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Witold Dyrka -force run

ID: 1504789081 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (151)
Sequences: 67 (39.5)
Seq/Len: 0.444
Nf(neff/√len): 3.2

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: 0.444).

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
14_E131_E2.2570.91
38_K44_G1.8080.74
115_R118_S1.6860.66
30_C43_L1.6510.64
110_F156_D1.6130.61
124_L127_L1.5460.56
32_E103_A1.4950.52
38_K155_E1.4930.52
88_I155_E1.4730.51
30_C66_P1.4560.49
34_K132_Q1.4310.47
30_C154_D1.4010.45
37_K122_K1.3910.45
28_K32_E1.3820.44
149_D156_D1.3690.43
55_E70_L1.3520.42
13_L122_K1.3450.41
131_E154_D1.3300.40
40_C136_V1.3270.40
51_I57_L1.3260.40
99_R119_D1.3230.40
42_R110_F1.3150.39
15_N112_D1.3140.39
37_K99_R1.3120.39
31_E113_V1.2980.38
36_C76_R1.2910.37
70_L99_R1.2800.37
131_E161_Q1.2800.37
36_C39_Q1.2760.36
20_I90_K1.2570.35
43_L51_I1.2290.33
33_M77_F1.2220.33
28_K41_R1.2190.32
14_E154_D1.1970.31
80_A120_V1.1960.31
29_R36_C1.1830.30
52_K104_S1.1810.30
50_L114_N1.1800.30
52_K118_S1.1780.30
51_I83_E1.1580.29
34_K47_V1.1570.29
84_A155_E1.1510.28
114_N129_Q1.1510.28
36_C57_L1.1500.28
53_P141_Q1.1470.28
151_Q155_E1.1420.28
103_A139_I1.1360.27
78_K85_N1.1350.27
108_I140_S1.1350.27
103_A134_M1.1330.27
75_N160_F1.1230.26
141_Q144_S1.1230.26
97_I141_Q1.1220.26
84_A101_L1.1070.26
34_K77_F1.1020.25
110_F149_D1.0940.25
66_P76_R1.0920.25
33_M115_R1.0880.25
33_M145_W1.0830.24
19_I122_K1.0730.24
82_E101_L1.0680.23
78_K99_R1.0660.23
88_I163_L1.0600.23
47_V97_I1.0590.23
19_I61_G1.0550.23
83_E130_V1.0510.23
76_R136_V1.0450.22
41_R47_V1.0400.22
19_I32_E1.0390.22
113_V137_S1.0320.22
23_G121_W1.0170.21
53_P58_Q1.0160.21
85_N136_V1.0160.21
116_K148_E1.0090.20
35_Y47_V1.0070.20
49_G150_Q1.0010.20
29_R76_R1.0000.20
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  
2msvA10.92771000.372Contact Map
4btfA10.7531000.585Contact Map
4dgwA10.74193.40.914Contact Map
3rfyA10.734993.20.914Contact Map
1y9jA10.680790.10.921Contact Map
1vptA10.777189.10.923Contact Map
1u60A40.337371.30.936Contact Map
2wvqA20.8313410.947Contact Map
4bqmA20.307231.30.95Contact Map
4bex110.656627.50.952Contact 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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