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tgac n term1

ID: 1506634791 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 326 (324)
Sequences: 1085 (984.4)
Seq/Len: 3.349
Nf(neff/√len): 54.7

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: 3.349).

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
42_F46_V2.7851.00
30_T33_G2.5481.00
307_L312_L2.5181.00
224_V267_V2.3611.00
261_W304_Q2.3231.00
240_T243_A2.2351.00
255_P259_L2.1181.00
41_R44_E2.1161.00
268_A304_Q2.0671.00
306_A315_R2.0121.00
221_L225_Q1.9851.00
61_E64_E1.9291.00
19_R23_D1.9281.00
256_L259_L1.8911.00
223_L238_L1.8590.99
79_W83_Q1.8500.99
305_M314_V1.8250.99
82_Q85_E1.8190.99
296_A305_M1.8120.99
44_E47_E1.8080.99
246_I313_F1.7980.99
220_T260_A1.7960.99
43_W46_V1.7830.99
99_R102_A1.7700.99
12_P15_F1.7680.99
134_A138_D1.7500.99
92_W95_R1.7500.99
79_W85_E1.7320.99
254_R257_Q1.7210.99
100_P103_S1.7130.99
266_V269_L1.7070.99
238_L264_G1.7020.99
43_W47_E1.6990.99
82_Q86_R1.6850.99
109_L162_A1.6680.98
60_V64_E1.6300.98
243_A261_W1.6180.98
279_L307_L1.6130.98
286_D289_A1.5990.98
42_F47_E1.5920.98
302_D316_R1.5600.97
236_L240_T1.5540.97
56_E66_R1.5440.97
40_S43_W1.5330.97
81_R85_E1.5180.97
115_L154_H1.5030.97
279_L293_L1.5000.96
293_L297_L1.4970.96
246_I306_A1.4370.95
261_W280_D1.4350.95
228_G274_R1.4220.95
220_T224_V1.4220.95
197_L239_L1.4160.95
176_R180_A1.4140.95
222_A225_Q1.4130.95
275_W303_D1.4000.94
133_G138_D1.3850.94
4_G7_R1.3840.94
268_A276_G1.3760.94
237_W277_G1.3610.93
267_V270_E1.3560.93
263_L270_E1.3500.93
99_R103_S1.3490.93
10_L13_Y1.3480.93
268_A275_W1.3370.92
7_R23_D1.3270.92
134_A137_A1.3180.92
41_R46_V1.3170.92
69_L74_P1.2990.91
44_E48_G1.2980.91
176_R181_A1.2950.91
79_W82_Q1.2900.90
134_A139_P1.2890.90
76_L79_W1.2880.90
8_V18_E1.2770.90
273_E301_E1.2760.90
217_L259_L1.2700.89
262_G265_R1.2700.89
133_G136_S1.2590.89
68_S71_A1.2510.88
123_A127_L1.2420.88
110_S114_L1.2400.88
239_L281_L1.2370.88
122_A125_E1.2330.88
238_L275_W1.2300.87
9_P78_R1.2280.87
221_L263_L1.2220.87
22_L25_P1.2170.87
10_L15_F1.2100.86
154_H166_P1.2090.86
46_V49_A1.2070.86
304_Q316_R1.2020.86
265_R304_Q1.2010.86
229_D232_I1.1950.85
57_A62_G1.1930.85
181_A185_E1.1920.85
122_A126_G1.1850.85
264_G275_W1.1830.84
221_L224_V1.1820.84
80_R83_Q1.1820.84
66_R71_A1.1820.84
163_E166_P1.1780.84
198_S202_L1.1780.84
101_L314_V1.1780.84
280_D308_R1.1770.84
255_P258_A1.1760.84
134_A146_G1.1740.84
11_P15_F1.1670.83
279_L282_P1.1670.83
50_D54_L1.1660.83
72_L75_V1.1660.83
267_V274_R1.1640.83
234_A237_W1.1640.83
98_W102_A1.1400.81
176_R225_Q1.1290.80
210_H214_P1.1290.80
79_W87_S1.1290.80
17_R23_D1.1260.80
305_M312_L1.1220.80
245_S250_D1.1180.80
306_A313_F1.1180.80
176_R229_D1.1100.79
107_G110_S1.1090.79
67_A71_A1.1070.79
99_R104_A1.1050.78
213_L216_G1.1040.78
81_R84_S1.1020.78
213_L217_L1.1010.78
159_E162_A1.0970.78
237_W276_G1.0920.77
123_A126_G1.0910.77
213_L219_L1.0900.77
33_G36_S1.0850.77
13_Y16_Q1.0800.76
269_L276_G1.0790.76
220_T238_L1.0790.76
231_A234_A1.0780.76
40_S44_E1.0750.76
245_S251_P1.0690.75
103_S106_G1.0670.75
277_G280_D1.0630.75
243_A280_D1.0620.74
182_R185_E1.0560.74
305_M320_A1.0540.74
19_R22_L1.0490.73
83_Q86_R1.0490.73
15_F21_W1.0440.73
128_S212_A1.0390.72
159_E166_P1.0390.72
247_G251_P1.0380.72
109_L112_R1.0380.72
254_R259_L1.0330.72
52_G56_E1.0320.71
241_R281_L1.0280.71
62_G68_S1.0270.71
100_P105_I1.0240.71
244_V261_W1.0220.70
49_A76_L1.0200.70
116_F223_L1.0200.70
237_W275_W1.0170.70
66_R72_L1.0140.69
96_V99_R1.0110.69
308_R313_F1.0090.69
55_T59_R1.0020.68
285_L310_S1.0020.68
57_A61_E1.0000.68
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  
4impA40.80981000.474Contact Map
4l4xA10.76691000.492Contact Map
3qp9A40.64721000.534Contact Map
3mjeA20.65031000.536Contact Map
2fr1A10.64421000.539Contact Map
2z5lA10.59821000.541Contact Map
4hxyA20.524599.90.578Contact Map
3slkA20.527699.60.722Contact Map
4j1qA10.490899.40.745Contact Map
4kc5A40.662699.10.781Contact 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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