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dbpa4

ID: 1502231822 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (451)
Sequences: 5781 (3812.8)
Seq/Len: 12.818
Nf(neff/√len): 179.5

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: 12.818).

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_L4.6431.00
61_L74_A3.9761.00
128_A133_L3.9691.00
29_V45_V3.7961.00
11_P63_Q3.7281.00
136_H141_T3.6321.00
78_C87_V3.4121.00
37_I181_L3.2511.00
41_K203_L3.2371.00
20_E97_F3.2341.00
318_L343_S2.9641.00
138_Q169_D2.7061.00
248_C254_C2.6581.00
91_L103_I2.6081.00
61_L151_V2.4861.00
251_K274_D2.4821.00
36_A203_L2.4561.00
309_S337_N2.4541.00
134_L169_D2.4211.00
90_E93_R2.3901.00
192_A204_A2.3821.00
77_L133_L2.3791.00
150_L171_I2.3011.00
266_Q294_V2.2701.00
20_E96_R2.2621.00
128_A142_V2.2231.00
248_C257_V2.2041.00
233_Q264_V2.1581.00
5_S19_N2.1421.00
217_E365_N2.1291.00
36_A205_I2.1281.00
134_L138_Q2.0901.00
329_I341_A2.0721.00
14_Q63_Q2.0251.00
217_E340_L1.9491.00
75_L147_L1.9401.00
319_A325_H1.9391.00
253_D317_E1.9311.00
23_Y55_A1.9061.00
215_P338_S1.9031.00
61_L149_T1.8911.00
315_N343_S1.8861.00
71_Q146_A1.8561.00
269_L292_A1.8551.00
104_L123_P1.8541.00
285_V289_N1.8321.00
12_P16_T1.8281.00
218_Q325_H1.8081.00
16_T97_F1.8071.00
254_C272_H1.7651.00
255_Q270_S1.7631.00
286_R291_S1.7491.00
218_Q329_I1.7331.00
216_I333_A1.7331.00
64_Q148_N1.7211.00
37_I43_V1.7141.00
17_N97_F1.6971.00
258_C268_A1.6891.00
88_A103_I1.6881.00
40_G179_Q1.6831.00
135_D139_K1.6601.00
228_K317_E1.6531.00
244_C314_V1.6331.00
88_A105_T1.6191.00
257_V296_V1.6181.00
73_Q148_N1.6041.00
42_D202_P1.6001.00
38_L63_Q1.5971.00
246_V294_V1.5951.00
258_C270_S1.5791.00
14_Q59_L1.5751.00
91_L125_I1.5741.00
157_R160_D1.5731.00
62_L98_L1.5701.00
199_Q202_P1.5531.00
116_R141_T1.5461.00
261_L296_V1.5451.00
269_L283_T1.5391.00
168_D197_R1.5281.00
66_D69_L1.5191.00
36_A39_A1.5101.00
297_A301_A1.4981.00
229_I260_A1.4711.00
46_Q206_E1.4691.00
76_V91_L1.4651.00
73_Q124_H1.4571.00
10_L59_L1.4561.00
113_G117_D1.4381.00
74_A149_T1.4381.00
406_G409_G1.4331.00
57_F87_V1.4291.00
315_N329_I1.4191.00
232_L316_F1.4091.00
91_L127_V1.4040.99
387_I400_V1.3940.99
235_L342_I1.3920.99
255_Q272_H1.3900.99
312_L342_I1.3870.99
85_D281_D1.3740.99
64_Q149_T1.3610.99
42_D200_R1.3560.99
164_S168_D1.3490.99
400_V425_V1.3460.99
18_L23_Y1.3410.99
7_L10_L1.3390.99
411_D414_D1.3320.99
401_L415_I1.3320.99
220_F345_C1.3310.99
219_Q367_Q1.3270.99
77_L128_A1.3210.99
41_K201_D1.3160.99
213_L216_I1.3160.99
219_Q340_L1.3120.99
45_V183_F1.3080.99
19_N24_L1.3050.99
21_L93_R1.3050.99
66_D124_H1.2940.99
88_A92_R1.2870.99
14_Q94_L1.2870.99
396_R399_D1.2860.99
126_I142_V1.2810.99
169_D173_F1.2790.99
32_A203_L1.2740.99
40_G64_Q1.2630.99
137_L173_F1.2630.99
254_C270_S1.2490.99
112_F116_R1.2350.98
237_S266_Q1.2290.98
244_C294_V1.2210.98
241_P244_C1.2200.98
242_S311_E1.2160.98
62_L95_A1.2150.98
232_L314_V1.2140.98
42_D180_T1.2080.98
301_A305_L1.2030.98
248_C296_V1.1990.98
175_P178_R1.1960.98
322_P359_M1.1940.98
224_S227_G1.1900.98
42_D178_R1.1900.98
229_I264_V1.1830.98
229_I257_V1.1800.98
134_L166_A1.1800.98
37_I60_G1.1780.98
357_S363_K1.1770.98
318_L356_I1.1680.97
436_K439_K1.1660.97
166_A169_D1.1570.97
269_L286_R1.1530.97
28_P32_A1.1520.97
3_A6_T1.1520.97
315_N341_A1.1480.97
104_L118_S1.1460.97
11_P14_Q1.1410.97
192_A196_G1.1410.97
23_Y94_L1.1390.97
425_V428_A1.1360.97
229_I316_F1.1280.97
112_F141_T1.1270.97
72_T126_I1.1170.96
16_T19_N1.1110.96
446_I451_C1.1050.96
102_K121_H1.1030.96
440_Q444_G1.1020.96
410_L414_D1.0980.96
36_A43_V1.0930.96
95_A101_T1.0880.96
412_G416_G1.0880.96
233_Q260_A1.0860.96
147_L174_A1.0820.96
244_C312_L1.0820.96
217_E338_S1.0800.95
389_G393_A1.0730.95
54_T87_V1.0710.95
33_A37_I1.0700.95
55_A94_L1.0680.95
245_V310_L1.0640.95
410_L415_I1.0640.95
232_L246_V1.0640.95
65_I101_T1.0630.95
287_F295_L1.0600.95
415_I418_I1.0480.94
33_A43_V1.0450.94
222_E347_P1.0360.94
75_L174_A1.0320.94
189_E193_A1.0310.94
65_I74_A1.0260.94
57_F78_C1.0240.93
67_A124_H1.0230.93
236_L294_V1.0210.93
169_D172_R1.0180.93
402_G406_G1.0170.93
18_L22_G1.0140.93
36_A41_K1.0110.93
42_D199_Q1.0090.93
399_D402_G1.0090.93
246_V316_F1.0070.93
230_P264_V1.0030.93
416_G420_V1.0020.92
400_V405_T1.0020.92
322_P326_V1.0010.92
16_T20_E1.0000.92
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  
4pxaA10.81841000.322Contact Map
2db3A40.80741000.33Contact Map
4nhoA10.80311000.339Contact Map
4ljyA10.84681000.342Contact Map
3sqwA10.97591000.346Contact Map
3fmpB20.44641000.347Contact Map
4d25A10.80961000.347Contact Map
3i5xA10.95621000.35Contact Map
4w7sA20.85121000.353Contact Map
4c9bA10.81181000.357Contact 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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