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Amy Keating

ID: 1504911862 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 189 (183)
Sequences: 260 (177.9)
Seq/Len: 1.421
Nf(neff/√len): 13.2

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: 1.421).

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
82_F141_Y4.3961.00
19_L152_V3.6141.00
11_A92_D2.6841.00
47_D161_R2.5741.00
82_F130_A2.0810.98
37_E63_E1.8260.96
77_G163_I1.7780.95
59_A62_E1.7460.94
54_D63_E1.7150.93
64_Y70_Q1.6310.91
82_F90_F1.5590.88
87_T129_Q1.5580.88
19_L81_V1.4990.85
61_Q70_Q1.4470.82
115_G130_A1.4300.81
86_N124_T1.4180.80
118_C150_Q1.4140.80
54_D64_Y1.3870.78
22_Q26_N1.3740.77
115_G143_E1.3640.77
113_L139_I1.3540.76
63_E70_Q1.3350.74
55_I76_E1.3060.72
46_I161_R1.3010.72
144_T147_K1.2970.71
56_L63_E1.2830.70
92_D129_Q1.2730.69
28_F59_A1.2700.69
17_S24_I1.2620.68
7_V25_Q1.2590.68
14_V146_A1.2550.68
175_D178_G1.2440.67
63_E96_Y1.2340.66
89_S114_V1.2250.65
14_V117_K1.2240.65
14_V145_S1.2200.65
20_T68_R1.2150.64
34_P63_E1.2100.64
32_Y125_V1.2090.64
8_V19_L1.2050.63
17_S120_L1.2030.63
143_E151_G1.1910.62
117_K145_S1.1840.61
12_G78_F1.1830.61
37_E83_A1.1490.58
12_G32_Y1.1440.57
26_N77_G1.1440.57
12_G37_E1.1400.57
113_L134_A1.1340.56
61_Q64_Y1.1320.56
18_A28_F1.1310.56
94_H149_R1.1150.54
23_L26_N1.1150.54
28_F147_K1.1150.54
127_S134_A1.1110.54
9_V72_M1.1070.53
130_A141_Y1.1030.53
93_I162_E1.1020.53
56_L160_V1.0970.52
83_A96_Y1.0970.52
26_N64_Y1.0970.52
68_R75_G1.0970.52
62_E90_F1.0950.52
19_L93_I1.0910.52
79_L105_D1.0850.51
31_E79_L1.0810.51
38_D42_K1.0790.51
62_E71_Y1.0790.51
80_C159_L1.0700.50
112_V155_A1.0670.49
128_R131_Q1.0640.49
33_D72_M1.0600.49
84_I107_D1.0570.48
32_Y37_E1.0570.48
25_Q67_M1.0510.48
80_C93_I1.0470.47
22_Q66_A1.0410.47
61_Q73_R1.0380.46
130_A143_E1.0330.46
114_V155_A1.0320.46
82_F151_G1.0310.46
37_E56_L1.0250.45
76_E99_Q1.0230.45
109_V180_G1.0200.45
20_T33_D1.0190.45
35_T60_G1.0190.45
144_T166_H1.0160.44
57_D60_G1.0150.44
22_Q29_V1.0130.44
34_P37_E1.0130.44
12_G75_G1.0110.44
117_K146_A1.0100.44
178_G181_C1.0090.44
63_E83_A1.0090.44
37_E96_Y1.0080.43
4_Y141_Y1.0070.43
51_C113_L1.0060.43
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  
2j0vA40.88361000.44Contact Map
2gf0A40.90481000.444Contact Map
2iwrA10.86771000.447Contact Map
1m7bA10.86241000.449Contact Map
4dsuA10.93651000.451Contact Map
3ihwA10.85191000.454Contact Map
3regA20.87831000.456Contact Map
2bovA10.90481000.456Contact Map
3conA10.82541000.458Contact Map
4klzA10.82011000.459Contact 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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