OPENSEQ.org
2ndY-based-concatenated

ID: 1517517198 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 397 (365)
Sequences: 968 (650.7)
Seq/Len: 2.652
Nf(neff/√len): 34.1

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: 2.652).

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_V5.1721.00
218_V237_A4.1841.00
116_G333_I3.5631.00
204_V249_L3.0771.00
152_R156_E2.8801.00
206_L245_V2.8411.00
206_L221_A2.7001.00
321_V332_V2.6921.00
159_I320_L2.6841.00
14_F22_W2.5191.00
166_V216_V2.3421.00
64_K254_Q2.2821.00
236_G247_R2.2151.00
210_P213_V2.1501.00
162_L332_V2.0991.00
115_E124_P2.0901.00
221_A248_A2.0111.00
152_R250_L2.0040.99
236_G250_L1.9640.99
159_I163_L1.9600.99
65_G74_S1.9340.99
247_R250_L1.9020.99
186_V206_L1.8950.99
184_L219_V1.8860.99
17_K69_I1.8630.99
94_R98_G1.8550.99
15_L18_E1.8430.99
334_E349_V1.7860.99
20_L73_V1.7710.98
116_G335_V1.7240.98
155_E314_E1.7030.98
19_T152_R1.7000.98
13_A153_L1.6420.97
149_S161_G1.6350.97
158_V334_E1.6220.97
125_V333_I1.5900.96
300_E303_D1.5900.96
238_S243_M1.5620.96
64_K74_S1.5550.96
50_R86_E1.5530.96
332_V351_V1.5420.95
221_A249_L1.5200.95
118_D331_K1.4980.94
96_P103_P1.4900.94
156_E236_G1.4830.94
210_P217_Y1.4750.94
151_G156_E1.4700.94
127_V350_R1.4690.94
203_R226_E1.4690.94
211_S214_E1.4670.94
97_E108_T1.4550.93
152_R236_G1.4490.93
129_A133_F1.4450.93
206_L219_V1.4440.93
127_V335_V1.4400.93
118_D332_V1.4110.92
85_A148_L1.4030.92
85_A337_L1.3910.91
36_E265_S1.3900.91
185_E300_E1.3800.91
74_S254_Q1.3740.90
11_F243_M1.3730.90
115_E126_Y1.3660.90
195_R199_R1.3650.90
243_M247_R1.3650.90
208_L217_Y1.3620.90
110_P127_V1.3600.90
46_P68_R1.3570.90
209_L218_V1.3440.89
18_E21_R1.3290.88
157_A347_V1.3090.87
158_V161_G1.3070.87
64_K236_G1.3020.87
134_H145_T1.2960.87
160_Q255_G1.2910.86
118_D121_T1.2900.86
162_L350_R1.2760.85
35_V38_F1.2750.85
158_V349_V1.2720.85
36_E51_R1.2710.85
146_N165_V1.2600.84
169_D367_M1.2460.84
165_V349_V1.2340.83
58_E264_E1.2330.83
16_P19_T1.2260.82
127_V333_I1.2250.82
120_T321_V1.2240.82
4_I9_E1.2190.82
219_V304_L1.2120.81
339_L343_D1.2090.81
78_E251_E1.2030.81
195_R198_E1.1940.80
159_I317_T1.1750.78
213_V367_M1.1710.78
152_R247_R1.1690.78
339_L345_P1.1690.78
12_R238_S1.1680.78
324_V354_A1.1630.77
167_E254_Q1.1620.77
208_L219_V1.1610.77
236_G254_Q1.1600.77
163_L237_A1.1590.77
338_T346_V1.1550.77
64_K167_E1.1470.76
154_R158_V1.1470.76
40_D45_I1.1460.76
84_A339_L1.1410.75
210_P214_E1.1390.75
355_S365_G1.1380.75
12_R247_R1.1320.75
210_P216_V1.1280.74
221_A252_V1.1280.74
87_P249_L1.1220.74
215_G332_V1.1190.73
223_T252_V1.1160.73
135_P261_R1.1150.73
149_S347_V1.1110.73
194_R204_V1.1100.73
234_G248_A1.1050.72
40_D256_L1.1050.72
132_V350_R1.1040.72
123_E315_K1.1030.72
62_A263_I1.0990.71
12_R156_E1.0960.71
64_K247_R1.0960.71
154_R336_D1.0950.71
4_I11_F1.0920.71
164_E251_E1.0870.70
157_A245_V1.0870.70
209_L220_G1.0860.70
184_L319_E1.0840.70
309_T316_L1.0800.70
321_V351_V1.0730.69
165_V351_V1.0680.68
12_R236_G1.0640.68
11_F16_P1.0640.68
309_T312_S1.0630.68
74_S250_L1.0560.67
78_E164_E1.0470.66
6_Y10_G1.0450.66
366_N369_E1.0440.66
65_G254_Q1.0420.66
35_V48_E1.0400.65
208_L343_D1.0400.65
163_L316_L1.0350.65
122_R300_E1.0330.65
40_D51_R1.0320.64
201_V305_D1.0270.64
6_Y9_E1.0240.64
114_V129_A1.0240.64
187_H299_V1.0210.63
183_E205_E1.0200.63
64_K150_A1.0190.63
36_E45_I1.0190.63
67_T70_Q1.0160.63
173_I210_P1.0150.63
65_G247_R1.0130.62
247_R254_Q1.0120.62
260_R263_I1.0110.62
77_M344_V1.0050.61
165_V354_A1.0030.61
14_F18_E1.0000.61
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  
4v1tA20.92441000.353Contact Map
4q86A80.93451000.384Contact Map
1hbnA20.634891.50.946Contact Map
3sqgA30.816177.40.955Contact Map
3adlA10.173818.30.97Contact Map
1ekzA10.176316.10.971Contact Map
3llhA20.158715.80.971Contact Map
2mdrA10.219113.30.972Contact Map
4j56E40.2393110.973Contact Map
4wyqB20.183910.40.973Contact 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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