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4ryr

ID: 1500381823 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 151 (145)
Sequences: 2559 (1975.6)
Seq/Len: 17.648
Nf(neff/√len): 164.1

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: 17.648).

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
109_A138_A3.9021.00
91_F104_D3.9021.00
112_T137_S3.0961.00
99_F148_Y3.0331.00
43_M47_M3.0001.00
38_W142_Y2.9401.00
62_I123_S2.7051.00
102_T145_W2.5991.00
84_F111_T2.1941.00
115_L130_L1.9821.00
102_T144_S1.9481.00
77_L118_F1.8791.00
146_T149_S1.8701.00
116_I127_A1.8321.00
120_S127_A1.8251.00
145_W149_S1.7891.00
60_V78_F1.7821.00
128_W131_I1.7681.00
77_L114_L1.7521.00
109_A137_S1.6831.00
109_A141_T1.6411.00
146_T150_I1.5761.00
115_L119_S1.5751.00
59_S130_L1.5661.00
29_W98_L1.5301.00
84_F107_L1.5241.00
105_C141_T1.5171.00
15_L86_Q1.5071.00
53_F85_N1.4671.00
88_F144_S1.3840.99
114_L118_F1.3660.99
35_K147_I1.3010.99
108_V133_Y1.2810.99
34_E150_I1.2770.99
142_Y146_T1.2750.99
29_W96_K1.2640.99
60_V75_W1.2640.99
91_F101_A1.2610.99
84_F104_D1.2370.98
63_I119_S1.2120.98
44_T48_I1.2040.98
74_F119_S1.1820.98
120_S124_K1.1810.98
109_A112_T1.1700.97
81_N111_T1.1660.97
105_C144_S1.1520.97
35_K39_T1.1440.97
97_N100_L1.1280.97
9_F60_V1.1280.97
62_I65_N1.1270.97
101_A104_D1.1170.96
38_W146_T1.1090.96
116_I130_L1.1030.96
59_S126_S1.0800.95
83_I87_A1.0750.95
76_F80_L1.0590.95
120_S128_W1.0560.95
102_T148_Y1.0560.95
54_G58_L1.0520.95
63_I74_F1.0510.94
116_I134_F1.0490.94
105_C137_S1.0470.94
67_Y71_P1.0400.94
81_N115_L1.0200.93
37_S146_T1.0180.93
113_L134_F1.0160.93
109_A113_L1.0160.93
63_I122_L1.0110.93
85_N133_Y1.0060.93
44_T139_F1.0010.92
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  
4ryoA101000Contact Map
4uc1A30.98011000.037Contact Map
2mgyA111000.067Contact Map
4ev6A50.410660.921Contact Map
4i0uA100.39744.80.924Contact Map
1rh5B10.20533.20.93Contact Map
4phzK30.72192.30.936Contact Map
2rlwA10.22521.50.942Contact Map
4qncA20.37091.40.943Contact Map
1yewC30.60931.20.945Contact 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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