OPENSEQ.org
txnl4b

ID: 1517314905 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 149 (98)
Sequences: 58794 (42240.1)
Seq/Len: 599.939
Nf(neff/√len): 4266.9

Jackhmmer Results: (2016_04)
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: 599.939).

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 > 50% 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
47_K99_H2.2441.00
26_L57_A2.1121.00
51_D103_V2.0471.00
103_V107_K2.0371.00
35_D38_C1.9881.00
63_V70_T1.9691.00
91_K105_S1.9031.00
25_V85_F1.8481.00
99_H103_V1.7931.00
24_K57_A1.7691.00
26_L59_Y1.7461.00
89_H92_V1.7311.00
52_L103_V1.6501.00
31_G60_L1.6451.00
98_D101_K1.6331.00
82_V92_V1.6161.00
42_D60_L1.5731.00
13_E17_A1.5521.00
44_I99_H1.5221.00
93_D97_P1.5091.00
52_L107_K1.5001.00
11_K68_V1.4461.00
51_D99_H1.4351.00
63_V78_I1.4271.00
81_T84_F1.4101.00
37_V40_Q1.4101.00
15_D72_Y1.4070.99
84_F88_Q1.3700.99
41_L81_T1.3690.99
29_R41_L1.3110.99
49_S53_S1.3030.99
44_I47_K1.2900.99
101_K104_G1.2890.99
73_F84_F1.2870.99
105_S108_T1.2560.99
40_Q96_S1.2440.98
42_D46_S1.2430.98
82_V89_H1.2220.98
48_T52_L1.2070.98
29_R42_D1.1730.98
32_R78_I1.1710.98
11_K69_Y1.1600.97
46_S50_S1.1310.97
29_R60_L1.1300.97
68_V72_Y1.1280.97
15_D19_K1.1260.97
33_D62_D1.1200.96
97_P101_K1.1180.96
11_K66_T1.1120.96
69_Y73_F1.0700.95
25_V83_F1.0510.94
84_F89_H1.0260.94
17_A59_Y1.0190.93
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  
1qgvA10.832299.80.344Contact Map
3gixA20.879299.80.35Contact Map
2av4A10.825599.80.355Contact Map
4oo4A20.704799.80.395Contact Map
2r2jA10.845699.80.397Contact Map
3f8uA20.966499.80.398Contact Map
3apoA10.90699.80.399Contact Map
4i6xA10.738399.80.401Contact Map
2yoiA20.711499.80.407Contact Map
1xwbA40.711499.80.409Contact 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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