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TR

ID: 1507799600 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 143 (136)
Sequences: 2556 (1826.9)
Seq/Len: 18.794
Nf(neff/√len): 156.7

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: 18.794).

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_R3.8481.00
17_A60_V3.3081.00
4_V31_V2.5951.00
3_D30_S2.2291.00
20_L60_V2.1961.00
57_F86_A1.9721.00
32_F38_L1.9141.00
21_K36_E1.8901.00
43_F119_N1.8661.00
8_Y13_G1.8501.00
7_S65_A1.7921.00
42_K46_K1.7781.00
63_P98_D1.7071.00
25_Q36_E1.7001.00
65_A79_V1.6881.00
63_P107_V1.6841.00
21_K25_Q1.6761.00
16_L60_V1.5981.00
7_S82_E1.5781.00
34_D38_L1.5761.00
18_S35_V1.5641.00
46_K49_Q1.5291.00
76_K79_V1.5081.00
123_W131_T1.5001.00
4_V58_V1.4631.00
59_L65_A1.4401.00
133_E137_R1.4221.00
38_L50_S1.3890.99
11_N64_G1.3850.99
32_F50_S1.3850.99
8_Y34_D1.3790.99
135_I139_L1.3610.99
62_S65_A1.3110.99
110_E113_Q1.2900.99
10_R34_D1.2810.99
83_I112_M1.2650.99
1_T53_G1.2530.99
29_F139_L1.2430.98
4_V29_F1.2260.98
2_P30_S1.2170.98
19_L23_H1.2150.98
127_Y130_A1.2090.98
49_Q53_G1.2080.98
33_I37_K1.1830.98
21_K33_I1.1810.98
131_T134_K1.1790.98
38_L46_K1.1720.98
41_G95_P1.1620.97
33_I36_E1.1500.97
4_V56_N1.1330.97
48_I52_M1.1020.96
56_N92_N1.1000.96
29_F140_Q1.0920.96
13_G35_V1.0920.96
38_L79_V1.0830.96
32_F47_L1.0820.96
84_V111_D1.0680.95
38_L43_F1.0640.95
137_R140_Q1.0490.94
59_L83_I1.0420.94
10_R43_F1.0170.93
2_P54_A1.0050.93
27_H132_I1.0030.93
9_R64_G1.0000.92
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  
2js7A10.895199.90.221Contact Map
4eo7A10.881199.90.245Contact Map
2j67A20.902199.80.25Contact Map
4om7A20.902199.80.25Contact Map
1fyxA10.888199.80.256Contact Map
3ub2A10.790299.80.258Contact Map
3h16A40.909199.80.268Contact Map
4lzpB40.888199.80.281Contact Map
1t3gA20.881199.80.287Contact Map
4lqcA20.909199.80.289Contact 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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