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OPENSEQ.org
gluti gapdh 2
Genes: A B A+B
Length: 504 531 937
Sequences: 25017 743 53
Seq/Len: 49.64 1.4 0.06
MirrorTree (Pazo et al. 2001) 0.19
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.04 0.00
2 0.07 0.04 0.00
5 0.09 0.04 0.02
10 0.11 0.05 0.03
20 0.14 0.05 0.05
100 0.22 0.05 0.16
∞ 0.28 0.07 0.34
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
288_N 335_V 1.69 0.19 0.00
199_L 341_M 1.45 0.14 0.00
385_P 26_L 1.41 0.13 0.00
210_S 153_I 1.35 0.12 0.00
187_P 112_W 1.31 0.11 0.00
154_G 55_M 1.30 0.11 0.00
113_S 72_A 1.22 0.10 0.00
378_F 157_F 1.20 0.09 0.00
207_C 456_F 1.19 0.09 0.00
84_G 448_V 1.18 0.09 0.00
273_L 73_L 1.18 0.09 0.00
32_V 63_S 1.16 0.09 0.00
347_C 194_S 1.16 0.09 0.00
462_E 153_I 1.16 0.09 0.00
88_N 456_F 1.15 0.09 0.00
70_A 422_G 1.15 0.09 0.00
93_R 372_Q 1.13 0.08 0.00
38_K 216_Y 1.13 0.08 0.00
450_F 448_V 1.12 0.08 0.00
227_V 430_L 1.11 0.08 0.00
64_L 395_L 1.10 0.08 0.00
187_P 301_E 1.10 0.08 0.00
405_A 487_V 1.09 0.08 0.00
430_G 494_L 1.09 0.08 0.00
201_C 235_L 1.08 0.08 0.00
323_V 99_C 1.08 0.08 0.00
34_N 192_L 1.07 0.08 0.00
352_T 29_V 1.06 0.07 0.00
374_G 12_Y 1.05 0.07 0.00
277_V 126_A 1.05 0.07 0.00
114_K 196_V 1.04 0.07 0.00
302_G 420_L 1.02 0.07 0.00
101_L 249_T 1.02 0.07 0.00
345_A 430_L 1.01 0.07 0.00
66_S 299_F 1.00 0.07 0.00
263_F 477_L 1.00 0.07 0.00
319_A 485_L 0.98 0.07 0.00
294_S 26_L 0.98 0.07 0.00
78_I 217_F 0.98 0.07 0.00
125_G 448_V 0.97 0.06 0.00
145_G 270_I 0.97 0.06 0.00
413_T 487_V 0.97 0.06 0.00
413_T 63_S 0.96 0.06 0.00
172_Q 341_M 0.96 0.06 0.00
170_I 506_L 0.96 0.06 0.00
292_Y 252_L 0.96 0.06 0.00
332_G 193_L 0.96 0.06 0.00
154_G 33_Y 0.96 0.06 0.00
374_G 431_L 0.94 0.06 0.00
297_I 193_L 0.94 0.06 0.00
187_P 479_L 0.93 0.06 0.00
373_F 33_Y 0.93 0.06 0.00
421_C 335_V 0.93 0.06 0.00
444_F 486_T 0.93 0.06 0.00
228_L 225_I 0.93 0.06 0.00
197_A 341_M 0.93 0.06 0.00
334_R 114_G 0.93 0.06 0.00
192_I 32_I 0.92 0.06 0.00
132_Y 42_T 0.92 0.06 0.00
338_L 254_V 0.92 0.06 0.00
154_G 320_S 0.92 0.06 0.00
71_I 6_I 0.92 0.06 0.00
113_S 499_R 0.92 0.06 0.00
86_F 243_F 0.92 0.06 0.00
346_G 270_I 0.91 0.06 0.00
417_I 7_R 0.91 0.06 0.00
402_A 270_I 0.91 0.06 0.00
187_P 357_A 0.91 0.06 0.00
78_I 284_M 0.91 0.06 0.00
145_G 196_V 0.91 0.06 0.00
387_P 448_V 0.91 0.06 0.00
189_L 7_R 0.91 0.06 0.00
296_S 505_C 0.91 0.06 0.00
120_E 232_I 0.91 0.06 0.00
413_T 448_V 0.90 0.06 0.00
41_E 7_R 0.90 0.06 0.00
72_F 120_L 0.90 0.06 0.00
147_V 341_M 0.90 0.06 0.00
399_P 493_L 0.90 0.06 0.00
178_S 2_L 0.90 0.06 0.00
224_A 459_I 0.89 0.06 0.00
78_I 270_I 0.89 0.06 0.00
162_L 195_L 0.89 0.06 0.00
78_I 52_R 0.89 0.06 0.00
338_L 204_F 0.89 0.06 0.00
272_I 335_V 0.89 0.06 0.00
112_F 252_L 0.89 0.06 0.00
159_L 455_L 0.89 0.06 0.00
418_V 450_T 0.89 0.06 0.00
145_G 66_V 0.88 0.06 0.00
199_L 63_S 0.88 0.06 0.00
16_V 32_I 0.88 0.06 0.00
324_S 63_S 0.88 0.06 0.00
101_L 7_R 0.88 0.06 0.00
220_E 119_L 0.88 0.06 0.00
438_T 7_R 0.88 0.06 0.00
83_V 270_I 0.88 0.06 0.00
425_V 462_I 0.87 0.06 0.00
153_R 481_F 0.87 0.05 0.00
443_L 403_I 0.87 0.05 0.00
186_W 78_P 0.86 0.05 0.00
186_W 79_L 0.86 0.05 0.00
186_W 83_G 0.86 0.05 0.00
186_W 144_F 0.86 0.05 0.00
186_W 222_R 0.86 0.05 0.00
186_W 297_L 0.86 0.05 0.00
186_W 325_D 0.86 0.05 0.00
186_W 354_H 0.86 0.05 0.00
186_W 376_V 0.86 0.05 0.00
186_W 378_E 0.86 0.05 0.00
186_W 380_R 0.86 0.05 0.00
186_W 480_P 0.86 0.05 0.00
186_W 503_L 0.86 0.05 0.00
186_W 507_D 0.86 0.05 0.00
197_A 474_P 0.86 0.05 0.00
311_I 63_S 0.86 0.05 0.00
95_S 459_I 0.86 0.05 0.00
244_M 119_L 0.86 0.05 0.00
298_F 193_L 0.86 0.05 0.00
418_V 32_I 0.86 0.05 0.00
334_R 153_I 0.85 0.05 0.00
195_I 485_L 0.85 0.05 0.00
318_T 406_A 0.85 0.05 0.00
352_T 221_L 0.85 0.05 0.00
417_I 246_D 0.85 0.05 0.00
347_C 431_L 0.85 0.05 0.00
63_T 419_S 0.85 0.05 0.00
148_S 7_R 0.85 0.05 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)
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