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OPENSEQ.org
ABCA4-593-922
ID: 1490921423 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 330 (298)
Sequences: 3227 (2313.5)
Seq/Len: 10.829
Nf(neff/√len): 134.0
Jackhmmer Results: (2016_04)
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: 10.829).

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 > 50% 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
83_V169_A3.6211.00
144_F213_G3.5401.00
79_V173_S3.2901.00
150_T255_A3.2681.00
17_A20_Q2.9601.00
158_L261_L2.6491.00
147_A252_L2.5651.00
252_L256_A2.2641.00
249_Q253_L2.2601.00
253_L257_V2.2061.00
301_A304_K2.1601.00
21_D25_Q2.1371.00
116_M149_S2.0071.00
147_A251_M1.9361.00
279_W282_L1.9311.00
302_L305_T1.9121.00
145_L210_F1.8711.00
87_E166_A1.8131.00
264_Y268_V1.7661.00
154_M255_A1.7561.00
151_A251_M1.6861.00
158_L206_S1.6431.00
226_G229_W1.6081.00
24_E27_I1.5941.00
147_A248_M1.5701.00
91_K266_D1.5691.00
206_S210_F1.5521.00
112_S157_F1.5521.00
105_W112_S1.5361.00
301_A305_T1.5081.00
10_R13_W1.4951.00
300_R303_E1.4861.00
172_C176_I1.4711.00
221_E226_G1.4441.00
197_E201_A1.4401.00
148_F207_P1.4321.00
12_I17_A1.4271.00
105_W157_F1.4241.00
139_F143_L1.4181.00
280_Y284_Q1.4050.99
299_E302_L1.3960.99
42_L45_M1.3930.99
212_F216_Y1.3920.99
296_T299_E1.3870.99
121_F125_I1.3850.99
117_S146_L1.3790.99
209_A251_M1.3740.99
298_E304_K1.3640.99
44_Q47_Y1.3550.99
161_T262_A1.3520.99
94_L99_V1.3450.99
250_M254_D1.3440.99
154_M262_A1.3440.99
94_L97_Q1.3430.99
206_S209_A1.3360.99
40_I44_Q1.3230.99
42_L46_P1.3210.99
213_G244_F1.3100.99
298_E301_A1.2980.99
298_E303_E1.2970.99
162_F265_L1.2920.99
105_W262_A1.2920.99
278_P282_L1.2920.99
295_S298_E1.2900.99
270_P274_G1.2900.99
299_E303_E1.2790.99
84_L88_L1.2750.99
297_R300_R1.2690.99
24_E28_T1.2650.99
268_V281_F1.2590.99
274_G281_F1.2570.99
264_Y281_F1.2560.99
15_G18_Y1.2560.99
95_K101_N1.2500.99
293_G301_A1.2480.99
150_T154_M1.2450.98
300_R304_K1.2390.98
299_E305_T1.2390.98
206_S258_Y1.2210.98
297_R305_T1.2180.98
296_T301_A1.2140.98
294_C297_R1.2050.98
294_C298_E1.2000.98
85_E91_K1.2000.98
279_W283_L1.1970.98
121_F142_F1.1910.98
157_F262_A1.1750.98
43_Q46_P1.1730.98
297_R302_L1.1710.98
280_Y283_L1.1700.97
254_D258_Y1.1640.97
38_V44_Q1.1610.97
227_L244_F1.1610.97
297_R301_A1.1610.97
181_Y184_H1.1600.97
21_D28_T1.1550.97
10_R14_G1.1550.97
267_Q277_L1.1530.97
80_K170_A1.1520.97
296_T300_R1.1500.97
171_A174_G1.1490.97
245_L249_Q1.1440.97
180_L207_P1.1390.97
120_I149_S1.1340.97
43_Q48_P1.1280.97
94_L108_W1.1230.97
285_E288_W1.1220.97
270_P273_Y1.1210.97
117_S142_F1.1190.96
291_G294_C1.1160.96
207_P210_F1.1090.96
203_S250_M1.0930.96
248_M252_L1.0910.96
137_D140_I1.0900.96
293_G297_R1.0900.96
85_E99_V1.0900.96
283_L286_S1.0900.96
27_I31_Q1.0890.96
294_C303_E1.0880.96
235_S238_E1.0840.96
298_E302_L1.0840.96
292_E295_S1.0830.96
285_E289_L1.0800.95
9_F12_I1.0770.95
105_W266_D1.0740.95
293_G298_E1.0670.95
298_E305_T1.0650.95
180_L183_P1.0610.95
203_S206_S1.0600.95
12_I18_Y1.0580.95
8_D12_I1.0560.95
87_E165_K1.0560.95
147_A255_A1.0540.95
251_M254_D1.0530.95
293_G303_E1.0510.94
297_R304_K1.0490.94
259_G263_W1.0440.94
63_F67_M1.0420.94
296_T303_E1.0420.94
44_Q48_P1.0320.94
92_E95_K1.0310.94
236_P239_G1.0290.94
100_S103_V1.0270.94
38_V42_L1.0220.93
42_L48_P1.0220.93
9_F44_Q1.0200.93
300_R305_T1.0190.93
104_I107_T1.0150.93
271_G276_P1.0150.93
296_T302_L1.0110.93
97_Q108_W1.0110.93
169_A175_V1.0040.93
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  
4ltoA40.40324.40.95Contact Map
3j9pD40.754518.70.952Contact Map
2k21A10.363618.60.952Contact Map
4cbcA40.272717.40.953Contact Map
2z73A20.89.20.958Contact Map
3oduA20.74247.80.96Contact Map
4pypA10.712160.962Contact Map
3wdoA10.872750.963Contact Map
3emlA10.72124.70.964Contact Map
2m0qA10.36973.90.965Contact 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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