GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ATG8

ID: 1506431523 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 122 (118)
Sequences: 545 (314.7)
Seq/Len: 4.619
Nf(neff/√len): 29.0

HHblits Results: (2016_02)
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: 4.619).

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
55_D60_Q2.5021.00
18_E26_Y2.0791.00
22_I31_P1.7321.00
12_L102_E1.6150.99
103_D107_Y1.6030.99
50_Y79_V1.5920.99
42_V112_G1.5800.99
107_Y110_Y1.5170.98
7_K101_D1.5110.98
46_D68_R1.5050.98
68_R71_L1.4600.98
73_A76_A1.4360.97
6_F9_S1.4320.97
60_Q64_V1.3900.97
107_Y117_G1.3300.96
57_T60_Q1.3260.95
6_F10_N1.3240.95
8_I12_L1.3160.95
16_M20_S1.2910.94
34_V61_F1.2900.94
64_V68_R1.2680.94
4_S8_I1.2620.94
11_P14_A1.2360.93
17_S21_R1.2150.92
7_K12_L1.2090.92
15_R18_E1.2080.91
111_S114_N1.2070.91
35_E58_V1.1910.91
87_P94_A1.1820.90
71_L78_F1.1810.90
56_L60_Q1.1670.90
79_V112_G1.1420.88
40_S44_D1.1350.88
7_K10_N1.1140.86
3_K8_I1.1040.86
44_D82_K1.0980.85
19_S23_R1.0950.85
94_A97_E1.0920.85
81_V86_P1.0870.85
2_A8_I1.0790.84
103_D106_L1.0790.84
25_K61_F1.0780.84
104_G112_G1.0740.84
36_K44_D1.0710.83
114_N117_G1.0700.83
113_E117_G1.0670.83
66_R76_A1.0670.83
15_R31_P1.0650.83
76_A81_V1.0650.83
51_L105_F1.0650.83
8_I11_P1.0630.83
77_I80_F1.0590.82
85_L88_T1.0570.82
57_T62_V1.0550.82
6_F12_L1.0540.82
52_V56_L1.0540.82
61_F67_K1.0530.82
61_F92_M1.0460.81
112_G116_F1.0440.81
79_V84_T1.0330.80
64_V79_V1.0300.80
10_N78_F1.0260.80
55_D61_F1.0230.79
43_P101_D1.0210.79
34_V72_G1.0160.79
104_G116_F1.0060.78
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: (06Aug15)
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  
3ruiB10.92621000.094Contact Map
3m95A20.95081000.095Contact Map
3w1yA20.90161000.103Contact Map
3h9dA20.93441000.11Contact Map
4eoyA30.94261000.115Contact Map
2zjdA20.97541000.117Contact Map
1eo6A20.9591000.119Contact Map
3wapA10.95081000.137Contact Map
3wamA10.92621000.142Contact Map
3vtwA30.95081000.148Contact 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.

Page generated in 0.1155 seconds.