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Target P05431_2_

ID: 1513365133 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 170 (158)
Sequences: 419 (304.2)
Seq/Len: 2.652
Nf(neff/√len): 24.2

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: 2.652).

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
127_C163_C3.0771.00
43_A98_M2.5391.00
1_M4_L2.2821.00
39_Q162_T1.9310.99
46_L98_M1.8810.99
35_T38_A1.8400.99
154_I159_L1.8210.99
44_I114_L1.7960.99
84_V96_A1.7690.98
5_Q22_I1.7340.98
33_D157_K1.7030.98
28_L33_D1.6440.97
1_M26_V1.5600.96
125_W163_C1.5240.95
39_Q49_G1.5130.95
16_V20_V1.4760.94
8_F12_E1.3980.91
6_K157_K1.3820.91
127_C160_P1.3600.90
15_I27_A1.3540.90
42_E46_L1.3530.89
115_W128_G1.3490.89
10_L19_I1.3300.88
65_P81_G1.3280.88
30_A34_Y1.3220.88
7_G12_E1.3130.88
42_E84_V1.3120.87
21_G35_T1.3040.87
6_K35_T1.3020.87
50_Q73_V1.3020.87
28_L158_H1.2510.84
161_S164_R1.2460.84
42_E83_Y1.2330.83
48_E158_H1.2270.82
44_I112_L1.2270.82
46_L84_V1.2100.81
57_Y63_E1.2100.81
3_T17_I1.2090.81
116_A164_R1.2010.80
43_A102_N1.1950.80
8_F11_I1.1880.79
69_T161_S1.1780.79
89_V116_A1.1720.78
38_A106_E1.1580.77
43_A84_V1.1520.76
2_N6_K1.1510.76
43_A46_L1.1470.76
41_S45_L1.1390.75
16_V19_I1.1370.75
92_G116_A1.1370.75
22_I41_S1.1360.75
42_E81_G1.1260.74
27_A31_Y1.1180.73
45_L48_E1.1110.73
7_G11_I1.1080.72
25_A30_A1.1070.72
99_A102_N1.0970.71
11_I14_M1.0860.70
160_P163_C1.0850.70
143_V146_A1.0830.70
1_M28_L1.0760.69
39_Q81_G1.0740.69
37_R114_L1.0720.69
46_L96_A1.0650.68
31_Y34_Y1.0620.68
37_R164_R1.0600.67
11_I19_I1.0560.67
17_I27_A1.0550.67
46_L59_L1.0390.65
15_I18_A1.0380.65
1_M6_K1.0330.65
57_Y65_P1.0240.64
5_Q91_N1.0190.63
9_T12_E1.0140.62
129_Q159_L1.0100.62
125_W164_R1.0090.62
7_G10_L1.0070.62
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  
2hi2A10.91761000.405Contact Map
3sokA20.79411000.443Contact Map
1oqwA20.77061000.472Contact Map
3jyzA10.752999.90.547Contact Map
1qveA20.682499.90.572Contact Map
1x6zA10.623599.80.609Contact Map
3sojA20.611899.80.642Contact Map
2m7gA10.358899.50.71Contact Map
4noaA10.6235980.831Contact Map
3g20A20.6412980.832Contact 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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