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T0814 1-120

ID: 1404851054 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 120 (115)
Sequences: 219 (208.3)
Seq/Len: 1.904
Nf(neff/√len): 19.4

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: 1.904).

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
82_N86_T4.5691.00
66_G74_Y2.4921.00
11_M51_Y2.3811.00
38_L62_I2.3611.00
40_V62_I2.3021.00
40_V60_I2.1580.99
80_H88_S1.9520.99
28_T31_N1.8280.98
92_P100_Q1.8010.97
52_I60_I1.6260.94
47_I119_N1.5380.92
69_S116_Q1.4840.90
75_A100_Q1.3740.84
76_Y98_G1.3580.83
52_I67_L1.3320.82
66_G114_T1.3090.80
42_V60_I1.2940.79
14_F19_G1.2500.76
115_T120_Y1.2450.75
35_I74_Y1.2350.74
47_I51_Y1.2330.74
77_N108_A1.2090.72
36_K74_Y1.2040.72
75_A103_T1.1970.71
14_F89_Q1.1860.70
73_R103_T1.1860.70
9_L16_L1.1840.70
38_L41_K1.1840.70
39_Q63_N1.1580.67
82_N94_E1.1490.67
49_E80_H1.1430.66
26_F81_C1.1380.66
9_L78_V1.1350.65
84_D88_S1.1200.64
30_V61_E1.1070.62
48_S56_G1.0990.62
70_G108_A1.0880.60
109_N118_S1.0700.58
71_Y75_A1.0640.58
61_E78_V1.0630.58
73_R83_A1.0620.58
66_G115_T1.0600.57
38_L93_I1.0300.54
7_S16_L1.0210.53
10_F17_S1.0130.52
71_Y109_N1.0110.52
82_N97_N1.0060.52
95_Y106_D1.0030.51
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: (05Jul14)
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  
4dw1A10.97521.80.93Contact Map
2qgmA10.7759.90.941Contact Map
4jg9A20.42590.941Contact Map
1utrA20.43338.80.942Contact Map
4bbwA10.64178.60.942Contact Map
1v10A10.755.40.947Contact Map
1ygpA20.96674.80.949Contact Map
4n4rB20.7254.70.949Contact Map
4nnrA20.54174.50.949Contact Map
2dckA10.7253.80.951Contact 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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