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T0808 19-150

ID: 1405531970 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 132 (122)
Sequences: 2298 (2131.3)
Seq/Len: 18.836
Nf(neff/√len): 193.0

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: 18.836).

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
68_G97_V4.0291.00
40_S100_D3.0071.00
38_I100_D2.7821.00
50_T90_D2.4301.00
93_Q97_V2.3821.00
64_K104_V1.9411.00
66_S102_Q1.8811.00
26_Q30_T1.8261.00
48_P94_A1.8201.00
25_T28_G1.8021.00
57_A76_L1.7811.00
44_Y96_Y1.7241.00
24_I28_G1.6911.00
56_Y116_Q1.6841.00
9_V13_G1.6661.00
9_V12_N1.6281.00
42_Y96_Y1.6031.00
23_R26_Q1.5811.00
66_S71_G1.5711.00
33_T103_G1.5571.00
9_V14_Y1.5341.00
42_Y98_R1.4701.00
21_G24_I1.4571.00
23_R28_G1.4471.00
34_N37_S1.4401.00
120_D124_G1.3540.99
8_G12_N1.3430.99
58_K84_V1.3390.99
84_V113_E1.3150.99
54_S120_D1.3120.99
9_V15_V1.2930.99
19_Q23_R1.2830.99
55_L74_V1.2780.99
61_S112_G1.2430.98
45_L91_I1.2240.98
40_S98_R1.2050.98
8_G11_G1.2020.98
65_V117_L1.1970.98
24_I29_V1.1850.98
30_T39_V1.1710.98
12_N18_Q1.1510.97
25_T116_Q1.1510.97
21_G25_T1.1510.97
14_Y41_I1.1440.97
45_L97_V1.1380.97
58_K113_E1.1300.97
12_N16_T1.1200.96
25_T29_V1.1160.96
55_L101_L1.1150.96
48_P93_Q1.1100.96
64_K102_Q1.1040.96
45_L51_A1.0820.96
67_Y99_I1.0750.95
63_I76_L1.0690.95
58_K79_N1.0570.95
54_S118_I1.0540.95
62_E75_N1.0460.94
31_H36_K1.0390.94
56_Y115_K1.0380.94
50_T88_S1.0350.94
57_A103_G1.0270.94
26_Q29_V1.0180.93
21_G29_V1.0140.93
15_V18_Q1.0080.93
67_Y97_V1.0040.93
80_D83_K1.0010.92
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: (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  
3zm8A10.94799.20.439Contact Map
2bgoA10.840999.20.445Contact Map
2vzsA2099.10.462Contact Map
4kmqA10.893999.10.47Contact Map
2wz8A10.871299.10.474Contact Map
3wnoA20.9848990.482Contact Map
2cdpA40.8864990.487Contact Map
2w87A20.9242990.493Contact Map
2vzpA20.856198.90.503Contact Map
2y8kA10.886498.90.505Contact 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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