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T0855

ID: 1405537039 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 119 (108)
Sequences: 362 (326.1)
Seq/Len: 3.352
Nf(neff/√len): 31.4

Jackhmmer Results: (2014_04_16)
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: 3.352).

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
75_I92_L2.0341.00
101_Q104_S1.7100.99
35_G63_I1.6380.98
73_V94_Q1.5350.97
77_Y100_Y1.5240.97
12_V16_L1.4970.96
77_Y90_L1.4970.96
71_Q96_K1.4830.96
79_S83_T1.4670.96
108_E111_D1.4420.95
81_R85_L1.4410.95
82_N96_K1.4270.95
40_S65_F1.4230.95
79_S85_L1.4190.95
76_K89_A1.4130.95
107_R110_D1.3800.94
29_A39_P1.3700.93
71_Q75_I1.3580.93
104_S114_A1.3460.93
11_G15_G1.2780.90
36_I49_D1.2690.89
31_Q34_Y1.2680.89
22_W35_G1.2560.89
32_L35_G1.2500.88
56_A59_Q1.2460.88
87_A107_R1.2380.88
84_K88_K1.2330.88
34_Y40_S1.2260.87
94_Q114_A1.2250.87
65_F115_G1.2150.86
29_A35_G1.1900.85
12_V15_G1.1880.85
11_G14_A1.1790.84
109_V113_V1.1720.84
53_L56_A1.1680.83
90_L101_Q1.1680.83
9_Q12_V1.1650.83
101_Q107_R1.1600.83
40_S47_V1.1520.82
108_E114_A1.1330.81
37_V42_T1.1310.81
90_L107_R1.1250.80
102_T107_R1.1210.80
95_L98_E1.1170.79
10_I15_G1.1160.79
88_K109_V1.1100.79
17_A21_E1.0830.76
76_K96_K1.0590.74
12_V17_A1.0560.74
30_N48_D1.0550.74
47_V59_Q1.0540.74
62_T80_Q1.0530.74
10_I14_A1.0490.73
54_V58_D1.0430.73
84_K89_A1.0390.72
80_Q84_K1.0340.72
27_I113_V1.0260.71
13_L16_L1.0240.71
108_E113_V1.0210.70
80_Q115_G1.0130.69
17_A22_W1.0050.69
107_R114_A1.0030.68
14_A18_I1.0010.68
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: (12Jul14)
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  
2kvzA10.43799.10.438Contact Map
2kt7A10.403498.80.513Contact Map
3i57A20.411896.50.698Contact Map
2kywA10.403491.40.765Contact Map
4m00A10.949687.80.781Contact Map
3lyyA20.579870.30.817Contact Map
2lfiA10.705970.10.817Contact Map
3nz3A10.529457.20.831Contact Map
2x5pA10.4706120.881Contact Map
3e8vA10.4118100.885Contact 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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