L2.1321.00
38_R91_A2.0401.00
61_P64_K1.9491.00
12_V16_E1.9211.00
39_Q45_L1.8631.00
24_V34_W1.8531.00
49_G69_I1.8521.00
97_W100_G1.8431.00
36_W80_L1.6151.00
48_I67_V1.5971.00
37_I47_W1.5951.00
12_V18_L1.5701.00
38_R46_E1.5371.00
100_G103_V1.5361.00
99_Q104_T1.5181.00
35_S47_W1.4861.00
19_S79_S1.4821.00
48_I63_L1.4801.00
19_S81_K1.4781.00
97_W103_V1.4521.00
101_T105_V1.4491.00
34_W78_F1.4311.00
35_S96_A1.4070.99
5_Q8_G1.3970.99
23_T77_Q1.3720.99
10_G18_L1.3540.99
102_L105_V1.3500.99
66_R89_D1.3150.99
33_Y50_Y1.2830.99
97_W102_L1.2800.99
18_L103_V1.2320.98
93_Y96_A1.1930.98
6_E9_P1.1900.98
15_S22_C1.1730.98
66_R82_L1.1650.97
98_G102_L1.1580.97
72_D75_K1.1480.97
51_I78_F1.1370.97
50_Y58_N1.1340.97
60_N63_L1.1300.97
65_S84_S1.1140.96
89_D93_Y1.1080.96
33_Y52_Y1.1040.96
98_G103_V1.0780.95
43_K46_E1.0680.95
2_V5_Q1.0660.95
99_Q102_L1.0360.94
7_S10_G1.0160.93
99_Q103_V1.0050.93
100_G105_V1.0050.93
73_T76_N1.0010.92
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  
4pfeA2099.80.189Contact Map
4ut7H10.990799.80.207Contact Map
1yjdC10.962699.80.237Contact Map
1dqtA40.953399.80.244Contact Map
3g9aB10.981399.70.254Contact Map
4qgyA2199.70.255Contact Map
3k3qA1199.70.261Contact Map
4qo1A10.990799.70.262Contact Map
4wemB1199.70.263Contact Map
4n8pA10.934699.70.265Contact 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.

Page generated in 0.0431 seconds.