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2bl2

ID: 1499474456 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 156 (149)
Sequences: 1263 (702.4)
Seq/Len: 8.477
Nf(neff/√len): 57.5

Jackhmmer Results: (2016_04)
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: 8.477).

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_I96_S3.5481.00
102_T145_G2.8091.00
21_T25_F2.4641.00
20_A24_I2.4611.00
96_S100_A2.3591.00
85_S88_Q2.2471.00
48_Q51_K2.0651.00
36_M115_A2.0061.00
65_Q103_G1.9261.00
71_V147_V1.8541.00
117_G135_A1.7381.00
72_I149_S1.7241.00
23_T73_A1.7221.00
84_M92_F1.6181.00
147_V150_F1.5671.00
65_Q106_S1.5441.00
29_G33_G1.5271.00
71_V140_T1.5161.00
18_A96_S1.4841.00
136_A140_T1.4670.99
104_L107_G1.4660.99
68_Y139_E1.4640.99
72_I150_F1.4290.99
107_G136_A1.3610.99
55_A121_L1.3430.99
58_L63_G1.3220.99
147_V151_L1.3060.99
129_T132_I1.2690.98
41_A57_I1.2480.98
26_S69_G1.2450.98
111_G115_A1.2270.98
25_F100_A1.2240.98
36_M108_I1.2170.97
43_A62_P1.2160.97
19_M95_A1.2160.97
64_T71_V1.1880.97
14_F90_L1.1850.97
54_Q130_K1.1790.97
89_G94_G1.1750.97
23_T95_A1.1750.97
29_G111_G1.1440.96
74_F150_F1.1430.96
113_V138_V1.1410.96
141_Y144_L1.1380.96
146_F150_F1.1360.96
114_A135_A1.1280.95
61_L64_T1.1150.95
22_A35_G1.1090.95
66_G141_Y1.1060.95
107_G111_G1.1010.95
120_I131_G1.0980.94
26_S71_V1.0810.94
75_L153_V1.0730.94
26_S103_G1.0690.93
94_G113_V1.0570.93
62_P65_Q1.0530.93
131_G135_A1.0520.93
57_I132_I1.0350.92
65_Q110_Q1.0310.92
32_K36_M1.0270.91
98_P149_S1.0240.91
109_A138_V1.0180.91
24_I36_M1.0170.91
120_I127_H1.0150.91
67_L144_L1.0110.91
27_G66_G1.0110.91
97_L104_L1.0090.91
21_T24_I1.0080.90
38_G42_A1.0070.90
32_K109_A1.0060.90
55_A134_F1.0050.90
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  
2bl2A1011000.159Contact Map
3j9tY1001000.21Contact Map
4bemJ10.987299.90.359Contact Map
2xquA50.474499.20.645Contact Map
4v1gA3099.20.646Contact Map
1wu0A10.435999.10.654Contact Map
1a91A10.474499.10.655Contact Map
4cbkA130.410399.10.66Contact Map
3zk1A220.599.10.661Contact Map
4bemA90.474499.10.667Contact 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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