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BCII

ID: 1515603041 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 257 (217)
Sequences: 3735 (2504.6)
Seq/Len: 17.212
Nf(neff/√len): 170.0

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: 17.212).

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
114_I125_I3.7811.00
85_V115_T3.3001.00
192_N234_N3.2491.00
224_E253_L2.9491.00
171_E189_P2.8731.00
139_A158_Q2.7981.00
50_Q53_K2.7391.00
134_K155_G2.5631.00
162_N169_K2.4671.00
87_S112_V2.2781.00
169_K190_Q2.2641.00
77_N107_K2.2441.00
157_L184_I2.0021.00
74_L195_V1.9831.00
227_L250_L1.9761.00
75_V101_V1.9611.00
111_D134_K1.9041.00
164_K169_K1.8801.00
162_N171_E1.8761.00
176_G185_V1.8621.00
95_K99_E1.8521.00
100_M103_K1.8261.00
111_D136_H1.7951.00
193_I237_V1.7941.00
85_V186_V1.7941.00
136_H155_G1.7801.00
187_W194_L1.7631.00
81_G110_T1.7591.00
50_Q54_N1.7511.00
75_V82_L1.7461.00
215_Y218_E1.7381.00
55_V193_I1.7001.00
54_N191_Y1.6751.00
224_E228_K1.6691.00
168_M191_Y1.6421.00
83_V170_V1.6091.00
188_L191_Y1.5941.00
77_N82_L1.5791.00
193_I235_A1.5781.00
112_V125_I1.5671.00
54_N168_M1.5651.00
121_R240_H1.5641.00
113_I186_V1.5601.00
183_N197_G1.4851.00
82_L105_F1.4791.00
238_P241_G1.4491.00
122_I145_A1.4491.00
86_D116_H1.4411.00
155_G161_T1.4391.00
142_A146_K1.4281.00
170_V188_L1.4231.00
178_G222_S1.4101.00
115_T186_V1.4060.99
79_S167_N1.3830.99
160_V171_E1.3810.99
195_V237_V1.3710.99
82_L101_V1.3700.99
56_W77_N1.3650.99
223_I249_L1.3640.99
138_T184_I1.3460.99
50_Q56_W1.3310.99
83_V113_I1.3280.99
116_H198_C1.3240.99
74_L237_V1.3130.99
140_L143_E1.3000.99
98_I102_E1.2970.99
185_V199_L1.2900.99
121_R198_C1.2840.99
91_D95_K1.2720.99
159_T225_N1.2560.99
129_K154_L1.2550.99
78_T166_G1.2450.98
164_K167_N1.2450.98
172_T186_V1.2440.98
87_S125_I1.2270.98
94_T127_T1.2220.98
244_G248_L1.2110.98
78_T83_V1.2070.98
157_L161_T1.2060.98
112_V128_L1.2020.98
139_A156_D1.1920.98
225_N228_K1.1870.98
75_V84_L1.1710.98
142_A156_D1.1630.97
120_D240_H1.1590.97
172_T184_I1.1580.97
80_K166_G1.1540.97
168_M188_L1.1310.97
111_D155_G1.1280.97
170_V186_V1.1230.97
83_V111_D1.1090.96
99_E103_K1.1050.96
118_H121_R1.0980.96
227_L253_L1.0910.96
171_E187_W1.0890.96
73_G88_S1.0860.96
158_Q161_T1.0720.95
194_L236_V1.0700.95
55_V76_L1.0670.95
116_H121_R1.0670.95
220_S224_E1.0670.95
115_T197_G1.0670.95
115_T195_V1.0660.95
178_G218_E1.0630.95
169_K189_P1.0500.94
58_H97_L1.0490.94
168_M190_Q1.0480.94
80_K110_T1.0330.94
98_I128_L1.0220.93
98_I127_T1.0190.93
54_N79_S1.0130.93
78_T81_G1.0100.93
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  
4c1hA10.85991000.417Contact Map
4d1tA10.86771000.424Contact Map
3l6nA10.83661000.429Contact Map
2yheA60.94551000.432Contact Map
1m2xA40.82491000.432Contact Map
1a7tA20.84821000.432Contact Map
2fhxA20.80931000.436Contact Map
4eybA20.88721000.441Contact Map
2zo4A10.78991000.442Contact Map
2yntA20.84051000.443Contact 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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