GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
NgPilE

ID: 1513816017 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 165 (162)
Sequences: 837 (590.6)
Seq/Len: 5.167
Nf(neff/√len): 46.4

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: 5.167).

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
1_M4_L3.1741.00
128_C158_C3.1401.00
43_A99_M2.5621.00
35_T38_A2.1811.00
130_Q154_L1.9241.00
8_F12_E1.8801.00
3_T6_K1.8461.00
149_I154_L1.7301.00
7_G12_E1.7241.00
116_W129_G1.7211.00
42_E46_L1.7021.00
9_T13_L1.6700.99
57_Y63_K1.6420.99
39_Q157_T1.6330.99
9_T12_E1.6280.99
16_V19_I1.6140.99
44_I115_L1.6130.99
1_M26_V1.5970.99
43_A85_V1.5840.99
56_E60_N1.5640.99
98_T112_K1.5570.99
15_I18_A1.5350.99
21_G35_T1.5090.99
21_G26_V1.4900.99
90_V93_G1.4730.98
11_I16_V1.4450.98
128_C155_P1.4280.98
48_E51_K1.4070.98
156_S159_R1.3800.97
57_Y61_H1.3690.97
25_A30_A1.3660.97
44_I113_L1.3640.97
36_A39_Q1.3640.97
47_A97_A1.3600.97
36_A153_H1.3470.97
33_D152_K1.3450.97
85_V97_A1.3120.96
41_S45_L1.3110.96
46_L99_M1.2980.96
45_L48_E1.2480.94
40_V149_I1.2400.94
57_Y65_P1.2400.94
126_W158_C1.2280.94
46_L97_A1.2270.94
17_I20_V1.2270.94
93_G126_W1.2200.93
50_Q73_V1.2190.93
16_V22_I1.2130.93
111_K150_D1.2120.93
49_G82_G1.2040.93
42_E84_Y1.1970.93
5_Q22_I1.1860.92
108_I111_K1.1630.91
9_T21_G1.1530.91
37_R159_R1.1490.90
43_A46_L1.1430.90
39_Q84_Y1.1350.90
35_T152_K1.1270.89
87_E100_L1.1200.89
6_K35_T1.1170.89
2_N26_V1.1050.88
1_M6_K1.1040.88
93_G117_A1.1030.88
12_E16_V1.0820.86
14_M18_A1.0650.85
7_G10_L1.0640.85
113_L148_E1.0630.85
39_Q82_G1.0570.85
141_A145_D1.0560.85
12_E19_I1.0530.84
42_E85_V1.0480.84
53_A57_Y1.0330.83
13_L16_V1.0270.82
46_L85_V1.0270.82
25_A33_D1.0240.82
16_V20_V1.0180.82
130_Q148_E1.0130.81
14_M19_I1.0070.81
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  
2hi2A10.95151000.341Contact Map
3sokA20.82421000.399Contact Map
1oqwA20.79391000.428Contact Map
3jyzA10.781899.90.513Contact Map
1qveA20.70399.80.554Contact Map
1x6zA10.642499.80.59Contact Map
3sojA20.630399.70.628Contact Map
2m7gA10.369799.50.671Contact Map
3g20A20.654598.40.789Contact Map
4noaA10.642497.90.81Contact 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 0.0389 seconds.