OPENSEQ.org
t4-2

ID: 1516630625 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 230 (224)
Sequences: 3463 (3064.1)
Seq/Len: 15.460
Nf(neff/√len): 204.7

Jackhmmer Results: (2016_04)
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: 15.460).

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
45_R57_E4.9321.00
56_E63_V4.3161.00
118_E166_T3.6261.00
46_A60_P3.3371.00
48_L63_V3.0591.00
116_F168_K3.0401.00
120_D164_L3.0191.00
116_F166_T2.9421.00
47_I57_E2.9371.00
50_H55_I2.7991.00
59_S62_T2.7451.00
98_R118_E2.7451.00
118_E164_L2.7441.00
22_H27_G2.7031.00
121_V163_Y2.6191.00
86_G196_H2.6191.00
101_S105_Y2.5671.00
138_D142_Q2.5461.00
56_E66_A2.4641.00
114_T170_P2.3991.00
114_T168_K2.3271.00
93_V124_K2.2901.00
48_L70_L2.2891.00
95_K122_E2.2101.00
47_I54_I2.2001.00
177_K205_E2.1891.00
96_E120_D2.1351.00
126_D160_K2.0461.00
100_K118_E2.0321.00
35_D38_A2.0071.00
126_D159_K1.9521.00
18_K21_E1.9491.00
109_F115_L1.9371.00
20_K23_K1.9201.00
23_K44_D1.9051.00
46_A63_V1.7691.00
106_T109_F1.7341.00
93_V122_E1.7291.00
48_L55_I1.7281.00
50_H70_L1.6861.00
21_E25_K1.6591.00
92_A184_L1.6141.00
20_K41_I1.6131.00
36_M64_T1.5841.00
58_G62_T1.5671.00
91_K125_E1.5651.00
198_I201_V1.4721.00
33_S39_V1.4701.00
40_K64_T1.4361.00
16_F22_H1.4201.00
110_P113_D1.4111.00
40_K61_E1.3980.99
39_V46_A1.3480.99
97_V182_V1.3470.99
48_L66_A1.3380.99
90_F93_V1.3350.99
15_C20_K1.3340.99
17_R21_E1.3170.99
23_K29_I1.3080.99
43_C60_P1.2700.99
133_G146_G1.2690.99
48_L56_E1.2480.99
7_G11_F1.2380.98
20_K24_Q1.2360.98
19_L42_L1.2350.98
133_G148_N1.2230.98
6_V12_Q1.2200.98
9_A13_Q1.2030.98
54_I57_E1.1990.98
136_I204_F1.1970.98
98_R120_D1.1910.98
31_F39_V1.1900.98
101_S106_T1.1890.98
102_E113_D1.1890.98
115_L171_L1.1770.98
16_F20_K1.1700.97
18_K27_G1.1690.97
6_V11_F1.1610.97
120_D162_K1.1560.97
101_S104_G1.1520.97
56_E62_T1.1500.97
109_F113_D1.1450.97
21_E24_Q1.1320.97
19_L22_H1.1310.97
159_K162_K1.1260.97
11_F15_C1.1220.97
33_S42_L1.1190.96
40_K65_Q1.1160.96
5_A15_C1.1120.96
159_K163_Y1.1040.96
58_G63_V1.1040.96
122_E162_K1.0970.96
119_L132_A1.0850.96
137_R143_D1.0780.95
12_Q16_F1.0370.94
31_F42_L1.0180.93
7_G14_K1.0170.93
123_A158_L1.0080.93
18_K22_H1.0060.93
50_H53_E1.0010.92
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  
2r5oA20.799.80.627Contact Map
3tuiC40.760999.60.668Contact Map
2oljA20.347899.60.67Contact Map
4u00A1099.60.671Contact Map
1b0uA10.369699.60.672Contact Map
4ymuJ2099.60.673Contact Map
1vplA10.352299.60.674Contact Map
2onkA40.38799.60.678Contact Map
4wbsA20.347899.60.679Contact Map
1g6hA10.347899.60.679Contact 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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