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ID: 1514270076 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 246 (242)
Sequences: 18069 (11233.4)
Seq/Len: 74.665
Nf(neff/√len): 722.1

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: 74.665).

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
22_A105_S3.9211.00
160_F164_Q3.8131.00
22_A71_V3.1471.00
163_A167_K2.7001.00
80_Y164_Q2.6881.00
74_V104_V2.6401.00
96_A100_I2.5951.00
157_V161_I2.3751.00
63_M109_I2.2631.00
80_Y85_H2.1701.00
29_V64_A2.1671.00
26_W67_A2.1601.00
50_V56_Y2.1501.00
164_Q167_K2.0541.00
22_A101_L1.9841.00
71_V101_L1.9801.00
67_A108_A1.9501.00
80_Y84_C1.9301.00
127_V131_V1.9301.00
73_L161_I1.8551.00
85_H88_K1.8481.00
49_P55_A1.8471.00
12_Q17_N1.8361.00
164_Q168_H1.7881.00
84_C168_H1.7861.00
18_T101_L1.7831.00
200_K245_I1.7711.00
59_T63_M1.7181.00
167_K171_K1.7151.00
155_F202_L1.7061.00
80_Y161_I1.7031.00
99_K102_L1.6841.00
19_C98_G1.6521.00
100_I103_L1.6371.00
166_S170_S1.6361.00
227_L231_S1.6191.00
27_E242_N1.6101.00
96_A99_K1.5811.00
88_K92_F1.5761.00
205_H235_V1.5741.00
168_H171_K1.5711.00
172_Y176_R1.5591.00
94_D97_R1.5571.00
24_A27_E1.5491.00
67_A105_S1.5281.00
113_T117_F1.5241.00
159_S163_A1.5051.00
95_T99_K1.5031.00
21_I25_A1.4961.00
48_S52_K1.4781.00
73_L157_V1.4561.00
77_I161_I1.4491.00
237_I241_C1.4191.00
26_W105_S1.4010.99
81_F85_H1.3940.99
27_E68_A1.3930.99
226_R230_V1.3910.99
18_T99_K1.3880.99
78_D82_A1.3850.99
210_L231_S1.3840.99
67_A71_V1.3770.99
223_T227_L1.3710.99
78_D93_G1.3670.99
59_T116_F1.3620.99
76_A162_A1.3600.99
242_N246_Y1.3590.99
26_W68_A1.3480.99
33_A36_F1.3310.99
66_Q150_L1.3140.99
23_L71_V1.3130.99
81_F92_F1.3060.99
71_V105_S1.3060.99
115_R118_E1.3020.99
15_R98_G1.2920.99
28_I31_M1.2880.99
30_L239_A1.2720.99
104_V108_A1.2720.99
80_Y160_F1.2680.99
19_C74_V1.2630.99
88_K91_R1.2550.99
72_V158_L1.2530.99
49_P120_S1.2450.98
210_L227_L1.2350.98
19_C75_M1.2180.98
108_A112_A1.2080.98
77_I81_F1.1990.98
70_W154_P1.1960.98
114_P118_E1.1900.98
48_S51_N1.1860.98
82_A87_L1.1680.97
17_N20_L1.1670.97
166_S191_D1.1660.97
232_N236_M1.1660.97
6_V21_I1.1660.97
52_K127_V1.1580.97
63_M112_A1.1560.97
70_W107_F1.1450.97
158_L198_I1.1450.97
19_C78_D1.1410.97
14_P17_N1.1390.97
17_N21_I1.1350.97
190_R193_L1.1210.97
82_A89_H1.1160.96
97_R100_I1.1150.96
84_C164_Q1.1090.96
202_L206_L1.1050.96
73_L158_L1.0950.96
19_C71_V1.0920.96
82_A86_P1.0860.96
188_Q192_Q1.0710.95
18_T22_A1.0560.95
103_L107_F1.0540.95
69_V201_F1.0520.95
151_Y206_L1.0520.95
187_D191_D1.0490.94
70_W104_V1.0440.94
34_S236_M1.0340.94
89_H93_G1.0290.94
196_I245_I1.0200.93
240_G243_V1.0180.93
169_M190_R1.0180.93
71_V104_V1.0060.93
62_N112_A1.0020.92
200_K241_C1.0010.92
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  
4iarA10.9351000.123Contact Map
3emlA10.99191000.134Contact Map
4pxzA10.95931000.135Contact Map
3oduA20.97971000.135Contact Map
3uonA10.96751000.136Contact Map
2rh1A10.98781000.138Contact Map
4bvnA10.96341000.141Contact Map
4eiyA10.99191000.145Contact Map
3pblA20.95931000.151Contact Map
4grvA10.97151000.155Contact 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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