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ID: 1501089758 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 264 (262)
Sequences: 69 (19.2)
Seq/Len: 0.263
Nf(neff/√len): 1.2

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: 0.263).

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 > 50% 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
53_A76_T3.8881.00
14_G30_C3.7571.00
15_G29_C3.5280.99
35_G46_G3.2490.98
13_T31_A3.1760.98
59_G70_C2.7290.94
36_C44_G2.6750.93
12_C32_G2.5260.90
58_G71_C2.2800.82
10_C34_G1.9690.68
38_C44_G1.9650.68
11_T33_A1.9640.67
52_T77_A1.8560.61
72_T135_V1.8090.58
57_T72_T1.7110.52
15_G30_C1.6640.49
90_A235_T1.6480.48
60_T69_A1.6460.48
37_C43_G1.6370.47
42_T217_L1.6350.47
33_A128_I1.6290.46
14_G29_C1.6240.46
8_A34_G1.5750.43
92_A184_I1.5440.41
114_N131_D1.5160.39
61_A68_T1.4670.36
54_C75_G1.4640.36
127_T134_E1.4210.34
41_G217_L1.3980.32
11_T31_A1.3950.32
135_V160_R1.3790.31
120_T153_I1.3700.31
107_T151_L1.3480.29
107_T251_F1.3480.29
151_L251_F1.3480.29
107_T139_D1.3310.29
139_D151_L1.3310.29
139_D251_F1.3310.29
220_N257_R1.3160.28
92_A238_V1.3080.27
200_V217_L1.2980.27
23_C26_A1.2960.27
92_A137_V1.2890.26
108_M116_A1.2890.26
52_T120_T1.2800.26
105_E188_S1.2790.26
128_I143_L1.2600.25
87_Y203_Q1.2550.25
37_C69_A1.2370.24
16_G28_C1.2290.23
35_G206_L1.2280.23
160_R182_V1.2280.23
37_C60_T1.2220.23
8_A58_G1.2120.23
125_G137_V1.2080.23
34_G46_G1.2070.22
77_A120_T1.2030.22
8_A71_C1.1910.22
105_E235_T1.1830.21
93_K134_E1.1810.21
52_T155_I1.1600.20
62_T243_V1.1590.20
86_D232_I1.1570.20
32_G63_C1.1530.20
218_M221_F1.1530.20
86_D221_F1.1400.20
86_D216_T1.1320.19
90_A189_K1.1290.19
90_A116_A1.1290.19
120_T243_V1.1230.19
127_T200_V1.1170.19
30_C239_I1.1130.18
171_I195_V1.1110.18
31_A156_V1.1100.18
34_G58_G1.1060.18
209_G248_S1.1050.18
145_D227_Q1.1040.18
128_I171_I1.1030.18
203_Q256_K1.0950.18
43_G69_A1.0890.18
77_A155_I1.0890.18
99_A136_E1.0880.18
26_A47_G1.0870.18
43_G60_T1.0860.17
10_C53_A1.0780.17
10_C76_T1.0780.17
105_E199_A1.0770.17
129_V160_R1.0740.17
53_A206_L1.0720.17
76_T206_L1.0720.17
31_A177_E1.0690.17
8_A11_T1.0630.17
177_E254_A1.0560.16
34_G71_C1.0550.16
18_T26_A1.0520.16
13_T33_A1.0490.16
108_M141_K1.0470.16
11_T128_I1.0460.16
48_C218_M1.0370.16
13_T30_C1.0340.16
187_T225_A1.0310.15
124_P240_G1.0290.15
206_L221_F1.0270.15
53_A71_C1.0260.15
71_C76_T1.0260.15
50_A218_M1.0180.15
133_K257_R1.0130.15
35_G135_V1.0120.15
186_N191_P1.0070.15
156_V232_I1.0060.15
181_G232_I1.0010.15
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  
3q3yA20.68561000.558Contact Map
2ijd120.69321000.558Contact Map
1cqqA10.68181000.561Contact Map
2b0fA10.68941000.572Contact Map
3qzrA20.68181000.574Contact Map
3zveA10.69321000.586Contact Map
4dcdA10.6971000.635Contact Map
2bhgA20.65531000.645Contact Map
2halA10.66671000.695Contact Map
1lvmA20.636498.40.929Contact 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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