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2bl2

ID: 1499447903 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 156 (147)
Sequences: 1049 (594.4)
Seq/Len: 7.136
Nf(neff/√len): 49.0

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: 7.136).

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_S3.1141.00
96_S100_A2.5751.00
102_T145_G2.5181.00
65_Q103_G2.0321.00
36_M115_A1.9671.00
29_G33_G1.8171.00
26_S69_G1.7591.00
136_A140_T1.7181.00
71_V147_V1.7141.00
48_Q51_K1.7051.00
43_A62_P1.6821.00
85_S88_Q1.6771.00
107_G111_G1.5881.00
135_A139_E1.5521.00
65_Q106_S1.5511.00
68_Y139_E1.5441.00
23_T73_A1.5360.99
147_V150_F1.5230.99
11_G89_G1.5160.99
71_V140_T1.5030.99
20_A24_I1.4790.99
21_T25_F1.3850.99
117_G135_A1.3830.99
104_L107_G1.3640.98
19_M95_A1.3380.98
57_I132_I1.3330.98
146_F150_F1.3010.98
15_A18_A1.2850.98
22_A73_A1.2740.97
24_I102_T1.2650.97
72_I149_S1.2470.97
28_I104_L1.2280.97
67_L71_V1.2240.96
36_M108_I1.2220.96
141_Y144_L1.2070.96
16_V19_M1.2000.96
62_P65_Q1.1990.96
72_I150_F1.1850.96
75_L153_V1.1600.95
109_A138_V1.1470.94
34_V63_G1.1460.94
58_L63_G1.1390.94
59_Q102_T1.1390.94
38_G43_A1.1340.94
14_F89_G1.1270.94
72_I99_I1.1170.93
65_Q68_Y1.1080.93
79_N154_L1.1070.93
25_F100_A1.1020.93
79_N92_F1.0960.92
55_A134_F1.0960.92
18_A96_S1.0840.92
72_I148_I1.0830.92
57_I155_N1.0760.92
65_Q110_Q1.0710.91
18_A93_L1.0650.91
59_Q143_I1.0630.91
23_T95_A1.0550.90
55_A121_L1.0550.90
40_A115_A1.0530.90
32_K109_A1.0530.90
16_V91_N1.0490.90
111_G115_A1.0420.90
74_F150_F1.0390.90
22_A149_S1.0320.89
63_G66_G1.0320.89
76_I153_V1.0280.89
41_A45_T1.0260.89
60_L74_F1.0220.88
109_A112_K1.0190.88
143_I147_V1.0190.88
32_K108_I1.0150.88
76_I92_F1.0140.88
17_L20_A1.0120.88
91_N153_V1.0110.88
28_I97_L1.0090.88
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  
2bl2A1011000.171Contact Map
3j9tY1001000.191Contact Map
4bemJ10.987299.90.335Contact Map
2xquA50.474499.20.648Contact Map
4v1gA3099.20.649Contact Map
1wu0A10.435999.20.655Contact Map
1a91A10.474499.20.657Contact Map
3zk1A220.544999.20.661Contact Map
4cbkA130.410399.10.668Contact Map
4bemA90.474499.10.672Contact 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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