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OPENSEQ.org

cI_NDUA_40_cIII_QCR2_40_mouse

Genes: A B A+B
Length: 377 453 730
Sequences: 10537 11365 173
Seq/Len: 27.95 25.09 0.24
MirrorTree (Pazo et al. 2001) 0.33
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.15 0.01
2 0.05 0.16 0.03
5 0.06 0.17 0.06
10 0.07 0.17 0.10
20 0.09 0.18 0.21
100 0.12 0.20 0.80
0.18 0.24 3.21
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution.
Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
58_V 366_L 1.45 0.33 0.00
354_R 197_M 1.34 0.27 0.00
188_E 224_G 1.20 0.21 0.00
199_I 182_Y 1.20 0.21 0.00
108_W 234_A 1.19 0.20 0.00
248_G 244_L 1.18 0.20 0.00
74_G 110_L 1.17 0.20 0.00
198_A 280_N 1.17 0.20 0.00
163_R 427_A 1.16 0.19 0.00
58_V 146_F 1.14 0.18 0.00
128_N 201_T 1.14 0.18 0.00
61_A 116_R 1.13 0.18 0.00
265_F 234_A 1.11 0.17 0.00
272_L 207_Y 1.11 0.17 0.00
263_F 222_G 1.10 0.17 0.00
242_V 90_T 1.09 0.17 0.00
58_V 207_Y 1.09 0.17 0.00
335_L 205_L 1.08 0.17 0.00
349_S 261_Q 1.07 0.16 0.00
280_I 382_Y 1.07 0.16 0.00
336_E 206_H 1.06 0.16 0.00
285_H 182_Y 1.06 0.16 0.00
143_D 44_P 1.05 0.15 0.00
128_N 232_Q 1.03 0.14 0.00
97_M 58_L 1.01 0.14 0.00
339_G 282_E 1.01 0.14 0.00
165_I 133_L 1.01 0.14 0.00
58_V 436_K 1.01 0.14 0.00
341_Q 48_V 1.00 0.14 0.00
71_N 436_K 0.98 0.13 0.00
80_V 294_G 0.98 0.13 0.00
188_E 238_L 0.97 0.13 0.00
112_D 72_E 0.96 0.13 0.00
58_V 231_K 0.96 0.13 0.00
184_K 224_G 0.96 0.13 0.00
278_K 323_V 0.95 0.12 0.00
58_V 210_Q 0.95 0.12 0.00
183_S 358_V 0.94 0.12 0.00
68_Y 69_S 0.94 0.12 0.00
58_V 89_L 0.93 0.12 0.00
124_N 440_A 0.93 0.12 0.00
191_V 111_S 0.92 0.12 0.00
183_S 352_N 0.92 0.11 0.00
191_V 322_D 0.91 0.11 0.00
58_V 293_L 0.91 0.11 0.00
312_P 366_L 0.90 0.11 0.00
80_V 239_N 0.89 0.11 0.00
251_N 130_I 0.88 0.10 0.00
224_L 148_R 0.88 0.10 0.00
349_S 179_D 0.87 0.10 0.00
261_K 139_N 0.87 0.10 0.00
150_R 331_S 0.85 0.10 0.00
65_L 427_A 0.85 0.10 0.00
145_F 182_Y 0.84 0.10 0.00
146_V 139_N 0.84 0.10 0.00
123_S 375_K 0.84 0.10 0.00
58_V 121_Y 0.84 0.10 0.00
297_V 220_L 0.84 0.10 0.00
61_A 282_E 0.83 0.09 0.00
149_P 133_L 0.83 0.09 0.00
151_A 247_A 0.83 0.09 0.00
124_N 67_A 0.83 0.09 0.00
78_S 182_Y 0.83 0.09 0.00
343_T 148_R 0.82 0.09 0.00
120_V 369_A 0.82 0.09 0.00
241_Y 289_L 0.82 0.09 0.00
336_E 50_A 0.82 0.09 0.00
184_K 78_G 0.81 0.09 0.00
226_V 66_K 0.81 0.09 0.00
123_S 211_N 0.81 0.09 0.00
169_H 359_K 0.81 0.09 0.00
241_Y 336_F 0.81 0.09 0.00
196_P 158_L 0.81 0.09 0.00
208_G 224_G 0.81 0.09 0.00
224_L 193_P 0.81 0.09 0.00
358_T 434_G 0.81 0.09 0.00
289_I 378_L 0.81 0.09 0.00
146_V 129_D 0.81 0.09 0.00
156_S 183_K 0.81 0.09 0.00
58_V 348_G 0.81 0.09 0.00
261_K 372_Q 0.81 0.09 0.00
97_M 320_P 0.81 0.09 0.00
242_V 128_S 0.81 0.09 0.00
116_I 242_G 0.81 0.09 0.00
246_S 238_L 0.80 0.09 0.00
276_L 296_G 0.80 0.09 0.00
196_P 366_L 0.80 0.09 0.00
55_V 79_T 0.80 0.09 0.00
260_G 313_V 0.80 0.09 0.00
246_S 257_E 0.80 0.09 0.00
61_A 395_E 0.80 0.09 0.00
225_A 80_S 0.80 0.09 0.00
184_K 68_G 0.79 0.09 0.00
165_I 176_N 0.79 0.09 0.00
248_G 189_P 0.79 0.09 0.00
153_A 318_H 0.79 0.09 0.00
276_L 358_V 0.79 0.09 0.00
246_S 251_A 0.79 0.09 0.00
155_A 114_A 0.79 0.09 0.00
76_M 373_A 0.79 0.09 0.00
282_G 55_Y 0.79 0.09 0.00
338_L 437_S 0.79 0.09 0.00
126_V 437_S 0.79 0.08 0.00
217_F 197_M 0.79 0.08 0.00
336_E 372_Q 0.78 0.08 0.00
219_N 110_L 0.78 0.08 0.00
160_G 238_L 0.78 0.08 0.00
241_Y 50_A 0.78 0.08 0.00
275_H 138_L 0.78 0.08 0.00
124_N 317_S 0.78 0.08 0.00
163_R 210_Q 0.78 0.08 0.00
58_V 108_G 0.78 0.08 0.00
338_L 62_G 0.78 0.08 0.00
109_D 68_G 0.77 0.08 0.00
74_G 234_A 0.77 0.08 0.00
104_T 134_M 0.77 0.08 0.00
160_G 336_F 0.77 0.08 0.00
263_F 286_F 0.77 0.08 0.00
165_I 440_A 0.77 0.08 0.00
126_V 413_L 0.77 0.08 0.00
69_V 216_A 0.77 0.08 0.00
202_R 417_D 0.77 0.08 0.00
160_G 91_T 0.76 0.08 0.00
170_L 244_L 0.76 0.08 0.00
339_G 205_L 0.76 0.08 0.00
126_V 259_R 0.76 0.08 0.00
349_S 382_Y 0.76 0.08 0.00
147_N 429_K 0.76 0.08 0.00
339_G 203_E 0.76 0.08 0.00
296_F 87_S 0.76 0.08 0.00
94_L 313_V 0.76 0.08 0.00
201_I 83_L 0.76 0.08 0.00
344_P 103_I 0.76 0.08 0.00
293_L 125_G 0.75 0.08 0.00
161_V 47_L 0.75 0.08 0.00
282_G 240_M 0.75 0.08 0.00
114_D 420_A 0.75 0.08 0.00
64_F 43_L 0.75 0.08 0.00
242_V 184_N 0.75 0.08 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

ID Seq/Len Name Options I_Prob Status
3513 0.24 cI_NDUA_40_cIII_QCR2_40_mouse Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3512 0 cI_NDUA_40_1_cIII_QCR2_40_1_mouse Δgene:(1, 20) A:(1E-40, 1) B:(1E-40, 1) msa: Jackhmmer (2015_06) Killed - Shared
3511 0.34 cI_NDUA_20_cIII_QCR2_20_mouse Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3510 0.25 cI_NDUA_6_cIII_QCR2_6_mouse Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared

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