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T0808 40-150

ID: 1405031738 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 111 (109)
Sequences: 122 (117.3)
Seq/Len: 1.119
Nf(neff/√len): 11.2

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: 1.119).

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
70_I73_A2.5741.00
85_K90_F1.8630.94
21_Y75_Y1.8140.93
22_F78_I1.7530.91
7_G75_Y1.7210.90
82_G90_F1.5960.85
30_A100_N1.5370.82
10_H86_S1.4510.76
28_T102_T1.4320.75
22_F98_A1.4150.74
30_A107_Y1.4100.73
19_S22_F1.3780.71
40_S90_F1.3700.70
8_V18_V1.3610.70
106_N110_D1.3610.70
7_G37_K1.3460.68
8_V63_V1.2620.61
103_G109_K1.2560.61
74_G87_G1.2540.60
42_I92_E1.2540.60
16_S55_L1.2400.59
55_L80_L1.2330.58
101_V109_K1.2240.58
51_F68_I1.2200.57
19_S79_D1.2150.57
80_L93_I1.2050.56
22_F76_V1.2040.56
34_L88_E1.2000.55
31_D64_P1.1920.55
3_I18_V1.1840.54
18_V33_S1.1640.52
43_K50_G1.1500.51
14_P96_L1.1370.49
42_I55_L1.1300.49
43_K52_K1.1300.49
8_V59_D1.1210.48
19_S77_R1.1210.48
52_K65_V1.1200.48
20_I30_A1.1150.47
18_V24_L1.1100.47
24_L78_I1.1080.47
12_T25_H1.1010.46
36_A55_L1.0970.46
38_G42_I1.0930.45
7_G21_Y1.0880.45
34_L73_A1.0850.44
28_T100_N1.0640.42
10_H87_G1.0640.42
82_G85_K1.0620.42
30_A102_T1.0590.42
7_G82_G1.0520.41
13_N43_K1.0470.41
24_L27_P1.0440.41
2_R104_K1.0390.40
35_Y40_S1.0320.39
45_S48_K1.0250.39
76_V80_L1.0180.38
23_Y40_S1.0180.38
15_K48_K1.0130.38
46_Y76_V1.0070.37
4_T105_S1.0070.37
13_N21_Y1.0030.37
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  
2bgoA10.8919980.725Contact Map
3zm8A10.955980.729Contact Map
4kmqA10.873997.90.734Contact Map
2vzpA20.846897.80.739Contact Map
2vzsA2097.80.739Contact Map
2w47A10.918997.70.743Contact Map
2w87A20.936997.60.749Contact Map
2w3jA10.945997.30.763Contact Map
2cdpA40.882997.20.767Contact Map
3wnoA20.98296.90.778Contact 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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