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T0848 1-170

ID: 1404966313 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 170 (156)
Sequences: 546 (511.1)
Seq/Len: 3.500
Nf(neff/√len): 40.9

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: 3.500).

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
76_K121_S3.8951.00
66_Q129_V3.2621.00
65_D129_V2.3631.00
74_A123_E2.3391.00
3_Q7_Y2.3041.00
48_K74_A2.0961.00
72_N125_N2.0601.00
67_L133_G1.9951.00
44_Q76_K1.8380.99
74_A121_S1.7480.99
19_T22_C1.7200.99
92_L138_L1.7110.99
154_T157_I1.6830.99
82_P115_T1.6040.98
117_N120_K1.5360.97
64_D129_V1.5320.97
52_Y69_L1.5260.97
3_Q9_V1.5030.97
98_K128_F1.5020.97
68_V127_F1.4170.95
3_Q8_A1.4140.95
65_D116_I1.4050.95
94_Q97_T1.4020.95
85_V90_F1.3940.95
62_T65_D1.3650.94
93_Y137_E1.3560.93
49_D106_D1.3550.93
15_L26_K1.3390.93
48_K72_N1.3210.92
86_D112_Q1.3150.92
8_A12_I1.2920.91
8_A13_L1.2740.90
20_A23_S1.2730.90
93_Y97_T1.2670.90
14_L35_E1.2520.89
70_K125_N1.2510.89
32_K36_T1.2450.89
89_D140_Y1.2400.89
44_Q78_T1.2290.88
5_K11_L1.2290.88
3_Q22_C1.2260.88
91_T98_K1.2240.88
97_T100_S1.2240.88
73_V92_L1.1850.85
13_L22_C1.1800.85
90_F140_Y1.1800.85
86_D89_D1.1520.83
73_V126_L1.1490.83
62_T129_V1.1420.82
66_Q117_N1.1350.82
93_Y98_K1.1330.82
35_E43_A1.1230.81
135_Q142_P1.1220.81
103_D133_G1.1170.81
143_E146_G1.1010.79
111_L124_G1.0920.78
86_D113_G1.0820.78
6_T10_F1.0740.77
23_S26_K1.0730.77
96_D100_S1.0680.76
28_S34_S1.0630.76
82_P117_N1.0540.75
89_D142_P1.0510.75
10_F14_L1.0450.74
16_M133_G1.0410.74
66_Q120_K1.0400.73
68_V129_V1.0340.73
70_K127_F1.0300.72
4_K20_A1.0280.72
86_D115_T1.0210.72
67_L85_V1.0200.71
3_Q6_T1.0190.71
15_L22_C1.0180.71
117_N129_V1.0070.70
88_M140_Y1.0060.70
14_L22_C1.0000.69
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  
3cfuA20.770699.60.551Contact Map
4lesA10.705999.40.605Contact Map
2llgA10.764798.30.741Contact Map
3qfgA20.676598.20.751Contact Map
2x3cA10.588296.90.807Contact Map
3ucpA10.717694.80.838Contact Map
3nrfA20.611894.70.839Contact Map
4lmhA40.711894.10.844Contact Map
3pmqA10.617691.60.856Contact Map
3o0lA20.6471830.875Contact 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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