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GREMLIN_4ote

ID: 1515599153 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 240 (239)
Sequences: 3141 (1875.8)
Seq/Len: 13.142
Nf(neff/√len): 121.3

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: 13.142).

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
128_T143_E3.8421.00
222_D226_S3.4991.00
7_V36_K3.2911.00
104_T151_K3.1821.00
103_D166_T3.1091.00
61_E65_K2.9921.00
9_G53_I2.9281.00
203_R206_D2.8531.00
74_K204_T2.8431.00
226_S230_E2.7001.00
93_I100_K2.5451.00
66_E70_A2.5411.00
91_Y163_P2.4111.00
5_K32_T2.4091.00
101_K147_G2.3901.00
78_G212_I2.3681.00
105_I167_A2.3371.00
104_T149_Q2.3311.00
106_A165_V2.3141.00
119_R122_E2.2551.00
25_L223_K2.2421.00
107_I114_C2.1751.00
21_E224_A2.1681.00
5_K34_E2.1331.00
100_K103_D2.1041.00
75_I201_A2.0891.00
76_M204_T2.0191.00
68_V73_Y1.9881.00
206_D209_S1.9871.00
7_V34_E1.9711.00
67_A73_Y1.9691.00
108_S117_N1.9621.00
49_N74_K1.9181.00
124_I188_Y1.9001.00
138_P152_E1.8921.00
29_K214_V1.8781.00
105_I148_I1.8181.00
94_K98_E1.7911.00
181_D184_K1.7831.00
27_K32_T1.7741.00
55_A215_L1.7741.00
226_S229_E1.7641.00
55_A202_F1.7551.00
99_F167_A1.7541.00
180_L185_N1.7411.00
88_L167_A1.7351.00
51_G203_R1.7251.00
29_K217_D1.7251.00
20_E23_K1.7191.00
200_L216_Q1.6691.00
107_I150_F1.6471.00
210_E214_V1.6441.00
46_E50_N1.5961.00
31_Y214_V1.5741.00
216_Q220_T1.5391.00
126_L148_I1.5181.00
93_I166_T1.4891.00
93_I103_D1.4801.00
99_F103_D1.4731.00
42_I63_Y1.4631.00
213_K217_D1.4551.00
222_D225_R1.4501.00
4_K211_K1.4481.00
110_N113_S1.4331.00
25_L28_E1.4321.00
61_E77_A1.4211.00
17_E231_K1.4171.00
128_T142_I1.4091.00
130_P142_I1.3900.99
227_L231_K1.3510.99
46_E67_A1.3280.99
130_P140_D1.3160.99
106_A161_S1.3110.99
123_S191_P1.2910.99
101_K146_K1.2660.99
79_K197_A1.2640.99
141_I150_F1.2450.98
31_Y211_K1.2370.98
96_V188_Y1.2350.98
209_S212_I1.2210.98
204_T207_K1.2110.98
25_L218_V1.2030.98
202_F206_D1.2020.98
87_I186_G1.2020.98
16_G37_N1.1960.98
48_L53_I1.1890.98
6_I211_K1.1890.98
9_G48_L1.1810.98
61_E199_L1.1750.98
181_D185_N1.1720.98
122_E128_T1.1580.97
49_N73_Y1.1480.97
10_A19_L1.1460.97
3_D32_T1.1430.97
158_I168_A1.1340.97
57_L81_L1.1240.97
129_L142_I1.1240.97
51_G205_E1.1230.97
95_S98_E1.1180.96
88_L169_F1.1130.96
78_G216_Q1.1020.96
21_E227_L1.0760.95
202_F205_E1.0730.95
208_D213_K1.0710.95
153_L158_I1.0710.95
21_E24_P1.0710.95
64_L68_V1.0680.95
64_L199_L1.0590.95
68_V74_K1.0570.95
17_E232_Y1.0570.95
25_L224_A1.0490.94
55_A212_I1.0430.94
9_G38_F1.0360.94
43_L46_E1.0100.93
68_V75_I1.0080.93
64_L201_A1.0080.93
167_A187_I1.0060.93
29_K218_V1.0050.93
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  
4qhqA10.98331000.327Contact Map
3ir1A60.97921000.402Contact Map
4oteA211000.421Contact Map
4ntlA10.99171000.423Contact Map
3up9A10.9751000.433Contact Map
1xs5A10.99171000.451Contact Map
4k3fA10.99581000.454Contact Map
3gxaA60.97921000.455Contact Map
3tqwA20.97081000.46Contact Map
4q5tA10.99581000.49Contact 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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