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cb2

ID: 1515193096 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 360 (291)
Sequences: 6680 (4280.2)
Seq/Len: 22.955
Nf(neff/√len): 250.9

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: 22.955).

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
47_S84_S5.7911.00
75_S158_W3.7341.00
132_Y137_Y3.3731.00
75_S123_S3.0531.00
207_Y211_H2.9681.00
106_F179_C2.5691.00
111_G115_M2.4781.00
210_G214_W2.4291.00
126_L157_M2.3321.00
204_G208_T2.2581.00
202_F255_L2.2531.00
64_L70_Y2.2251.00
99_G102_S2.0911.00
103_K107_L2.0911.00
148_G152_V2.0581.00
126_L153_T2.0331.00
55_L74_G2.0311.00
246_T302_R1.9721.00
71_L154_L1.9711.00
104_A108_L1.8961.00
132_Y211_H1.8911.00
258_W288_C1.8861.00
253_V298_I1.8811.00
77_A80_D1.8561.00
58_I74_G1.8441.00
55_L81_F1.8291.00
137_Y140_S1.7971.00
115_M162_A1.7841.00
134_C138_P1.7651.00
80_D295_N1.7481.00
263_A267_H1.7111.00
48_A81_F1.6751.00
79_A119_A1.6731.00
80_D120_S1.6711.00
34_T38_V1.6661.00
75_S154_L1.6641.00
166_Y170_M1.6561.00
111_G169_L1.6421.00
290_I294_V1.6281.00
52_V56_Y1.6211.00
50_E293_M1.6071.00
47_S293_M1.5911.00
271_T275_D1.5701.00
124_L205_I1.5481.00
151_L155_G1.5181.00
211_H214_W1.5031.00
146_T149_R1.4571.00
82_L116_T1.4561.00
72_F150_A1.4561.00
128_A208_T1.4561.00
158_W296_P1.4501.00
130_D134_C1.4371.00
123_S158_W1.4321.00
295_N299_Y1.4181.00
125_L208_T1.4171.00
61_S309_S1.4131.00
249_L298_I1.3820.99
148_G151_L1.3750.99
133_L144_L1.3560.99
129_I208_T1.3540.99
211_H215_K1.3530.99
56_Y313_C1.3520.99
67_K70_Y1.3330.99
102_S105_V1.3310.99
168_P171_G1.3220.99
121_V254_L1.3010.99
253_V294_V1.2950.99
72_F127_T1.2910.99
152_V156_I1.2870.99
44_G84_S1.2860.99
264_L284_C1.2850.99
206_I210_G1.2800.99
249_L302_R1.2790.99
214_W217_H1.2760.99
119_A161_S1.2690.99
79_A120_S1.2630.99
57_L310_A1.2620.99
48_A84_S1.2590.99
132_Y136_R1.2550.99
80_D291_N1.2540.99
54_V296_P1.2540.99
259_F263_A1.2480.99
125_L205_I1.2460.98
79_A158_W1.2430.98
311_H315_A1.2360.98
83_A292_S1.2310.98
280_A284_C1.2160.98
194_W198_I1.2110.98
153_T157_M1.2040.98
136_R215_K1.1940.98
155_G159_V1.1840.98
122_G160_L1.1800.98
119_A158_W1.1740.98
308_S311_H1.1720.98
122_G201_L1.1710.98
125_L204_G1.1680.97
152_V155_G1.1620.97
132_Y208_T1.1550.97
115_M165_S1.1530.97
46_L293_M1.1530.97
37_A96_V1.1450.97
73_I300_A1.1370.97
133_L137_Y1.1340.97
119_A123_S1.1300.97
213_L244_A1.1180.96
157_M161_S1.1150.96
76_L123_S1.1090.96
55_L78_G1.1090.96
53_A57_L1.1070.96
241_V245_K1.1030.96
132_Y207_Y1.0920.96
135_L138_P1.0870.96
123_S154_L1.0870.96
58_I64_L1.0820.96
133_L141_Y1.0750.95
84_S293_M1.0750.95
120_S295_N1.0700.95
60_S309_S1.0700.95
147_R151_L1.0690.95
250_V299_Y1.0640.95
279_K283_F1.0630.95
306_I310_A1.0630.95
71_L151_L1.0610.95
291_N295_N1.0600.95
54_V295_N1.0570.95
216_A243_L1.0380.94
52_V81_F1.0290.94
257_C291_N1.0270.94
219_H222_S1.0210.93
248_G252_A1.0210.93
201_L205_I1.0200.93
73_I135_L1.0190.93
136_R212_V1.0180.93
37_A41_T1.0150.93
292_S295_N1.0150.93
156_I160_L1.0120.93
38_V42_L1.0100.93
72_F126_L1.0090.93
31_P35_A1.0080.93
240_D243_L1.0040.93
44_G89_C1.0040.93
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  
3uonA10.78891000.389Contact Map
4pxzA10.76671000.391Contact Map
3emlA10.80561000.406Contact Map
4iarA10.79441000.407Contact Map
4eiyA10.80561000.407Contact Map
2rh1A10.79171000.407Contact Map
3v2yA10.84441000.411Contact Map
3pblA20.76941000.412Contact Map
3vw7A10.77221000.412Contact Map
4grvA10.79441000.413Contact 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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