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cbd

ID: 1516628646 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 216 (211)
Sequences: 3047 (2730.7)
Seq/Len: 14.441
Nf(neff/√len): 188.0

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: 14.441).

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
31_R43_E5.0681.00
42_E49_V4.5391.00
104_E152_T3.8301.00
32_A46_P3.4971.00
34_L49_V3.3831.00
102_F152_T3.0151.00
102_F154_K3.0051.00
84_R104_E2.9761.00
8_H13_G2.9171.00
33_I43_E2.8321.00
36_H41_I2.7971.00
124_D128_Q2.7581.00
87_S91_Y2.7421.00
42_E52_A2.6351.00
79_V110_K2.6011.00
100_T154_K2.5521.00
72_G182_H2.4841.00
100_T156_P2.4591.00
45_S48_T2.4471.00
81_K108_E2.3871.00
34_L56_L2.3831.00
163_K191_E2.3391.00
107_V149_Y2.2641.00
82_E106_D2.2531.00
112_D145_K2.1681.00
86_K104_E2.1551.00
21_D24_A2.1481.00
112_D146_K2.1161.00
4_K7_E2.0041.00
32_A49_V1.9571.00
33_I40_I1.9471.00
104_E150_L1.8901.00
106_D150_L1.8771.00
6_K9_K1.8761.00
9_K30_D1.8621.00
34_L41_I1.8501.00
78_A170_L1.8181.00
36_H56_L1.8141.00
95_F101_L1.7821.00
79_V108_E1.6751.00
22_M50_T1.6441.00
83_V168_V1.5751.00
122_I190_F1.5711.00
77_K111_E1.5491.00
7_E11_K1.5181.00
6_K27_I1.5071.00
26_K47_E1.5011.00
108_E149_Y1.4941.00
9_K15_I1.4931.00
184_I187_V1.4761.00
34_L52_A1.4761.00
4_K13_G1.4701.00
96_P99_D1.4301.00
19_S25_V1.4261.00
26_K50_T1.4241.00
2_F8_H1.4211.00
44_G48_T1.4030.99
3_R7_E1.3960.99
5_L28_L1.3790.99
7_E10_Q1.3600.99
88_E99_D1.3250.99
119_G132_G1.3240.99
5_L8_H1.3130.99
84_R106_D1.3100.99
76_F79_V1.2950.99
19_S28_L1.2870.99
123_R129_D1.2810.99
26_K51_Q1.2800.99
6_K10_Q1.2780.99
108_E148_K1.2760.99
40_I43_E1.2750.99
34_L42_E1.2730.99
101_L157_L1.2640.99
17_F25_V1.2520.99
106_D148_K1.2020.98
25_V32_A1.2020.98
119_G134_N1.2000.98
4_K8_H1.1920.98
122_I159_L1.1730.98
95_F99_D1.1710.98
84_R92_T1.1360.97
42_E48_T1.1340.97
2_F6_K1.1180.96
105_L118_A1.1030.96
109_A144_L1.0800.95
17_F24_A1.0500.94
2_F13_G1.0270.94
87_S90_G1.0220.93
23_N27_I1.0180.93
49_V52_A1.0170.93
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  
2r5oA20.745499.80.58Contact Map
1vplA10.3102990.755Contact Map
2oljA20.305698.90.757Contact Map
1b0uA10.310298.90.76Contact Map
4u00A1098.90.76Contact Map
4ymuJ2098.90.762Contact Map
4wbsA20.300998.90.763Contact Map
1g6hA10.305698.80.765Contact Map
4rvcA10.319498.80.766Contact Map
3tuiC40.703798.80.766Contact 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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