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GremlinQ

ID: 1513820351 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 152 (145)
Sequences: 3476 (3184.1)
Seq/Len: 23.972
Nf(neff/√len): 264.4

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: 23.972).

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
54_V58_W2.4611.00
39_A43_L2.2411.00
45_G48_S2.2251.00
32_Q35_A2.0681.00
55_R59_L2.0141.00
28_F32_Q2.0051.00
28_F31_L1.9171.00
22_A25_I1.8771.00
53_I57_K1.8171.00
44_G48_S1.6941.00
46_A50_A1.6291.00
11_V31_L1.5681.00
27_K30_D1.5501.00
32_Q36_K1.5501.00
115_I119_Y1.5011.00
140_T143_K1.4591.00
95_I98_A1.4491.00
30_D34_D1.4341.00
33_K37_I1.4151.00
101_Y104_K1.4000.99
129_C133_Y1.3970.99
95_I99_I1.3790.99
4_G7_L1.3620.99
17_L45_G1.3200.99
25_I29_A1.3020.99
11_V29_A1.2940.99
31_L34_D1.2910.99
39_A42_G1.2880.99
33_K36_K1.2820.99
40_V43_L1.2770.99
24_A28_F1.2690.99
34_D57_K1.2440.98
141_S144_V1.2210.98
4_G12_I1.2200.98
128_K132_K1.2170.98
101_Y105_T1.2070.98
7_L12_I1.2060.98
40_V44_G1.2050.98
137_D140_T1.2030.98
105_T108_L1.2030.98
43_L46_A1.1930.98
30_D33_K1.1810.98
38_S41_K1.1570.97
12_I28_F1.1530.97
17_L34_D1.1520.97
104_K108_L1.1510.97
29_A32_Q1.1430.97
138_N141_S1.1300.97
49_A53_I1.1280.97
15_V29_A1.1090.96
41_K48_S1.1050.96
27_K31_L1.0990.96
8_I24_A1.0940.96
15_V31_L1.0930.96
46_A49_A1.0890.96
59_L64_V1.0850.96
35_A38_S1.0830.96
134_D145_T1.0730.95
27_K34_D1.0700.95
25_I45_G1.0680.95
69_I74_K1.0570.95
101_Y106_Y1.0550.95
41_K45_G1.0540.95
11_V15_V1.0520.95
54_V64_V1.0520.95
74_K78_V1.0420.94
12_I29_A1.0400.94
20_L28_F1.0330.94
11_V27_K1.0280.94
80_T83_N1.0250.93
11_V34_D1.0220.93
42_G45_G1.0180.93
51_K88_P1.0150.93
41_K44_G1.0140.93
51_K54_V1.0130.93
97_A100_D1.0010.92
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  
2hi2A10.901399.60.506Contact Map
3sokA20.914599.50.514Contact Map
1oqwA20.881699.50.533Contact Map
2m7gA10.401399.30.568Contact Map
3g20A20.743497.20.768Contact Map
1x6zA10.677677.40.865Contact Map
3jyzA10.756675.40.867Contact Map
2m3kA10.671173.90.869Contact Map
1qveA20.697473.10.87Contact Map
4noaA10.657973.10.87Contact 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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