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T0808 19-150 -force run

ID: 1405530975 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 132 (128)
Sequences: 92 (83.6)
Seq/Len: 0.719
Nf(neff/√len): 7.4

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: 0.719).

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
43_F99_I2.3960.98
103_G111_F1.8140.86
72_F89_I1.7890.85
16_T40_S1.7420.82
51_A121_N1.6400.77
57_A76_L1.6380.77
91_I94_A1.6170.75
7_V39_V1.6160.75
44_Y114_I1.5350.70
42_Y96_Y1.5260.69
127_N131_D1.5200.69
51_A128_Y1.5200.69
28_G96_Y1.4990.67
45_L48_P1.4010.60
43_F119_A1.4000.59
43_F100_D1.3750.57
59_G112_G1.3320.54
14_Y20_D1.3260.53
7_V84_V1.3200.53
96_Y112_G1.2910.50
74_V114_I1.2630.48
103_G106_K1.2530.47
62_E120_D1.2280.45
99_I111_F1.2110.44
40_S43_F1.2080.43
49_T123_T1.1960.42
8_G131_D1.1920.42
24_I28_G1.1770.41
65_V86_V1.1770.41
45_L99_I1.1740.40
84_V117_L1.1740.40
108_G113_E1.1650.40
53_L100_D1.1600.39
7_V101_L1.1580.39
76_L128_Y1.1540.39
40_S100_D1.1410.38
37_S122_V1.1270.37
13_G117_L1.1180.36
15_V81_F1.1170.36
57_A60_H1.1140.36
49_T121_N1.1070.35
107_S131_D1.0930.34
27_R55_L1.0910.34
41_I89_I1.0850.33
48_P128_Y1.0830.33
107_S112_G1.0810.33
25_T63_I1.0810.33
97_V100_D1.0780.33
46_H67_Y1.0780.33
66_S93_Q1.0740.33
40_S98_R1.0730.33
33_T46_H1.0690.32
25_T53_L1.0630.32
14_Y40_S1.0590.32
10_S131_D1.0440.30
34_N42_Y1.0430.30
39_V54_S1.0420.30
39_V89_I1.0420.30
12_N41_I1.0390.30
39_V122_V1.0390.30
31_H107_S1.0330.30
112_G127_N1.0300.29
34_N76_L1.0230.29
75_N117_L1.0220.29
20_D39_V1.0170.29
23_R48_P1.0160.28
35_P103_G1.0110.28
63_I99_I1.0110.28
16_T102_Q1.0110.28
64_K71_G1.0050.28
65_V87_G1.0030.28
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  
2bgoA10.818297.60.8Contact Map
3zm8A10.931897.20.813Contact Map
4kmqA10.8636970.82Contact Map
2vzsA20.0682970.82Contact Map
2w87A20.924296.70.827Contact Map
2vzpA20.840996.70.827Contact Map
2w47A10.893996.30.835Contact Map
3wnoA20.954595.50.845Contact Map
2w3jA10.924294.80.851Contact Map
2cdpA40.886494.60.853Contact 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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