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4ipu

ID: 1500382060 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 137 (136)
Sequences: 1054 (842.2)
Seq/Len: 7.750
Nf(neff/√len): 72.2

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: 7.750).

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
12_Q16_E3.3271.00
28_E32_Q3.1781.00
39_Q51_S2.9501.00
41_L51_S2.8701.00
25_A38_I2.7641.00
28_E31_S2.7281.00
24_Y64_L2.1871.00
22_L86_L2.1441.00
6_T10_E1.9831.00
21_M50_L1.8701.00
35_A87_T1.8631.00
55_L59_S1.7951.00
37_S87_T1.7711.00
29_A92_G1.7481.00
101_T115_V1.7001.00
32_Q36_I1.6121.00
53_G57_S1.5931.00
4_P8_R1.5451.00
117_S125_Q1.5361.00
85_H100_R1.5231.00
115_V127_E1.4240.99
7_E107_N1.4180.99
21_M67_H1.3920.99
11_L106_Q1.3330.98
21_M24_Y1.3330.98
39_Q53_G1.3270.98
24_Y52_I1.3250.98
7_E10_E1.2920.98
18_L38_I1.2790.98
16_E23_Q1.2620.98
15_A126_L1.2620.98
21_M52_I1.2510.97
105_C115_V1.2330.97
19_N23_Q1.2310.97
101_T117_S1.2190.97
53_G61_A1.2140.97
22_L38_I1.2020.97
40_A46_W1.1630.96
21_M49_G1.1630.96
103_A115_V1.1330.95
37_S85_H1.1260.95
45_D48_K1.1110.94
131_K136_C1.1050.94
11_L104_I1.1030.94
16_E20_A1.0950.93
70_F104_I1.0830.93
89_T116_L1.0810.93
116_L124_I1.0780.93
37_S53_G1.0730.92
46_W49_G1.0660.92
74_T86_L1.0490.91
38_I52_I1.0480.91
19_N116_L1.0360.91
117_S127_E1.0320.90
100_R118_I1.0260.90
57_S61_A1.0240.90
14_A75_L1.0240.90
88_F124_I1.0050.89
105_C117_S1.0050.89
30_V66_K1.0000.88
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  
4ipuA411000.118Contact Map
4dq9A20.875997.30.744Contact Map
2knqA10.883282.10.845Contact Map
2iz6A20.48915.80.922Contact Map
1oqwA20.78834.90.925Contact Map
1xccA40.5624.40.926Contact Map
1prxA20.56933.50.929Contact Map
4i99C20.33582.10.937Contact Map
4kf9A10.627720.938Contact Map
4fczB20.197120.938Contact 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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