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OPENSEQ.org

ABCA4-1-592 -force run

ID: 1490921365 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 592 (590)
Sequences: 427 (250.7)
Seq/Len: 0.724
Nf(neff/√len): 10.3

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: 0.724).

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
10_L13_K2.3540.97
10_L20_R2.3330.97
6_Q20_R2.2650.97
13_K20_R2.2230.96
6_Q10_L2.1470.95
12_W20_R2.0590.93
10_L14_N2.0500.93
6_Q13_K2.0210.92
14_N20_R1.9630.91
523_D555_D1.9280.90
531_E570_K1.9170.90
11_L20_R1.9150.90
6_Q11_L1.8870.89
9_L12_W1.8830.88
6_Q12_W1.8770.88
403_D408_R1.8740.88
6_Q14_N1.8590.88
7_I20_R1.7200.81
9_L13_K1.7170.81
370_C392_P1.7110.81
9_L14_N1.7090.81
387_W391_K1.6650.78
75_C81_C1.6510.78
405_P482_L1.6490.78
32_P36_F1.5980.74
11_L14_N1.5960.74
33_L38_V1.5840.73
519_C541_L1.5820.73
396_G519_C1.5770.73
62_P75_C1.5640.72
572_R581_T1.5620.72
63_S75_C1.5570.72
9_L20_R1.5520.71
7_I13_K1.5470.71
387_W392_P1.5470.71
7_I10_L1.5430.71
393_L399_L1.5410.71
270_L278_S1.5400.70
28_E36_F1.5380.70
205_C230_C1.5310.70
28_E32_P1.5280.70
32_P39_L1.5050.68
392_P396_G1.5040.68
6_Q9_L1.5030.68
28_E39_L1.4920.67
75_C79_N1.4810.66
553_F581_T1.4800.66
13_K18_R1.4780.66
6_Q18_R1.4760.66
404_S523_D1.4740.66
32_P43_R1.4710.65
54_C81_C1.4680.65
28_E43_R1.4620.65
9_L16_T1.4500.64
8_Q19_K1.4420.63
12_W18_R1.4370.63
69_W72_G1.4290.62
12_W19_K1.4220.61
10_L18_R1.4180.61
61_M394_L1.4130.61
36_F43_R1.4130.61
519_C524_K1.4090.60
370_C396_G1.4080.60
33_L37_L1.3930.59
7_I12_W1.3880.59
275_G279_D1.3870.59
370_C519_C1.3870.59
401_T455_L1.3860.59
57_P69_W1.3830.58
5_R15_W1.3780.58
58_N69_W1.3730.57
276_I280_M1.3680.57
7_I14_N1.3670.57
25_F48_L1.3600.56
370_C387_W1.3480.55
32_P35_L1.3440.55
104_R109_F1.3420.55
9_L19_K1.3390.55
270_L274_G1.3390.55
248_V253_L1.3370.54
551_V569_Y1.3330.54
37_L41_W1.3320.54
575_I585_K1.3220.53
284_I562_S1.3190.53
28_E35_L1.3120.52
57_P60_A1.3110.52
33_L39_L1.3090.52
573_M578_V1.3040.52
411_L525_F1.3030.52
397_K526_E1.2990.51
264_R269_N1.2980.51
24_R31_W1.2920.51
571_I581_T1.2890.50
9_L21_Q1.2890.50
181_L232_L1.2890.50
279_D283_R1.2890.50
28_E33_L1.2860.50
47_P82_F1.2860.50
286_E291_P1.2820.50
33_L36_F1.2750.49
14_N18_R1.2700.49
55_H58_N1.2670.48
36_F39_L1.2660.48
24_R40_I1.2620.48
553_F564_P1.2600.48
59_K79_N1.2520.47
267_G281_S1.2500.47
550_G570_K1.2480.47
56_F78_N1.2470.47
69_W76_N1.2420.46
12_W21_Q1.2400.46
32_P38_V1.2380.46
537_R540_S1.2360.46
13_K19_K1.2340.46
411_L551_V1.2300.45
287_F294_Q1.2280.45
13_K22_K1.2250.45
3_F7_I1.2220.45
10_L16_T1.2190.44
10_L21_Q1.2180.44
27_V34_S1.2150.44
65_G71_Q1.2080.43
16_T19_K1.2080.43
407_A530_D1.2070.43
341_E344_N1.2010.43
547_F550_G1.1990.43
86_T96_N1.1990.43
6_Q21_Q1.1980.43
32_P65_G1.1940.42
24_R46_N1.1930.42
244_L249_D1.1930.42
11_L15_W1.1900.42
553_F569_Y1.1880.42
500_R506_T1.1880.42
18_R21_Q1.1850.42
7_I11_L1.1840.41
69_W79_N1.1810.41
89_E92_G1.1800.41
104_R108_D1.1770.41
10_L17_L1.1750.41
538_A541_L1.1740.41
140_R143_P1.1730.41
39_L43_R1.1710.40
125_I128_E1.1700.40
3_F20_R1.1670.40
291_P294_Q1.1670.40
274_G279_D1.1670.40
265_S269_N1.1670.40
62_P65_G1.1660.40
573_M576_D1.1650.40
570_K591_S1.1640.40
553_F571_I1.1630.40
103_A113_L1.1630.40
278_S281_S1.1620.40
11_L18_R1.1620.40
69_W73_I1.1600.40
24_R47_P1.1600.40
12_W22_K1.1590.39
57_P80_P1.1560.39
181_L539_L1.1560.39
12_W16_T1.1500.39
144_E249_D1.1490.39
10_L19_K1.1440.38
547_F585_K1.1430.38
17_L20_R1.1420.38
17_L24_R1.1420.38
572_R591_S1.1400.38
69_W80_P1.1390.38
8_Q15_W1.1380.38
3_F6_Q1.1360.38
261_L401_T1.1360.38
186_V452_R1.1350.37
234_Q532_T1.1340.37
134_Q532_T1.1330.37
233_S530_D1.1310.37
4_V17_L1.1310.37
157_L163_L1.1310.37
24_R45_A1.1300.37
489_S492_D1.1300.37
574_D578_V1.1270.37
17_L22_K1.1260.37
3_F10_L1.1250.37
324_C573_M1.1230.37
63_S71_Q1.1200.36
11_L22_K1.1200.36
526_E537_R1.1190.36
181_L214_I1.1190.36
175_D186_V1.1160.36
378_E391_K1.1150.36
411_L533_Q1.1140.36
270_L276_I1.1120.36
28_E38_V1.1100.36
522_L575_I1.1090.35
14_N19_K1.1080.35
62_P81_C1.1050.35
11_L21_Q1.1040.35
167_L249_D1.1000.35
383_T387_W1.1000.35
27_V41_W1.1000.35
3_F13_K1.0980.35
11_L17_L1.0970.35
13_K16_T1.0970.35
192_A196_P1.0960.34
553_F572_R1.0940.34
287_F295_D1.0930.34
55_H81_C1.0910.34
7_I19_K1.0910.34
398_I409_R1.0900.34
180_L184_S1.0890.34
238_Q254_F1.0890.34
370_C391_K1.0870.34
421_L447_Q1.0850.34
45_A51_H1.0830.33
63_S67_L1.0830.33
25_F38_V1.0830.33
428_V510_L1.0830.33
72_G86_T1.0820.33
3_F22_K1.0810.33
46_N538_A1.0800.33
106_Y117_P1.0800.33
547_F578_V1.0770.33
172_G516_Y1.0770.33
547_F573_M1.0760.33
104_R113_L1.0750.33
3_F12_W1.0730.33
35_L46_N1.0690.32
63_S81_C1.0680.32
21_Q55_H1.0680.32
31_W39_L1.0630.32
13_K28_E1.0600.32
569_Y581_T1.0600.32
316_M323_L1.0600.32
55_H69_W1.0600.32
391_K396_G1.0590.32
371_N451_I1.0550.31
11_L19_K1.0550.31
3_F14_N1.0550.31
519_C573_M1.0540.31
24_R41_W1.0530.31
552_V570_K1.0530.31
7_I15_W1.0520.31
103_A106_Y1.0520.31
535_T539_L1.0520.31
58_N89_E1.0510.31
70_L75_C1.0490.31
418_F574_D1.0480.31
73_I80_P1.0480.31
24_R383_T1.0470.31
324_C370_C1.0470.31
401_T552_V1.0470.31
276_I311_T1.0450.31
233_S551_V1.0440.31
403_D406_A1.0440.31
312_F317_G1.0440.31
273_W284_I1.0440.31
129_L153_I1.0410.30
24_R35_L1.0410.30
55_H59_K1.0390.30
253_L516_Y1.0380.30
59_K81_C1.0380.30
324_C396_G1.0370.30
387_W396_G1.0370.30
312_F343_N1.0360.30
58_N72_G1.0360.30
62_P79_N1.0360.30
12_W43_R1.0360.30
76_N80_P1.0360.30
570_K581_T1.0360.30
14_N17_L1.0350.30
97_Y100_S1.0340.30
47_P76_N1.0330.30
276_I476_E1.0330.30
351_I355_R1.0310.30
92_G100_S1.0310.30
38_V42_L1.0310.30
42_L48_L1.0300.30
170_N178_V1.0300.30
5_R8_Q1.0290.29
120_Q136_M1.0290.29
402_P571_I1.0290.29
578_V586_D1.0280.29
20_R32_P1.0270.29
392_P519_C1.0270.29
531_E591_S1.0260.29
396_G524_K1.0250.29
69_W89_E1.0230.29
574_D585_K1.0230.29
11_L16_T1.0220.29
25_F33_L1.0180.29
270_L275_G1.0180.29
210_L214_I1.0160.29
550_G585_K1.0160.29
24_R50_S1.0160.29
45_A48_L1.0150.29
524_K548_W1.0150.29
553_F591_S1.0140.28
265_S270_L1.0130.28
174_S228_A1.0130.28
343_N587_R1.0130.28
524_K541_L1.0130.28
13_K21_Q1.0130.28
86_T89_E1.0130.28
580_K590_D1.0110.28
55_H79_N1.0100.28
72_G76_N1.0090.28
548_W574_D1.0080.28
12_W17_L1.0080.28
119_S133_S1.0070.28
113_L117_P1.0070.28
59_K75_C1.0040.28
31_W36_F1.0040.28
507_D514_N1.0020.28
573_M586_D1.0020.28
5_R17_L1.0020.28
6_Q17_L1.0010.28
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  
2m9xA10.155444.40.981Contact Map
3aagA20.138513.20.985Contact Map
4khbA40.104712.70.985Contact Map
4zheA409.30.986Contact Map
1v9vA10.17067.10.987Contact Map
3fx7A20.11665.90.987Contact Map
3bq7A60.10985.70.987Contact Map
3hd7A20.064250.988Contact Map
2gkpA10.091250.988Contact Map
2f3nA30.10814.80.988Contact 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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