OPENSEQ.org
10_1titpdb

ID: 1516869732 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 89 (87)
Sequences: 14808 (10008.8)
Seq/Len: 170.207
Nf(neff/√len): 1073.1

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: 170.207).

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
35_K74_Q3.5241.00
13_V63_C2.7061.00
20_H59_I2.3701.00
18_T59_I2.3431.00
18_T61_H2.2141.00
27_E31_H2.1231.00
20_H57_I2.0801.00
33_Q76_A2.0501.00
33_Q40_P1.9341.00
35_K72_S1.8641.00
36_L71_V1.8151.00
14_F17_E1.7891.00
46_D67_M1.7391.00
13_V19_A1.7041.00
35_K40_P1.6691.00
36_L69_G1.6461.00
25_L75_A1.6111.00
70_E83_N1.6111.00
37_K72_S1.5921.00
21_F84_L1.5761.00
22_E57_I1.5531.00
33_Q74_Q1.5071.00
15_V65_L1.4871.00
3_E26_S1.4721.00
25_L32_G1.4581.00
32_G73_F1.4050.99
51_E56_H1.4010.99
48_E61_H1.2690.99
23_I73_F1.2480.99
19_A63_C1.2340.98
37_K41_L1.2310.98
77_N80_S1.2300.98
19_A60_L1.1930.98
50_I59_I1.1850.98
4_V7_P1.1790.98
64_Q67_M1.1550.97
13_V17_E1.1490.97
19_A84_L1.1470.97
32_G56_H1.1460.97
14_F87_K1.1420.97
6_K24_E1.1290.97
4_V25_L1.1200.96
24_E55_K1.1080.96
67_M71_V1.0870.96
11_V19_A1.0870.96
5_E24_E1.0760.95
8_L80_S1.0550.95
10_G83_N1.0420.94
38_G72_S1.0070.93
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  
1waaA4198.70.012Contact Map
3utoA2198.70.033Contact Map
2edfA1198.70.041Contact Map
2e7bA1198.60.046Contact Map
3b43A1198.60.057Contact Map
2enyA1198.60.062Contact Map
1x44A1198.60.064Contact Map
2edhA10.988898.60.065Contact Map
2e6pA1198.60.069Contact Map
1pd6A10.988898.60.07Contact 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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