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KNL1_C -force run

ID: 1506329112 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 206 (206)
Sequences: 69 (48.2)
Seq/Len: 0.335
Nf(neff/√len): 3.4

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: 0.335).

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 > 50% 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
18_F101_S1.9700.75
159_Y193_Y1.8160.66
13_D19_T1.7990.65
160_P193_Y1.7470.61
25_I59_E1.6760.57
140_F149_F1.6730.56
96_M126_L1.5860.50
76_Y85_K1.5850.50
159_Y187_V1.5730.50
96_M108_R1.4410.41
160_P187_V1.4260.40
87_C96_M1.4130.39
38_F41_L1.3680.36
3_L95_K1.3560.35
185_S193_Y1.3240.33
25_I73_I1.3110.32
29_I93_L1.3040.32
3_L24_T1.3040.32
11_W16_A1.2910.31
190_E196_N1.2870.31
70_H87_C1.2860.31
94_P201_I1.2830.31
124_Y129_I1.2830.31
178_D195_K1.2750.30
97_L104_V1.2680.30
93_L166_S1.2630.29
23_D31_F1.2590.29
20_F55_S1.2490.29
129_I170_N1.2420.28
62_A65_S1.2400.28
54_Q71_K1.2370.28
67_L90_Q1.2270.27
2_S24_T1.2260.27
106_H112_E1.2250.27
87_C168_I1.2220.27
110_L113_E1.2150.27
1_L67_L1.2000.26
13_D29_I1.2000.26
116_Y184_L1.1890.25
60_D127_M1.1890.25
114_I178_D1.1880.25
5_E31_F1.1830.25
117_L121_G1.1750.25
25_I203_Q1.1720.24
66_S86_T1.1700.24
168_I179_D1.1670.24
63_P66_S1.1670.24
45_Y131_I1.1640.24
102_L106_H1.1620.24
92_Q199_K1.1590.24
88_T172_V1.1530.24
90_Q195_K1.1520.23
70_H129_I1.1510.23
29_I151_I1.1420.23
53_F121_G1.1400.23
141_S148_K1.1350.23
30_T36_V1.1300.22
182_T188_P1.1280.22
3_L18_F1.1220.22
65_S94_P1.1220.22
4_S85_K1.1200.22
85_K88_T1.1170.22
58_D146_F1.1130.22
69_V76_Y1.1130.22
102_L131_I1.1050.21
177_Q196_N1.1050.21
83_W154_F1.1030.21
59_E138_L1.1000.21
13_D93_L1.0970.21
96_M109_L1.0960.21
136_L194_L1.0960.21
64_P184_L1.0950.21
11_W31_F1.0940.21
1_L4_S1.0900.21
102_L112_E1.0900.21
2_S45_Y1.0890.20
24_T59_E1.0860.20
169_Q182_T1.0820.20
53_F58_D1.0790.20
183_I202_Y1.0750.20
3_L138_L1.0660.19
3_L7_D1.0550.19
9_V138_L1.0500.19
113_E148_K1.0500.19
102_L111_G1.0440.19
61_Q184_L1.0420.18
19_T29_I1.0410.18
55_S81_E1.0410.18
29_I184_L1.0400.18
147_A155_L1.0370.18
2_S9_V1.0360.18
76_Y197_V1.0340.18
130_D184_L1.0310.18
8_V126_L1.0300.18
133_N180_I1.0290.18
13_D151_I1.0280.18
1_L70_H1.0270.18
2_S38_F1.0250.18
23_D138_L1.0220.18
87_C108_R1.0160.17
94_P120_W1.0110.17
59_E87_C1.0100.17
4_S95_K1.0100.17
141_S201_I1.0080.17
67_L100_F1.0050.17
98_E151_I1.0020.17
3_L44_R1.0010.17
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  
4nfaA10.9806100-0.012Contact Map
4y1lC1057.50.951Contact Map
1jatB10.480653.80.952Contact Map
1jatA10.490333.30.957Contact Map
2ebkA10.514632.40.958Contact Map
4ccgA20.5049310.958Contact Map
2r0jA10.456327.70.959Contact Map
2dawA10.5485270.959Contact Map
2yz0A10.524323.60.96Contact Map
1ayzA30.4757230.961Contact 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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