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pig_p1

ID: 1514410183 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 213 (195)
Sequences: 1128 (984)
Seq/Len: 5.785
Nf(neff/√len): 70.5

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: 5.785).

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
62_V111_I4.8731.00
127_H133_Q4.5531.00
41_Q44_M3.6971.00
140_Q198_Q3.6491.00
66_E107_R3.2341.00
73_Y103_M2.4281.00
70_F112_L2.3521.00
73_Y99_L2.3451.00
27_Q68_K2.3441.00
62_V67_M2.2901.00
139_L143_F2.2631.00
31_P142_S2.0761.00
129_L201_V2.0211.00
175_L182_K2.0061.00
38_M117_V1.9831.00
77_T88_I1.9401.00
39_V64_L1.8671.00
159_L181_R1.8211.00
80_S96_N1.8021.00
36_K64_L1.8021.00
74_M108_F1.7981.00
48_K120_F1.7911.00
170_C185_L1.7451.00
36_K40_V1.7331.00
119_A122_S1.7241.00
26_F30_V1.7221.00
160_I187_V1.6981.00
35_L67_M1.6641.00
141_N145_S1.6611.00
38_M67_M1.6421.00
35_L64_L1.6421.00
46_A59_W1.6391.00
35_L68_K1.6341.00
86_L109_E1.5890.99
62_V66_E1.5590.99
167_I183_F1.5550.99
37_N138_S1.4980.99
136_L199_I1.4940.99
190_C193_T1.4920.99
116_H131_K1.4830.99
90_S94_Y1.4710.99
82_C96_N1.4550.99
49_F114_Y1.4380.98
35_L39_V1.4340.98
95_S100_A1.4260.98
70_F111_I1.4230.98
138_S142_S1.3700.98
39_V62_V1.3670.98
38_M115_F1.3590.98
67_M111_I1.3570.98
144_D198_Q1.3510.97
44_M48_K1.3380.97
156_H179_K1.3260.97
188_R196_I1.3010.97
45_Y116_H1.2870.96
120_F131_K1.2770.96
116_H120_F1.2720.96
175_L183_F1.2600.96
118_V130_Y1.2550.96
69_A102_V1.2410.95
34_V138_S1.2410.95
166_F170_C1.2080.94
153_Q197_I1.2030.94
41_Q120_F1.1940.94
46_A114_Y1.1940.94
39_V111_I1.1910.94
42_T62_V1.1700.93
34_V135_F1.1630.93
180_K183_F1.1580.92
23_V27_Q1.1550.92
83_E87_S1.1540.92
143_F195_F1.1450.92
34_V38_M1.1440.92
27_Q32_D1.1260.91
128_G171_T1.1120.90
156_H180_K1.1060.90
87_S90_S1.1050.90
140_Q199_I1.0970.89
150_S193_T1.0930.89
174_E186_W1.0840.89
32_D64_L1.0730.88
39_V67_M1.0680.88
76_S94_Y1.0680.88
26_F75_I1.0620.87
140_Q144_D1.0620.87
41_Q119_A1.0580.87
147_F190_C1.0410.86
174_E202_H1.0370.86
28_L146_A1.0370.86
29_F143_F1.0350.85
63_T111_I1.0340.85
39_V43_N1.0330.85
167_I175_L1.0300.85
47_K61_E1.0210.84
64_L68_K1.0210.84
143_F198_Q1.0200.84
32_D68_K1.0200.84
44_M119_A1.0060.83
46_A110_K1.0060.83
142_S145_S1.0040.83
118_V134_P1.0020.83
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  
3kh0A20.20665.80.964Contact Map
1bcoA10.2775.60.964Contact Map
4ujrH10.40385.20.965Contact Map
3j61U10.41314.90.965Contact Map
1ef5A10.15964.90.965Contact Map
4w20U10.39444.60.966Contact Map
4y21A104.50.966Contact Map
4by6A20.84513.80.967Contact Map
1rlfA10.1693.60.968Contact Map
1lfdA20.15963.40.968Contact 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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