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OPENSEQ.org
cI_NDUA_20_cIII_QCR2_20_mouse
Genes: A B A+B
Length: 377 453 732
Sequences: 17493 11958 250
Seq/Len: 46.4 26.4 0.34
MirrorTree (Pazo et al. 2001) 0.23
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 0.09 0.18 0.01
2 0.10 0.19 0.03
5 0.13 0.20 0.08
10 0.15 0.20 0.14
20 0.17 0.21 0.30
100 0.20 0.23 1.22
∞ 0.25 0.28 4.03
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
334_G 367_S 1.52 0.47 0.00
199_I 182_Y 1.20 0.26 0.00
58_V 210_Q 1.13 0.23 0.00
263_F 222_G 1.12 0.22 0.00
285_H 182_Y 1.06 0.19 0.00
160_G 336_F 1.04 0.18 0.00
146_V 139_N 1.03 0.18 0.00
202_R 417_D 1.03 0.18 0.00
293_L 420_A 1.00 0.17 0.00
94_L 315_K 0.99 0.17 0.00
191_V 322_D 0.98 0.16 0.00
94_L 313_V 0.98 0.16 0.00
354_R 197_M 0.94 0.15 0.00
127_I 126_I 0.94 0.14 0.00
172_A 212_H 0.93 0.14 0.00
353_L 441_S 0.93 0.14 0.00
128_N 201_T 0.93 0.14 0.00
341_Q 358_V 0.92 0.14 0.00
278_K 323_V 0.92 0.14 0.00
126_V 339_Y 0.91 0.14 0.00
275_H 87_S 0.90 0.13 0.00
69_V 130_I 0.90 0.13 0.00
160_G 293_L 0.90 0.13 0.00
275_H 393_L 0.89 0.13 0.00
112_D 288_V 0.89 0.13 0.00
151_A 361_V 0.89 0.13 0.00
122_H 221_V 0.89 0.13 0.00
145_F 397_G 0.88 0.13 0.00
248_G 86_A 0.88 0.13 0.00
115_S 313_V 0.87 0.12 0.00
354_R 208_F 0.86 0.12 0.00
291_Y 356_N 0.85 0.12 0.00
115_S 362_A 0.85 0.12 0.00
143_D 44_P 0.84 0.12 0.00
163_R 289_L 0.84 0.12 0.00
165_I 331_S 0.84 0.12 0.00
58_V 366_L 0.83 0.11 0.00
154_Q 440_A 0.83 0.11 0.00
333_P 352_N 0.83 0.11 0.00
299_S 195_Y 0.83 0.11 0.00
97_M 58_L 0.83 0.11 0.00
189_K 86_A 0.83 0.11 0.00
83_P 240_M 0.83 0.11 0.00
152_I 336_F 0.83 0.11 0.00
160_G 91_T 0.82 0.11 0.00
59_F 208_F 0.82 0.11 0.00
280_I 382_Y 0.81 0.11 0.00
163_R 427_A 0.81 0.11 0.00
109_D 79_T 0.81 0.11 0.00
263_F 205_L 0.81 0.11 0.00
128_N 232_Q 0.81 0.11 0.00
162_E 420_A 0.80 0.10 0.00
263_F 385_S 0.80 0.10 0.00
261_K 338_I 0.80 0.10 0.00
200_I 270_A 0.80 0.10 0.00
61_A 44_P 0.80 0.10 0.00
165_I 361_V 0.80 0.10 0.00
280_I 355_Y 0.80 0.10 0.00
316_K 223_L 0.80 0.10 0.00
258_A 63_L 0.80 0.10 0.00
297_V 220_L 0.79 0.10 0.00
58_V 272_V 0.79 0.10 0.00
183_S 132_I 0.79 0.10 0.00
255_D 60_R 0.79 0.10 0.00
265_F 234_A 0.79 0.10 0.00
118_K 437_S 0.79 0.10 0.00
58_V 273_A 0.79 0.10 0.00
59_F 68_G 0.79 0.10 0.00
112_D 72_E 0.79 0.10 0.00
58_V 228_S 0.78 0.10 0.00
109_D 144_P 0.78 0.10 0.00
269_N 225_V 0.78 0.10 0.00
159_A 428_A 0.78 0.10 0.00
151_A 226_S 0.77 0.10 0.00
200_I 338_I 0.77 0.10 0.00
131_G 86_A 0.77 0.10 0.00
261_K 431_F 0.77 0.10 0.00
159_A 241_R 0.76 0.10 0.00
109_D 68_G 0.76 0.10 0.00
261_K 375_K 0.76 0.10 0.00
74_G 394_S 0.76 0.10 0.00
335_L 205_L 0.76 0.09 0.00
155_A 205_L 0.76 0.09 0.00
151_A 366_L 0.76 0.09 0.00
246_S 341_I 0.76 0.09 0.00
294_P 322_D 0.76 0.09 0.00
103_L 340_T 0.76 0.09 0.00
112_D 241_R 0.75 0.09 0.00
272_L 410_S 0.75 0.09 0.00
263_F 426_K 0.75 0.09 0.00
183_S 138_L 0.75 0.09 0.00
246_S 53_E 0.75 0.09 0.00
146_V 207_Y 0.75 0.09 0.00
357_R 424_V 0.75 0.09 0.00
339_G 211_N 0.75 0.09 0.00
253_T 183_K 0.75 0.09 0.00
148_I 432_V 0.74 0.09 0.00
169_H 311_Q 0.74 0.09 0.00
60_G 224_G 0.74 0.09 0.00
63_G 224_G 0.74 0.09 0.00
349_S 382_Y 0.74 0.09 0.00
120_V 369_A 0.74 0.09 0.00
126_V 427_A 0.74 0.09 0.00
67_R 116_R 0.74 0.09 0.00
116_I 425_V 0.74 0.09 0.00
76_M 363_Q 0.74 0.09 0.00
336_E 206_H 0.74 0.09 0.00
261_K 139_N 0.74 0.09 0.00
108_W 249_A 0.74 0.09 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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