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Gavriel Co Evolution

ID: 1513365121 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 171 (166)
Sequences: 175 (152.6)
Seq/Len: 1.054
Nf(neff/√len): 11.8

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: 1.054).

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
62_G66_R3.1131.00
54_Q143_E2.6951.00
54_Q120_K2.5670.99
31_V45_L2.4610.99
25_I29_V2.2560.98
31_V36_I2.0220.96
61_V124_G1.8390.93
51_K58_R1.8380.93
4_E9_F1.8160.92
53_K66_R1.7680.91
3_T6_K1.7260.89
45_L49_T1.6450.86
6_K16_K1.6450.86
79_A86_G1.5380.80
9_F12_H1.5150.79
8_K11_Q1.5030.78
1_M6_K1.4780.77
36_I45_L1.4290.73
23_T26_E1.3970.71
7_A12_H1.3870.70
54_Q122_Y1.3380.66
36_I49_T1.3370.66
62_G65_N1.3130.64
5_F18_R1.3100.64
2_K20_E1.3090.63
22_F26_E1.2920.62
50_N72_Y1.2790.61
31_V47_S1.2750.60
31_V38_A1.2470.58
48_Q51_K1.2430.58
62_G73_L1.2420.57
35_G39_A1.2310.56
95_N122_Y1.2300.56
72_Y86_G1.2140.55
24_L39_A1.2090.54
79_A108_V1.2080.54
86_G141_L1.2030.54
4_E12_H1.1940.53
26_E37_L1.1810.52
128_T137_T1.1750.51
21_G27_L1.1640.50
10_L18_R1.1630.50
29_V42_L1.1540.49
3_T9_F1.1520.49
66_R139_A1.1370.48
53_K131_I1.1300.47
58_R143_E1.1290.47
27_L41_A1.1270.47
29_V37_L1.1230.46
5_F15_L1.1130.45
24_L37_L1.1090.45
61_V64_M1.1040.45
73_L137_T1.1010.44
5_F20_E1.0980.44
76_N131_I1.0950.44
2_K12_H1.0920.43
59_N63_A1.0860.43
99_S110_N1.0850.43
73_L139_A1.0830.43
144_A152_D1.0800.42
144_A147_P1.0760.42
94_V133_N1.0660.41
97_K131_I1.0660.41
23_T29_V1.0580.40
23_T37_L1.0570.40
8_K12_H1.0550.40
156_A162_T1.0550.40
33_I39_A1.0520.40
100_F109_G1.0480.39
96_F122_Y1.0460.39
114_A121_P1.0420.39
120_K143_E1.0390.39
7_A10_L1.0350.38
127_W152_D1.0300.38
64_M86_G1.0270.38
66_R73_L1.0250.37
73_L126_V1.0250.37
61_V121_P1.0250.37
32_I35_G1.0230.37
64_M83_A1.0210.37
55_V141_L1.0180.37
66_R69_Q1.0070.36
108_V112_A1.0050.36
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  
2hi2A10.836399.40.757Contact Map
3sokA20.795399.30.771Contact Map
1oqwA20.771999.20.782Contact Map
2m7gA10.356799.20.79Contact Map
3g20A20.637497.90.857Contact Map
4noaA10.584881.90.925Contact Map
4d40A2069.60.932Contact Map
2m3kA10.590658.60.937Contact Map
3gn9A30.590640.30.943Contact Map
2kepA10.5848350.945Contact 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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