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OPENSEQ.org
M-L
Genes: A B A+B
Length: 484 134 616
Sequences: 250 201 209
Seq/Len: 0.52 1.5 0.34
MirrorTree (Pazo et al. 2001) 0.70
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 0.00 0.00 0.34
2 0.00 0.00 0.34
5 0.00 0.00 0.34
10 0.00 0.00 0.34
20 0.00 0.00 0.34
100 0.00 0.00 0.34
∞ 0.00 0.00 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
64_I 86_Q 1.60 0.52 0.00
353_A 92_E 1.52 0.46 0.00
53_V 93_M 1.40 0.38 0.00
322_V 115_S 1.31 0.32 0.00
299_I 14_L 1.23 0.28 0.00
356_S 133_E 1.22 0.27 0.00
463_T 117_N 1.20 0.26 0.00
30_T 64_N 1.18 0.25 0.00
214_D 134_Q 1.17 0.25 0.00
172_A 111_L 1.17 0.24 0.00
205_S 93_M 1.14 0.23 0.00
182_V 81_D 1.11 0.22 0.00
250_N 86_Q 1.08 0.20 0.00
453_G 104_N 1.08 0.20 0.00
173_A 120_A 1.07 0.20 0.00
183_K 132_K 1.06 0.19 0.00
230_L 89_Y 1.06 0.19 0.00
29_L 4_E 1.05 0.19 0.00
230_L 12_W 1.05 0.19 0.00
10_M 48_M 1.05 0.19 0.00
193_A 81_D 1.03 0.18 0.00
10_M 82_S 1.02 0.17 0.00
163_F 84_A 1.01 0.17 0.00
66_T 85_G 1.01 0.17 0.00
299_I 92_E 1.00 0.17 0.00
329_A 65_S 1.00 0.17 0.00
17_A 115_S 0.99 0.16 0.00
15_E 9_E 0.98 0.16 0.00
273_F 28_E 0.98 0.16 0.00
13_K 131_L 0.98 0.16 0.00
354_T 123_E 0.98 0.16 0.00
20_S 120_A 0.97 0.16 0.00
277_G 115_S 0.97 0.16 0.00
275_E 72_A 0.97 0.16 0.00
202_A 85_G 0.97 0.16 0.00
453_G 19_L 0.96 0.15 0.00
481_Y 117_N 0.96 0.15 0.00
171_S 73_A 0.95 0.15 0.00
451_G 13_T 0.95 0.15 0.00
369_D 98_A 0.95 0.15 0.00
158_Y 93_M 0.95 0.15 0.00
302_D 69_F 0.95 0.15 0.00
4_I 103_L 0.95 0.15 0.00
66_T 57_E 0.95 0.15 0.00
161_Y 92_E 0.94 0.15 0.00
449_R 124_I 0.94 0.15 0.00
105_T 79_T 0.94 0.14 0.00
10_M 81_D 0.93 0.14 0.00
21_S 129_A 0.93 0.14 0.00
412_D 93_M 0.93 0.14 0.00
115_I 69_F 0.93 0.14 0.00
466_V 94_S 0.92 0.14 0.00
366_K 4_E 0.92 0.14 0.00
235_E 131_L 0.92 0.14 0.00
141_K 134_Q 0.92 0.14 0.00
409_L 119_Q 0.92 0.14 0.00
49_T 100_M 0.91 0.14 0.00
142_K 56_G 0.91 0.14 0.00
454_D 16_Y 0.91 0.14 0.00
230_L 19_L 0.91 0.14 0.00
357_V 74_K 0.91 0.14 0.00
430_P 128_A 0.91 0.14 0.00
300_S 93_M 0.91 0.14 0.00
32_L 72_A 0.91 0.14 0.00
229_V 110_Q 0.91 0.14 0.00
411_F 69_F 0.91 0.14 0.00
351_T 9_E 0.91 0.14 0.00
172_A 80_V 0.91 0.14 0.00
441_A 24_A 0.90 0.13 0.00
465_L 108_K 0.90 0.13 0.00
111_I 127_N 0.90 0.13 0.00
316_S 4_E 0.90 0.13 0.00
299_I 128_A 0.89 0.13 0.00
453_G 26_K 0.89 0.13 0.00
456_V 98_A 0.89 0.13 0.00
76_E 54_V 0.88 0.13 0.00
417_L 108_K 0.88 0.13 0.00
329_A 113_S 0.88 0.13 0.00
251_G 46_D 0.88 0.13 0.00
381_P 113_S 0.88 0.13 0.00
320_A 82_S 0.88 0.13 0.00
298_T 93_M 0.88 0.13 0.00
290_V 43_Q 0.88 0.13 0.00
301_A 2_A 0.87 0.12 0.00
178_W 115_S 0.87 0.12 0.00
287_K 91_E 0.87 0.12 0.00
371_K 103_L 0.87 0.12 0.00
264_E 91_E 0.87 0.12 0.00
414_E 133_E 0.87 0.12 0.00
484_Q 117_N 0.87 0.12 0.00
218_Y 134_Q 0.87 0.12 0.00
81_T 13_T 0.86 0.12 0.00
155_K 100_M 0.85 0.12 0.00
387_G 66_I 0.85 0.12 0.00
394_G 117_N 0.85 0.12 0.00
36_A 16_Y 0.85 0.12 0.00
270_Q 93_M 0.85 0.12 0.00
358_T 8_D 0.85 0.12 0.00
415_V 95_M 0.85 0.12 0.00
418_D 86_Q 0.85 0.12 0.00
381_P 108_K 0.84 0.12 0.00
170_A 86_Q 0.84 0.12 0.00
269_G 89_Y 0.84 0.12 0.00
225_T 77_S 0.83 0.11 0.00
443_C 109_V 0.83 0.11 0.00
437_N 76_I 0.83 0.11 0.00
322_V 123_E 0.83 0.11 0.00
154_I 86_Q 0.83 0.11 0.00
471_Y 94_S 0.83 0.11 0.00
419_V 2_A 0.83 0.11 0.00
211_V 66_I 0.83 0.11 0.00
193_A 68_N 0.83 0.11 0.00
372_T 98_A 0.83 0.11 0.00
189_V 128_A 0.83 0.11 0.00
229_V 72_A 0.82 0.11 0.00
162_H 4_E 0.82 0.11 0.00
334_L 93_M 0.82 0.11 0.00
458_I 2_A 0.82 0.11 0.00
90_D 103_L 0.82 0.11 0.00
234_D 72_A 0.82 0.11 0.00
429_Q 72_A 0.82 0.11 0.00
218_Y 131_L 0.82 0.11 0.00
214_D 47_A 0.82 0.11 0.00
383_G 96_A 0.82 0.11 0.00
228_V 13_T 0.82 0.11 0.00
259_A 2_A 0.82 0.11 0.00
317_V 93_M 0.81 0.11 0.00
409_L 102_S 0.81 0.11 0.00
44_A 26_K 0.81 0.11 0.00
21_S 111_L 0.81 0.11 0.00
59_E 57_E 0.81 0.11 0.00
120_S 119_Q 0.81 0.11 0.00
24_T 92_E 0.81 0.11 0.00
399_L 9_E 0.81 0.11 0.00
112_I 134_Q 0.81 0.11 0.00
264_E 126_E 0.81 0.11 0.00
234_D 3_F 0.81 0.11 0.00
418_D 31_A 0.81 0.11 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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