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dbpa2

ID: 1502211160 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 445 (416)
Sequences: 8917 (4261.3)
Seq/Len: 21.435
Nf(neff/√len): 208.9

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: 21.435).

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
55_T68_S4.7321.00
274_R279_S4.5521.00
371_A374_C4.1841.00
257_L280_A3.7511.00
52_W85_G3.7401.00
255_S281_R3.3751.00
105_A109_E3.3191.00
242_C258_A2.8571.00
270_Q274_R2.8081.00
70_E85_G2.8051.00
66_K137_Q2.7811.00
107_V134_K2.5931.00
106_L113_S2.5441.00
59_V68_S2.5061.00
106_L110_I2.4471.00
40_N53_Y2.4291.00
246_C258_A2.4051.00
69_I119_T2.3471.00
278_G281_R2.2951.00
123_Q128_S2.2951.00
82_S86_N2.2861.00
35_I189_E2.2801.00
271_T280_A2.2701.00
297_S325_S2.2591.00
232_H297_S2.2441.00
118_M128_S2.2051.00
198_A326_S2.1941.00
71_E120_L2.1691.00
231_D325_S2.1541.00
273_V277_N2.0981.00
43_Y164_R2.0891.00
239_V262_D2.0661.00
115_Q129_L2.0621.00
387_D392_L2.0311.00
257_L274_R2.0171.00
115_Q120_L2.0041.00
72_V81_I1.9951.00
347_M367_A1.9871.00
214_Q302_V1.9871.00
306_L331_S1.9691.00
85_G114_S1.9661.00
254_Q282_I1.9571.00
47_S183_L1.9401.00
257_L271_T1.9351.00
26_Q92_L1.9311.00
59_V112_S1.9231.00
69_I138_Q1.9201.00
35_I38_T1.9051.00
88_C294_D1.8421.00
342_N346_E1.8411.00
307_A313_H1.8411.00
235_G289_A1.8271.00
246_C250_N1.8031.00
44_L57_Y1.7971.00
84_F88_C1.7971.00
84_F294_D1.7851.00
65_V137_Q1.7791.00
301_V320_T1.7731.00
246_C284_V1.7711.00
243_Q247_D1.7711.00
170_A184_M1.7101.00
343_I368_A1.7041.00
113_S119_T1.6821.00
300_L330_I1.6771.00
38_T42_I1.6571.00
32_D49_L1.6441.00
110_I113_S1.6421.00
69_I135_T1.6381.00
17_C57_Y1.6371.00
342_N345_S1.6351.00
343_I371_A1.6171.00
264_E267_D1.6081.00
95_G111_R1.5951.00
269_D273_V1.5811.00
26_Q91_R1.5731.00
42_I183_L1.5571.00
79_I83_E1.5511.00
121_S125_A1.5411.00
52_W90_G1.5301.00
95_G105_A1.5191.00
195_T326_S1.5141.00
22_V25_L1.5031.00
423_Q427_K1.4951.00
30_L37_I1.4831.00
367_A371_A1.4661.00
233_G282_I1.4621.00
215_T219_A1.4591.00
243_Q258_A1.4501.00
221_N231_D1.4501.00
34_P190_N1.4291.00
68_S142_L1.4291.00
276_A294_D1.4271.00
249_L256_A1.4251.00
287_D316_R1.4181.00
231_D299_E1.4161.00
103_I129_L1.4111.00
103_I123_Q1.3970.99
18_T22_V1.3850.99
367_A370_M1.3800.99
141_S159_N1.3770.99
256_A284_V1.3760.99
24_T53_Y1.3710.99
259_L268_R1.3650.99
421_V424_K1.3480.99
102_N118_M1.3350.99
246_C256_A1.3320.99
40_N44_L1.3300.99
215_T252_V1.3230.99
147_A307_A1.3220.99
236_F245_V1.3190.99
135_T138_Q1.3180.99
245_V248_A1.3080.99
95_G109_E1.3070.99
254_Q281_R1.3010.99
377_G439_C1.2970.99
199_S317_I1.2940.99
55_T142_L1.2920.99
424_K427_K1.2730.99
241_D244_A1.2700.99
247_D250_N1.2690.99
418_R422_A1.2580.99
41_I44_L1.2550.99
252_V282_I1.2540.99
83_E294_D1.2540.99
68_S85_G1.2500.99
20_L57_Y1.2390.98
424_K428_Q1.2370.98
198_A328_L1.2350.98
41_I45_I1.2320.98
418_R421_V1.2310.98
103_I128_S1.2300.98
247_D251_A1.2300.98
245_V284_V1.2180.98
55_T112_S1.2180.98
62_I112_S1.2150.98
85_G112_S1.2070.98
54_M140_A1.2070.98
72_V78_S1.2050.98
417_V421_V1.2000.98
48_L178_R1.1990.98
173_A177_A1.1980.98
25_L30_L1.1910.98
317_I329_A1.1910.98
99_L128_S1.1810.98
23_D56_C1.1740.98
52_W89_A1.1710.98
42_I185_V1.1680.97
242_C260_H1.1640.97
70_E81_I1.1610.97
105_A110_I1.1610.97
67_K139_S1.1590.97
196_D326_S1.1590.97
56_C60_V1.1550.97
199_S331_S1.1550.97
235_G282_I1.1550.97
233_G302_V1.1520.97
373_L385_P1.1490.97
263_L271_T1.1460.97
58_L139_S1.1330.97
34_P38_T1.1310.97
129_L135_T1.1290.97
259_L271_T1.1290.97
67_K111_R1.1270.97
37_I41_I1.1130.96
32_D40_N1.1130.96
301_V329_A1.1120.96
42_I45_I1.1120.96
24_T37_I1.1110.96
40_N54_M1.1040.96
219_A254_Q1.0980.96
217_I330_I1.0980.96
422_A426_W1.0910.96
295_I298_L1.0890.96
271_T274_R1.0750.95
60_V111_R1.0690.95
303_N317_I1.0640.95
99_L103_I1.0600.95
289_A293_L1.0560.95
419_Q423_Q1.0540.95
29_F49_L1.0510.94
259_L285_A1.0350.94
216_N220_L1.0340.94
20_L53_Y1.0250.93
235_G245_V1.0230.93
122_E126_A1.0220.93
370_M374_C1.0140.93
425_A428_Q1.0080.93
434_I439_C1.0060.93
195_T324_G1.0040.93
34_P37_I1.0010.92
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  
4pxaA10.78881000.455Contact Map
3sqwA10.95061000.457Contact Map
3i5xA10.95281000.463Contact Map
2db3A40.77531000.463Contact Map
3fmpB20.40671000.476Contact Map
4nhoA10.77081000.479Contact Map
4w7sA20.82021000.48Contact Map
4d25A10.77531000.481Contact Map
4ljyA10.83151000.485Contact Map
4c9bA10.7821000.494Contact 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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