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bv1 30-245 20-216 -force run 1-185 -force run

ID: 1513452947 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 185 (185)
Sequences: 152 (50.7)
Seq/Len: 0.822
Nf(neff/√len): 3.7

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: 0.822).

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
4_N50_L2.0680.95
5_Q38_Y2.0560.95
56_Q108_S1.7720.87
53_E119_I1.6810.82
3_E15_N1.6170.79
108_S114_K1.6140.79
65_I149_Y1.6090.78
50_L160_R1.5580.75
12_L24_Y1.5390.74
76_I127_V1.5380.74
28_V144_L1.5190.73
49_T105_G1.4650.69
3_E38_Y1.4510.68
21_F61_M1.4460.67
97_F116_R1.4290.66
164_N168_G1.4100.64
65_I147_K1.3950.63
82_P98_G1.3840.62
15_N38_Y1.3220.57
11_V23_T1.3120.56
148_R177_V1.3040.55
92_T149_Y1.2970.55
22_V136_I1.2930.54
70_G97_F1.2850.54
70_G116_R1.2850.54
3_E107_L1.2810.53
38_Y76_I1.2790.53
23_T26_R1.2750.53
6_F168_G1.2600.52
71_V132_D1.2360.49
80_R119_I1.2330.49
26_R160_R1.2270.49
45_R119_I1.2260.49
62_D175_L1.2250.48
5_Q163_C1.2030.47
22_V31_V1.2000.46
175_L185_A1.1950.46
66_S119_I1.1900.45
9_E21_F1.1890.45
77_V117_Y1.1880.45
156_S171_T1.1810.45
18_L28_V1.1810.45
19_S102_H1.1730.44
1_V153_A1.1720.44
178_Y184_D1.1690.44
76_I87_S1.1670.43
14_Q112_A1.1580.43
90_L176_L1.1550.42
1_V177_V1.1530.42
174_A179_Y1.1510.42
119_I176_L1.1400.41
113_L138_L1.1380.41
23_T45_R1.1350.41
35_T80_R1.1270.40
24_Y85_G1.1220.40
145_S172_K1.1160.39
152_W155_F1.1140.39
152_W157_D1.1140.39
98_G116_R1.1130.39
20_T29_R1.1100.39
79_G97_F1.1070.38
79_G116_R1.1070.38
26_R159_E1.1060.38
8_P106_N1.1050.38
41_L90_L1.1020.38
82_P97_F1.0960.37
82_P116_R1.0960.37
79_G98_G1.0950.37
79_G82_P1.0790.36
181_W184_D1.0790.36
155_F165_G1.0770.36
155_F167_Y1.0770.36
157_D165_G1.0770.36
157_D167_Y1.0770.36
52_I95_A1.0750.36
108_S138_L1.0680.35
12_L156_S1.0590.34
178_Y181_W1.0580.34
78_V125_R1.0550.34
74_M159_E1.0510.34
56_Q62_D1.0450.33
165_G173_N1.0440.33
167_Y173_N1.0440.33
122_V128_S1.0390.33
5_Q45_R1.0370.33
65_I175_L1.0350.33
21_F125_R1.0300.32
22_V177_V1.0300.32
23_T138_L1.0290.32
6_F160_R1.0270.32
57_G64_P1.0240.32
18_L134_L1.0200.31
84_V159_E1.0200.31
62_D161_D1.0200.31
2_Q71_V1.0110.31
12_L47_K1.0110.31
13_S24_Y1.0080.30
173_N183_S1.0070.30
67_T106_N1.0070.30
73_S76_I1.0070.30
53_E108_S1.0050.30
6_F50_L1.0020.30
76_I96_L1.0000.30
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  
2ixkA20.627220.967Contact Map
1nxmA20.610880.973Contact Map
1ep0A10.63787.90.973Contact Map
1dzrA20.59464.20.976Contact Map
1bnxA10.11894.10.976Contact Map
4hdqC10.0273.40.977Contact Map
4bz7A40.34053.30.977Contact Map
3ilcA10.50272.70.978Contact Map
3k44A40.26492.60.979Contact Map
2xk0A10.35682.40.979Contact 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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