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TR

ID: 1507797556 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 143 (134)
Sequences: 2827 (2055.5)
Seq/Len: 21.097
Nf(neff/√len): 177.6

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: 21.097).

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
3_D55_R3.6871.00
4_V31_V2.8051.00
17_A60_V2.5451.00
3_D30_S2.2031.00
32_F38_L2.0521.00
7_S82_E1.9731.00
7_S65_A1.9271.00
20_L60_V1.9131.00
57_F86_A1.9121.00
62_S65_A1.8171.00
65_A79_V1.7131.00
21_K36_E1.7061.00
76_K79_V1.6781.00
56_N92_N1.5911.00
21_K25_Q1.4831.00
34_D38_L1.4831.00
43_F119_N1.4671.00
6_I60_V1.4481.00
32_F50_S1.4261.00
133_E137_R1.4231.00
123_W131_T1.4221.00
4_V58_V1.4141.00
59_L65_A1.4091.00
25_Q36_E1.3930.99
97_I122_K1.3810.99
56_N94_V1.3470.99
38_L46_K1.3320.99
63_P107_V1.3160.99
9_R64_G1.2800.99
135_I139_L1.2800.99
48_I52_M1.2750.99
133_E136_I1.2700.99
18_S35_V1.2610.99
128_Q132_I1.2590.99
16_L60_V1.2510.99
5_F76_K1.2440.98
130_A133_E1.2330.98
1_T53_G1.2280.98
2_P30_S1.2240.98
27_H136_I1.2060.98
131_T134_K1.2040.98
25_Q30_S1.1810.98
19_L23_H1.1750.98
18_S22_V1.1700.97
21_K33_I1.1640.97
46_K49_Q1.1620.97
60_V98_D1.1370.97
83_I112_M1.1090.96
29_F140_Q1.1020.96
57_F65_A1.1000.96
33_I36_E1.0940.96
32_F47_L1.0930.96
63_P99_G1.0910.96
133_E138_F1.0880.96
4_V29_F1.0840.96
32_F46_K1.0810.95
81_K85_T1.0800.95
8_Y13_G1.0790.95
23_H26_L1.0750.95
76_K82_E1.0720.95
11_N64_G1.0490.94
8_Y34_D1.0480.94
84_V111_D1.0470.94
62_S98_D1.0370.94
38_L79_V1.0200.93
79_V83_I1.0130.93
130_A134_K1.0120.93
48_I51_V1.0100.93
33_I37_K1.0060.93
41_G95_P1.0030.93
9_R76_K1.0000.92
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  
2js7A10.895199.90.216Contact Map
4om7A20.909199.80.227Contact Map
2j67A20.902199.80.229Contact Map
1fyxA10.888199.80.239Contact Map
4eo7A10.881199.80.241Contact Map
3h16A40.909199.80.267Contact Map
4lzpB40.888199.80.279Contact Map
4lqcA20.909199.80.282Contact Map
3ub2A10.776299.80.284Contact Map
1t3gA20.916199.80.294Contact 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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