OPENSEQ.org
Ta-based-concatenated

ID: 1517517305 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 397 (363)
Sequences: 961 (637)
Seq/Len: 2.647
Nf(neff/√len): 33.4

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: 2.647).

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
162_L351_V5.1791.00
218_V237_A4.3191.00
116_G333_I3.6361.00
204_V249_L3.0111.00
321_V332_V2.9061.00
206_L245_V2.8951.00
152_R156_E2.8631.00
206_L221_A2.8301.00
159_I320_L2.6181.00
14_F22_W2.5221.00
210_P213_V2.2951.00
236_G247_R2.2721.00
166_V216_V2.1791.00
184_L219_V2.1601.00
236_G250_L2.1041.00
64_K254_Q2.1011.00
162_L332_V2.0961.00
115_E124_P2.0080.99
221_A248_A1.9940.99
152_R250_L1.9480.99
334_E349_V1.9140.99
247_R250_L1.8890.99
15_L18_E1.8640.99
159_I163_L1.8560.99
17_K69_I1.8380.99
116_G335_V1.8290.99
186_V206_L1.8230.99
20_L73_V1.7750.98
65_G74_S1.7730.98
158_V334_E1.6900.98
149_S161_G1.6690.97
155_E314_E1.6500.97
19_T152_R1.6410.97
125_V333_I1.6130.97
300_E303_D1.5750.96
13_A153_L1.5630.96
127_V335_V1.5380.95
238_S243_M1.5300.95
129_A133_F1.5270.95
210_P217_Y1.5240.95
152_R236_G1.5130.95
206_L219_V1.5000.95
118_D332_V1.4840.94
64_K74_S1.4760.94
46_P68_R1.4630.94
158_V161_G1.4610.93
156_E236_G1.4510.93
151_G156_E1.4350.93
118_D331_K1.4270.92
195_R199_R1.4220.92
203_R226_E1.4200.92
36_E265_S1.4020.91
158_V349_V1.4020.91
127_V350_R1.3940.91
332_V351_V1.3940.91
134_H145_T1.3890.91
115_E126_Y1.3770.91
221_A249_L1.3750.90
11_F243_M1.3690.90
195_R198_E1.3600.90
50_R86_E1.3470.89
339_L345_P1.3370.89
213_V367_M1.3360.89
36_E51_R1.3180.88
96_P108_T1.3010.87
219_V304_L1.2850.86
18_E21_R1.2830.86
157_A347_V1.2810.86
74_S254_Q1.2720.85
211_S214_E1.2700.85
152_R247_R1.2660.85
321_V351_V1.2660.85
35_V38_F1.2640.85
243_M247_R1.2500.84
4_I11_F1.2490.84
123_E315_K1.2490.84
151_G236_G1.2480.84
127_V333_I1.2450.83
165_V349_V1.2390.83
149_S347_V1.2340.83
146_N165_V1.2280.82
221_A252_V1.2280.82
118_D121_T1.2240.82
78_E251_E1.2200.82
163_L237_A1.2160.81
64_K236_G1.2080.81
122_R300_E1.2070.81
120_T321_V1.2010.80
12_R238_S1.1910.80
339_L343_D1.1900.79
169_D367_M1.1800.79
208_L217_Y1.1800.79
110_P127_V1.1790.79
16_P19_T1.1770.78
185_E300_E1.1700.78
324_V354_A1.1590.77
12_R247_R1.1580.77
162_L350_R1.1510.76
62_A263_I1.1500.76
355_S365_G1.1470.76
74_S250_L1.1430.76
204_V303_D1.1400.75
64_K247_R1.1360.75
236_G254_Q1.1340.75
309_T315_K1.1310.74
12_R236_G1.1270.74
132_V350_R1.1240.74
160_Q255_G1.1240.74
223_T252_V1.1230.74
209_L218_V1.1180.73
12_R156_E1.1160.73
159_I317_T1.1120.73
154_R336_D1.1090.72
58_E264_E1.1070.72
35_V48_E1.1040.72
164_E251_E1.1040.72
85_A148_L1.1000.72
4_I9_E1.0990.71
167_E217_Y1.0950.71
123_E326_E1.0930.71
40_D256_L1.0920.71
85_A337_L1.0910.71
135_P261_R1.0900.71
234_G252_V1.0890.70
312_S315_K1.0810.70
274_F278_G1.0780.69
208_L219_V1.0780.69
37_K48_E1.0740.69
93_E97_E1.0720.69
84_A339_L1.0670.68
40_D45_I1.0640.68
78_E164_E1.0630.68
154_R158_V1.0630.68
268_R273_E1.0610.68
146_N168_R1.0600.67
65_G250_L1.0570.67
206_L332_V1.0520.67
309_T316_L1.0510.66
247_R254_Q1.0500.66
67_T70_Q1.0480.66
163_L316_L1.0450.66
220_G235_F1.0440.66
197_L249_L1.0430.66
48_E75_A1.0380.65
157_A245_V1.0360.65
210_P214_E1.0360.65
234_G248_A1.0310.64
23_I73_V1.0290.64
36_E45_I1.0290.64
151_G254_Q1.0290.64
3_D8_V1.0240.64
6_Y10_G1.0190.63
210_P216_V1.0140.62
64_K150_A1.0130.62
338_T343_D1.0120.62
114_V129_A1.0120.62
209_L220_G1.0100.62
65_G277_P1.0080.62
194_R204_V1.0060.62
11_F16_P1.0050.61
64_K167_E1.0050.61
173_I210_P1.0040.61
91_I126_Y1.0010.61
338_T346_V1.0000.61
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  
4v1tA20.9271000.361Contact Map
4q86A80.9271000.384Contact Map
3sqgA30.652493.70.943Contact Map
1hbnA20.642391.80.946Contact Map
4j56E40.239317.40.971Contact Map
1ekzA10.1763170.971Contact Map
3llhA20.158716.60.971Contact Map
2mdrA10.19913.50.972Contact Map
3adlA10.173813.20.973Contact Map
4wyqB20.183913.10.973Contact 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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