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dbpa3

ID: 1502231798 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (451)
Sequences: 5634 (3820.5)
Seq/Len: 12.492
Nf(neff/√len): 179.9

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: 12.492).

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
58_G91_L4.7791.00
61_L74_A4.0341.00
128_A133_L3.9651.00
11_P63_Q3.8711.00
29_V45_V3.8571.00
136_H141_T3.6211.00
37_I181_L3.3581.00
78_C87_V3.2691.00
20_E97_F3.0941.00
318_L343_S3.0591.00
41_K203_L3.0251.00
90_E93_R2.6131.00
248_C254_C2.5911.00
251_K274_D2.5871.00
309_S337_N2.5841.00
138_Q169_D2.5541.00
91_L103_I2.5471.00
61_L151_V2.5471.00
266_Q294_V2.3701.00
248_C257_V2.3651.00
192_A204_A2.3481.00
134_L169_D2.3441.00
128_A142_V2.2951.00
150_L171_I2.2591.00
36_A203_L2.2491.00
77_L133_L2.2451.00
20_E96_R2.2261.00
329_I341_A2.2101.00
36_A205_I2.1271.00
233_Q264_V2.1161.00
253_D317_E2.0431.00
134_L138_Q2.0401.00
75_L147_L2.0031.00
23_Y55_A1.9671.00
269_L292_A1.9651.00
315_N343_S1.9591.00
285_V289_N1.9411.00
319_A325_H1.9231.00
71_Q146_A1.8831.00
5_S19_N1.8641.00
17_N97_F1.8621.00
218_Q325_H1.8611.00
104_L123_P1.8581.00
216_I333_A1.8461.00
286_R291_S1.8361.00
217_E340_L1.8301.00
64_Q148_N1.8271.00
257_V296_V1.8181.00
88_A103_I1.8131.00
218_Q329_I1.8111.00
14_Q63_Q1.7871.00
255_Q270_S1.7821.00
37_I43_V1.7721.00
215_P338_S1.7261.00
258_C268_A1.7241.00
12_P16_T1.6621.00
135_D139_K1.6601.00
61_L149_T1.6571.00
254_C272_H1.6491.00
228_K317_E1.6361.00
10_L59_L1.6291.00
261_L296_V1.6261.00
62_L98_L1.6201.00
91_L125_I1.6201.00
229_I260_A1.6001.00
269_L283_T1.5921.00
14_Q59_L1.5881.00
157_R160_D1.5831.00
40_G179_Q1.5791.00
232_L314_V1.5751.00
38_L63_Q1.5631.00
258_C270_S1.5551.00
85_D281_D1.5461.00
73_Q148_N1.5391.00
312_L342_I1.5341.00
244_C314_V1.5311.00
36_A39_A1.5031.00
232_L316_F1.5011.00
16_T97_F1.5001.00
88_A105_T1.4901.00
168_D197_R1.4891.00
42_D200_R1.4871.00
73_Q124_H1.4841.00
370_P375_I1.4661.00
297_A301_A1.4631.00
42_D202_P1.4571.00
411_D414_D1.4501.00
113_G117_D1.4441.00
18_L23_Y1.4121.00
116_R141_T1.4040.99
57_F87_V1.4040.99
66_D69_L1.4040.99
199_Q202_P1.3890.99
7_L10_L1.3870.99
217_E365_N1.3720.99
46_Q206_E1.3720.99
246_V294_V1.3710.99
164_S168_D1.3650.99
255_Q272_H1.3610.99
315_N329_I1.3570.99
137_L173_F1.3350.99
74_A149_T1.3340.99
45_V183_F1.3310.99
387_I400_V1.3310.99
28_P32_A1.3290.99
220_F345_C1.3180.99
213_L216_I1.3160.99
219_Q340_L1.3130.99
396_R399_D1.3110.99
406_G409_G1.3100.99
400_V425_V1.2920.99
401_L415_I1.2880.99
62_L95_A1.2860.99
237_S266_Q1.2840.99
248_C296_V1.2800.99
91_L127_V1.2790.99
318_L356_I1.2770.99
219_Q367_Q1.2720.99
32_A203_L1.2650.99
370_P374_S1.2600.99
192_A196_G1.2550.99
37_I60_G1.2530.99
77_L128_A1.2500.99
41_K201_D1.2460.98
76_V91_L1.2400.98
72_T126_I1.2370.98
235_L342_I1.2330.98
19_N24_L1.2310.98
21_L93_R1.2250.98
412_G416_G1.2210.98
224_S227_G1.2200.98
64_Q149_T1.2190.98
245_V310_L1.2190.98
269_L286_R1.2050.98
371_A374_S1.2000.98
241_P244_C1.1770.98
36_A41_K1.1760.98
16_T19_N1.1680.97
371_A375_I1.1620.97
229_I316_F1.1620.97
315_N341_A1.1600.97
42_D199_Q1.1570.97
88_A92_R1.1460.97
254_C270_S1.1460.97
3_A6_T1.1460.97
244_C294_V1.1450.97
42_D180_T1.1440.97
175_P178_R1.1400.97
65_I101_T1.1380.97
169_D173_F1.1370.97
66_D124_H1.1340.97
112_F116_R1.1190.96
357_S363_K1.1130.96
229_I264_V1.1120.96
40_G64_Q1.1100.96
57_F78_C1.1080.96
301_A305_L1.1080.96
233_Q260_A1.0980.96
229_I257_V1.0920.96
42_D178_R1.0860.96
23_Y94_L1.0840.96
364_L370_P1.0830.96
65_I124_H1.0820.96
387_I390_G1.0750.95
58_G103_I1.0750.95
33_A37_I1.0740.95
55_A94_L1.0730.95
399_D402_G1.0670.95
147_L174_A1.0590.95
11_P14_Q1.0590.95
166_A169_D1.0540.95
322_P326_V1.0480.94
242_S311_E1.0450.94
403_A407_D1.0420.94
287_F295_L1.0400.94
389_G393_A1.0390.94
67_A124_H1.0380.94
405_T408_I1.0380.94
412_G415_I1.0380.94
104_L118_S1.0370.94
112_F141_T1.0340.94
217_E338_S1.0330.94
134_L166_A1.0270.94
18_L22_G1.0160.93
232_L257_V1.0120.93
89_G288_A1.0110.93
397_P401_L1.0110.93
382_M385_L1.0080.93
14_Q94_L1.0040.93
126_I142_V1.0030.93
435_H439_K1.0020.92
260_A264_V1.0000.92
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  
4pxaA10.81841000.309Contact Map
2db3A40.80741000.319Contact Map
4nhoA10.80091000.329Contact Map
4ljyA10.84681000.332Contact Map
4d25A10.80961000.337Contact Map
3fmpB20.44641000.338Contact Map
3sqwA10.97591000.34Contact Map
3i5xA10.97591000.342Contact Map
4c9bA10.81181000.348Contact Map
4w7sA20.85121000.348Contact 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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