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4cu5A

ID: 1500380795 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 85 (82)
Sequences: 2181 (1745.5)
Seq/Len: 26.598
Nf(neff/√len): 192.8

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: 26.598).

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
65_I82_F3.2191.00
78_K81_D2.9011.00
76_L80_L2.7271.00
47_V54_E2.6681.00
17_A48_V2.6331.00
51_G56_I2.5691.00
16_S76_L2.4231.00
4_H46_Y2.1851.00
74_D78_K2.1701.00
3_K43_Q2.0741.00
56_I59_I1.9961.00
71_D74_D1.9701.00
12_V72_R1.8221.00
47_V59_I1.8191.00
4_H44_N1.7731.00
5_T42_T1.7241.00
68_K78_K1.6081.00
32_C54_E1.5851.00
44_N65_I1.5601.00
45_L64_F1.5541.00
45_L62_E1.5351.00
32_C38_V1.3400.99
20_V26_D1.2990.99
77_Y81_D1.2310.98
70_N74_D1.2210.98
9_D53_C1.1920.98
72_R75_T1.1910.98
49_G66_M1.1760.98
53_C75_T1.1750.98
20_V83_I1.1400.97
67_I78_K1.1330.97
6_I21_G1.1300.97
4_H24_Y1.1290.97
20_V79_A1.1280.97
50_G72_R1.1160.96
50_G68_K1.0990.96
13_D50_G1.0890.96
19_V22_W1.0670.95
18_T22_W1.0670.95
44_N63_K1.0630.95
67_I82_F1.0500.94
68_K75_T1.0130.93
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  
4cu2A10.917699.70.011Contact Map
4cu5A61990.329Contact Map
1kl7A20.870618.40.838Contact Map
2eguA10.847116.10.842Contact Map
4ql4A10.847114.40.845Contact Map
4r2vA20.847114.30.846Contact Map
1y7lA10.8471140.846Contact Map
3dwgA20.847113.80.846Contact Map
2pqmA20.847113.10.848Contact Map
3x44A2012.60.849Contact 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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