GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
3ze3

ID: 1500381969 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (115)
Sequences: 2493 (1811.6)
Seq/Len: 21.678
Nf(neff/√len): 168.9

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: 21.678).

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
74_V85_S3.3611.00
14_K86_G3.0261.00
20_W30_G2.9881.00
19_A65_L2.8651.00
63_V66_L2.4081.00
58_M102_D2.3411.00
33_V57_V2.2961.00
17_R21_I2.1531.00
76_R85_S1.9831.00
45_V110_L1.8521.00
16_L94_A1.8431.00
63_V99_A1.8181.00
73_V88_A1.7931.00
62_I99_A1.7791.00
40_A50_R1.7171.00
72_A87_R1.6791.00
20_W31_V1.6171.00
108_A112_W1.5731.00
49_T114_H1.5391.00
59_L99_A1.5371.00
46_D49_T1.4821.00
26_F61_M1.4611.00
68_S91_L1.4461.00
18_A87_R1.4331.00
48_V52_L1.4161.00
44_D50_R1.4050.99
22_N87_R1.3900.99
60_V96_V1.3900.99
65_L94_A1.3760.99
65_L91_L1.3550.99
19_A26_F1.3440.99
26_F29_E1.3330.99
63_V95_A1.3100.99
19_A91_L1.2930.99
52_L56_S1.2900.99
54_I102_D1.2880.99
73_V77_I1.2850.99
49_T110_L1.2830.99
11_Y14_K1.2590.99
84_L88_A1.2180.98
7_K10_G1.1980.98
65_L98_I1.1900.98
37_V57_V1.1890.98
12_S93_S1.1720.98
60_V103_A1.1710.98
5_I24_A1.1670.97
5_I9_A1.1500.97
5_I28_Q1.1430.97
38_V42_W1.1040.96
55_S102_D1.1030.96
23_E72_A1.1030.96
45_V53_L1.0910.96
29_E96_V1.0620.95
77_I85_S1.0590.95
56_S106_T1.0150.93
28_Q32_A1.0070.93
25_A28_Q1.0050.93
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  
3ze3A611000.017Contact Map
4w25210.41387.80.932Contact Map
1rh5B10.33625.60.937Contact Map
3b8cA20.9312.90.945Contact Map
4b03D30.56032.70.946Contact Map
4k1cA20.90522.70.946Contact Map
2lzrA10.32762.50.947Contact Map
3mp7B10.37072.10.949Contact Map
3wajA10.76721.90.95Contact Map
1pi7A10.16381.80.95Contact 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 0.015 seconds.