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Fz4CRD

ID: 1499875641 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 122 (117)
Sequences: 1389 (881.6)
Seq/Len: 11.872
Nf(neff/√len): 81.5

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: 11.872).

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
11_I64_V3.1721.00
7_D33_Q2.5701.00
8_P21_V2.0261.00
79_G111_P1.9801.00
80_G111_P1.9331.00
16_N56_Q1.9281.00
52_S85_V1.9211.00
79_G83_L1.8891.00
19_Y22_T1.8571.00
32_L35_D1.7301.00
52_S88_R1.6701.00
54_Q84_S1.6381.00
85_V88_R1.6301.00
62_V109_F1.6001.00
26_N30_H1.5781.00
90_E94_K1.5561.00
51_C89_C1.5521.00
24_M36_A1.5491.00
66_M120_M1.5401.00
114_D117_H1.4881.00
84_S88_R1.4831.00
59_L63_Y1.4681.00
101_P104_L1.4541.00
93_L98_F1.4141.00
25_P30_H1.4141.00
62_V104_L1.4091.00
83_L87_R1.3930.99
9_I19_Y1.3340.99
37_E41_T1.3090.99
57_F61_S1.2450.98
13_M47_I1.2380.98
44_T48_Q1.2350.98
33_Q36_A1.2330.98
66_M75_I1.2260.98
112_Q117_H1.2260.98
66_M81_M1.1970.98
25_P28_V1.1910.98
77_P120_M1.1790.98
51_C67_C1.1630.97
86_K90_E1.1300.97
35_D46_L1.1230.97
9_I17_L1.1220.97
42_T49_Y1.1200.96
40_L47_I1.1000.96
52_S84_S1.0850.96
24_M33_Q1.0750.95
83_L86_K1.0740.95
11_I36_A1.0580.95
14_C60_C1.0570.95
41_T55_L1.0470.94
67_C78_C1.0430.94
29_G35_D1.0400.94
50_G92_V1.0320.94
106_C110_P1.0250.93
22_T33_Q1.0230.93
41_T48_Q1.0230.93
99_A102_E1.0200.93
86_K100_W1.0150.93
7_D36_A1.0110.93
78_C82_C1.0080.93
49_Y96_F1.0070.93
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  
1ijyA20.98361000.058Contact Map
5bpbA401000.061Contact Map
1ijxA60.9591000.087Contact Map
4c7aA20.89341000.187Contact Map
2mahA10.89341000.196Contact Map
3hklA20.967297.90.739Contact Map
4ywtA4055.40.885Contact Map
3odnA10.868933.20.899Contact Map
1hdlA10.40162.90.939Contact Map
1ug2A10.47542.20.943Contact 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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