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4ipu

ID: 1501760637 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 137 (128)
Sequences: 753 (746)
Seq/Len: 5.883
Nf(neff/√len): 65.9

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: 5.883).

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
28_E32_Q3.3261.00
117_S125_Q2.4101.00
6_T10_E2.2661.00
12_Q16_E2.2221.00
25_A38_I2.2101.00
11_L104_I2.1121.00
21_M50_L2.1051.00
22_L38_I2.0781.00
46_W49_G1.9901.00
19_N116_L1.9881.00
39_Q51_S1.9031.00
17_E21_M1.8121.00
39_Q105_C1.7401.00
28_E31_S1.7391.00
22_L124_I1.7341.00
101_T117_S1.6891.00
39_Q53_G1.6060.99
37_S87_T1.5990.99
32_Q36_I1.5880.99
40_A46_W1.5330.99
15_A126_L1.5020.99
118_I124_I1.4290.98
88_F124_I1.4040.98
19_N23_Q1.3890.98
11_L106_Q1.3030.97
119_S125_Q1.2980.97
25_A36_I1.2980.97
35_A87_T1.2880.96
33_R90_A1.2850.96
11_L15_A1.2820.96
118_I122_G1.2730.96
101_T115_V1.2360.95
2_I6_T1.2290.95
94_L100_R1.2200.95
14_A17_E1.2090.94
101_T123_R1.1820.94
28_E36_I1.1780.93
37_S53_G1.1760.93
115_V127_E1.1670.93
22_L34_R1.1560.93
12_Q114_R1.1470.92
20_A121_A1.1310.91
24_Y52_I1.1270.91
55_L59_S1.1250.91
30_V92_G1.1020.90
15_A116_L1.1000.90
38_I82_A1.0960.90
88_F116_L1.0850.89
53_G59_S1.0800.89
33_R123_R1.0670.88
23_Q124_I1.0560.87
117_S123_R1.0510.87
5_F8_R1.0440.86
37_S84_E1.0410.86
23_Q26_R1.0170.84
120_Q124_I1.0090.84
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  
4ipuA4199.80.086Contact Map
4dq9A20.868698.50.536Contact Map
2knqA10.905197.60.633Contact Map
1oqwA20.883210.80.881Contact Map
1s21A10.408820.916Contact Map
2w87A20.94161.70.92Contact Map
4wt3A101.60.922Contact Map
4i4oA20.74451.40.923Contact Map
3dwlE20.18251.30.926Contact Map
4xesA101.10.929Contact 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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