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T domain short module

ID: 1506977639 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 254 (239)
Sequences: 3126 (2547.9)
Seq/Len: 13.079
Nf(neff/√len): 164.8

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: 13.079).

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
94_F99_A3.4411.00
71_L147_R3.2871.00
69_D147_R3.2611.00
91_S140_A3.1631.00
81_E110_R2.7941.00
89_G92_Q2.6281.00
75_L111_L2.6191.00
93_S96_E2.5471.00
68_L90_R2.4461.00
79_W139_V2.3741.00
100_D103_I2.3181.00
93_S137_P2.2261.00
196_M216_G2.1241.00
35_P47_L2.1131.00
76_A90_R2.0551.00
72_E90_R2.0451.00
189_F192_V2.0391.00
90_R139_V2.0071.00
82_A107_V1.9981.00
242_A246_M1.9881.00
190_H241_Y1.9291.00
234_I238_A1.9121.00
79_W99_A1.8531.00
138_T141_D1.8261.00
132_Q145_F1.8221.00
191_A198_I1.8091.00
76_A139_V1.7791.00
74_I114_K1.7541.00
129_L132_Q1.7351.00
31_V34_L1.7271.00
186_R215_V1.7101.00
70_E73_S1.6541.00
78_L107_V1.5701.00
73_S77_K1.5671.00
233_L236_T1.5131.00
110_R114_K1.4861.00
79_W142_L1.4531.00
76_A80_A1.4351.00
12_E16_K1.4301.00
68_L140_A1.4161.00
80_A87_S1.4131.00
190_H196_M1.4121.00
136_Y145_F1.4050.99
69_D73_S1.4030.99
95_Y134_L1.4010.99
71_L74_I1.3880.99
7_R10_E1.3870.99
75_L139_V1.3850.99
75_L143_A1.3740.99
68_L72_E1.3730.99
190_H199_F1.3630.99
185_L213_S1.3500.99
79_W94_F1.3450.99
65_E90_R1.3450.99
75_L142_L1.3380.99
106_Q110_R1.3380.99
77_K114_K1.3110.99
220_A240_D1.3070.99
108_A112_R1.2930.99
19_V23_M1.2930.99
188_V196_M1.2920.99
191_A241_Y1.2890.99
189_F203_L1.2740.99
69_D90_R1.2620.99
88_I97_H1.2580.99
232_E236_T1.2550.99
90_R140_A1.2530.99
14_F18_H1.2480.99
82_A103_I1.2330.98
240_D244_C1.2320.98
24_L28_L1.2270.98
64_S87_S1.2190.98
12_E28_L1.2180.98
79_W107_V1.2160.98
69_D72_E1.2120.98
72_E143_A1.2110.98
231_A240_D1.2090.98
191_A199_F1.1900.98
163_I167_N1.1840.98
71_L115_L1.1820.98
92_Q97_H1.1810.98
65_E91_S1.1590.97
80_A86_V1.1530.97
163_I166_Q1.1520.97
20_P23_M1.1520.97
191_A197_D1.1450.97
72_E140_A1.1430.97
203_L214_I1.1400.97
244_C247_A1.1370.97
233_L237_V1.1340.97
190_H194_G1.1290.97
243_E247_A1.1260.97
29_Q48_A1.1250.97
75_L78_L1.1220.97
243_E246_M1.1210.97
187_V245_L1.1110.96
136_Y141_D1.1020.96
10_E14_F1.0980.96
184_L212_G1.0930.96
43_D46_T1.0850.96
31_V47_L1.0740.95
37_T43_D1.0720.95
25_P41_K1.0700.95
108_A133_M1.0620.95
231_A237_V1.0510.94
237_V240_D1.0510.94
76_A88_I1.0500.94
71_L146_I1.0470.94
188_V214_I1.0400.94
99_A103_I1.0250.93
112_R127_D1.0240.93
95_Y137_P1.0120.93
88_I92_Q1.0000.92
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  
2vsqA10.8151000.308Contact Map
4r0mB20.53151000.462Contact Map
4dg8A10.20081000.462Contact Map
4iz6A20.53151000.468Contact Map
4f6lB20.366199.90.535Contact Map
4oqjA10.129999.90.54Contact Map
3tejA20.645799.90.554Contact Map
2vz8A20.177299.80.622Contact Map
2jgpA10.62299.70.644Contact Map
2cq8A10.425299.70.646Contact 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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