GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
pfam_helo

ID: 1505138585 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 66 (65)
Sequences: 411 (361.6)
Seq/Len: 6.323
Nf(neff/√len): 44.9

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: 6.323).

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
16_K20_E2.5961.00
26_L30_I1.5620.99
40_T54_V1.5210.99
22_L25_D1.4990.99
27_A31_T1.4460.99
4_T8_K1.4330.99
48_N51_D1.4290.99
14_R37_I1.3570.98
5_L23_I1.3140.97
3_T26_L1.3040.97
4_T33_L1.2310.96
17_Q24_R1.2270.96
37_I57_I1.2230.96
23_I31_T1.1900.95
20_E31_T1.1830.94
20_E24_R1.1730.94
22_L63_L1.1610.94
43_Q48_N1.1480.93
14_R53_D1.1290.92
15_D23_I1.1120.92
12_A17_Q1.1100.91
60_L64_K1.0930.91
25_D32_S1.0880.90
8_K11_W1.0820.90
21_I64_K1.0770.90
59_G62_N1.0720.89
47_R52_D1.0720.89
20_E27_A1.0640.89
15_D18_K1.0410.88
17_Q21_I1.0380.87
17_Q28_D1.0230.86
15_D54_V1.0200.86
19_F47_R1.0180.86
45_A48_N1.0180.86
46_L50_A1.0160.86
7_N15_D1.0130.86
27_A32_S1.0090.85
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  
2wvqA20.954599.20.072Contact Map
4y21A106.80.829Contact Map
1vptA10.90916.20.833Contact Map
1a31A10.33334.90.841Contact Map
3magA10.92424.70.842Contact Map
3re2A10.96974.20.846Contact Map
3l9aX10.84854.10.846Contact Map
4dynA20.969740.847Contact Map
3fp5A10.83333.60.851Contact Map
3k93A10.62123.40.853Contact 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.

Page generated in 0.035 seconds.