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ID: 1507728746 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 221 (218)
Sequences: 1078 (779.2)
Seq/Len: 4.945
Nf(neff/√len): 52.8

Jackhmmer Results: (2016_04)
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: 4.945).

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
110_L137_A3.6551.00
117_A137_A3.1761.00
117_A134_S2.6741.00
94_L109_T2.2861.00
177_L203_A2.2511.00
5_V9_L2.2061.00
55_S123_K2.1361.00
6_L10_L2.1111.00
64_R128_E2.0951.00
49_G88_G2.0471.00
38_A101_R1.9891.00
8_L12_C1.8921.00
41_L98_L1.8861.00
53_L88_G1.8841.00
82_L209_G1.7911.00
106_W141_A1.7711.00
96_Q162_Y1.7531.00
55_S129_E1.7151.00
123_K129_E1.7141.00
56_G84_A1.6860.99
110_L141_A1.6640.99
184_V190_L1.6330.99
45_V98_L1.6170.99
137_A141_A1.5660.99
123_K126_D1.5300.99
111_V115_V1.5180.99
48_S133_L1.5000.98
114_L137_A1.4590.98
41_L143_F1.4010.97
46_F92_L1.3630.97
109_T113_L1.3500.96
186_Y189_Q1.3460.96
1_L5_V1.3450.96
38_A42_A1.3410.96
46_F95_A1.3150.96
189_Q192_W1.2970.95
23_L27_R1.2940.95
9_L13_L1.2880.95
21_R25_V1.2650.94
58_T129_E1.2600.94
42_A99_R1.2500.94
188_N192_W1.2450.94
55_S128_E1.2440.94
127_W131_S1.2300.93
13_L25_V1.2270.93
173_S177_L1.2220.93
56_G85_S1.2140.93
83_V119_L1.2090.92
98_L106_W1.1900.92
24_W27_R1.1860.91
188_N191_W1.1840.91
95_A113_L1.1780.91
83_V86_L1.1750.91
103_S150_P1.1670.91
12_C16_L1.1670.91
56_G64_R1.1610.90
87_I112_L1.1590.90
172_A176_L1.1580.90
124_G129_E1.1540.90
53_L57_A1.1490.90
167_I171_G1.1390.89
10_L138_A1.1370.89
199_D207_A1.1340.89
103_S152_R1.1230.88
12_C39_P1.1220.88
186_Y194_F1.1110.87
97_G105_A1.1040.87
210_S213_L1.1040.87
169_V215_L1.0910.86
98_L140_L1.0820.86
86_L91_C1.0810.86
66_E144_R1.0700.85
175_W190_L1.0680.85
209_G213_L1.0580.84
77_I196_L1.0560.84
117_A212_L1.0540.84
46_F165_A1.0510.83
208_L211_C1.0510.83
68_L73_P1.0460.83
89_V93_L1.0370.82
98_L109_T1.0370.82
126_D129_E1.0350.82
138_A142_M1.0320.82
187_S191_W1.0250.81
106_W110_L1.0220.81
102_L106_W1.0210.81
78_D202_R1.0170.80
102_L149_R1.0160.80
25_V218_A1.0160.80
118_L178_L1.0150.80
20_A26_T1.0150.80
11_A42_A1.0060.79
22_R27_R1.0030.79
9_L16_L1.0010.79
212_L215_L1.0000.79
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  
4us3A10.950241.60.923Contact Map
2ostA40.22626.60.947Contact Map
3nd0A20.29416.30.947Contact Map
4cadC40.66065.70.949Contact Map
4yayA1050.95Contact Map
4eneA20.35294.50.951Contact Map
1lnqA80.28514.40.951Contact Map
3dh4A40.96384.20.952Contact Map
2z73A20.941230.955Contact Map
2xq2A10.96382.90.956Contact 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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