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1CDH

ID: 1515662558 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 178 (173)
Sequences: 20880 (14305.8)
Seq/Len: 120.694
Nf(neff/√len): 1087.6

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: 120.694).

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
131_R160_T3.6931.00
29_K85_E3.0471.00
6_G74_L2.8981.00
13_E70_I2.6031.00
81_T94_Q2.5321.00
7_K10_D2.4831.00
11_T70_I2.3971.00
156_T171_K2.3481.00
158_T169_E2.3441.00
81_T92_E2.3351.00
16_C84_C2.2451.00
13_E68_P2.2101.00
156_T173_D2.2041.00
115_T145_S2.1691.00
118_L159_C2.1631.00
113_S147_S2.1231.00
115_T143_T2.0971.00
20_Q24_I2.0791.00
109_L112_Q2.0441.00
11_T72_K2.0331.00
117_T143_T2.0031.00
30_N80_D2.0031.00
108_L149_L1.9801.00
129_Q160_T1.9551.00
131_R158_T1.9471.00
160_T169_E1.9091.00
129_Q162_L1.9051.00
29_K83_I1.9011.00
15_T68_P1.8951.00
113_S145_S1.8861.00
132_S155_G1.8511.00
122_P126_P1.8501.00
162_L167_K1.8201.00
133_P137_N1.8141.00
27_H85_E1.7741.00
158_T171_K1.7321.00
27_H87_E1.6801.00
120_S161_V1.6051.00
12_V95_L1.6021.00
54_R78_D1.5921.00
108_L114_L1.5881.00
8_K76_I1.5611.00
116_L174_I1.5521.00
6_G12_V1.5441.00
30_N82_Y1.5391.00
114_L174_I1.5281.00
83_I92_E1.5241.00
127_S162_L1.4891.00
31_S83_I1.4851.00
131_R136_K1.4831.00
120_S128_V1.4761.00
31_S35_K1.4581.00
133_P158_T1.4391.00
5_L96_L1.4371.00
56_D72_K1.4050.99
132_S157_W1.3860.99
18_A86_V1.3440.99
11_T73_N1.3240.99
129_Q136_K1.3120.99
58_R70_I1.2890.99
110_Q151_L1.2830.99
114_L146_V1.2820.99
18_A26_F1.2780.99
107_H175_V1.2650.99
113_S148_Q1.2470.99
128_V142_K1.2410.98
116_L172_I1.2130.98
5_L98_F1.2040.98
31_S81_T1.2030.98
4_V12_V1.2000.98
114_L149_L1.1890.98
108_L112_Q1.1500.97
160_T167_K1.1390.97
7_K98_F1.1320.97
27_H34_I1.1190.96
154_S176_V1.1030.96
28_W69_L1.0870.96
55_A71_I1.0840.96
15_T66_N1.0770.95
79_S97_V1.0700.95
132_S135_G1.0640.95
56_D70_I1.0600.95
12_V71_I1.0540.95
6_G10_D1.0480.94
122_P163_Q1.0450.94
128_V161_V1.0320.94
29_K34_I1.0290.94
14_L95_L1.0170.93
130_C144_L1.0090.93
108_L174_I1.0050.93
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  
1wioA2199.90.028Contact Map
4q6iC4199.90.056Contact Map
4h8wC10.988899.90.059Contact Map
1qz1A10.898999.80.12Contact Map
1cs6A10.870899.80.126Contact Map
2rikA10.904599.80.129Contact Map
3kldA10.88299.80.13Contact Map
3b43A10.904599.80.13Contact Map
2v5mA10.910199.80.135Contact Map
2v5tA10.870899.80.136Contact 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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