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OPENSEQ.org
SpA-C
Genes: A B A+B
Length: 516 79 577
Sequences: 36789 194 215
Seq/Len: 71.3 2.46 0.37
MirrorTree (Pazo et al. 2001) 0.84
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 0.08 0.08 0.04
2 0.10 0.08 0.36
5 0.14 0.08 0.36
10 0.17 0.08 0.36
20 0.18 0.08 0.36
100 0.23 0.08 0.36
∞ 0.29 0.09 0.38
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
309_L 29_D 1.52 0.48 0.00
154_I 66_A 1.48 0.46 0.00
227_T 36_M 1.46 0.45 0.00
173_L 66_A 1.42 0.41 0.00
409_I 51_I 1.40 0.40 0.00
305_A 64_N 1.39 0.40 0.00
472_A 7_V 1.30 0.34 0.00
217_G 41_L 1.29 0.33 0.00
327_I 16_M 1.28 0.33 0.00
281_V 46_E 1.26 0.31 0.00
60_V 11_I 1.26 0.31 0.00
240_L 56_T 1.23 0.29 0.00
146_K 36_M 1.23 0.29 0.00
209_W 57_E 1.23 0.29 0.00
420_D 51_I 1.18 0.27 0.00
509_L 46_E 1.16 0.26 0.00
242_I 62_D 1.16 0.26 0.00
455_L 50_D 1.14 0.24 0.00
515_K 29_D 1.13 0.24 0.00
45_L 66_A 1.12 0.23 0.00
207_M 66_A 1.12 0.23 0.00
154_I 41_L 1.10 0.22 0.00
49_I 19_V 1.10 0.22 0.00
229_D 36_M 1.10 0.22 0.00
420_D 23_M 1.09 0.22 0.00
11_E 12_D 1.09 0.22 0.00
285_Q 7_V 1.09 0.22 0.00
375_A 43_V 1.08 0.21 0.00
282_K 10_I 1.07 0.21 0.00
254_M 40_E 1.07 0.21 0.00
169_S 15_F 1.07 0.21 0.00
504_I 6_E 1.05 0.20 0.00
105_P 15_F 1.04 0.20 0.00
77_L 15_F 1.04 0.20 0.00
5_P 74_V 1.04 0.19 0.00
124_I 41_L 1.03 0.19 0.00
275_D 11_I 1.03 0.19 0.00
125_N 8_I 1.02 0.18 0.00
506_I 19_V 1.02 0.18 0.00
91_S 30_A 1.01 0.18 0.00
416_I 55_V 1.01 0.18 0.00
235_A 5_S 1.01 0.18 0.00
246_T 15_F 1.01 0.18 0.00
483_S 52_R 1.01 0.18 0.00
247_S 24_D 1.01 0.18 0.00
238_F 55_V 0.99 0.17 0.00
66_Q 55_V 0.99 0.17 0.00
489_K 43_V 0.99 0.17 0.00
319_L 49_F 0.99 0.17 0.00
159_T 16_M 0.99 0.17 0.00
265_K 56_T 0.98 0.17 0.00
492_Y 54_P 0.98 0.17 0.00
451_A 60_R 0.97 0.17 0.00
247_S 65_T 0.96 0.16 0.00
448_N 16_M 0.96 0.16 0.00
246_T 55_V 0.96 0.16 0.00
449_L 60_R 0.95 0.16 0.00
506_I 25_E 0.95 0.16 0.00
367_N 16_M 0.95 0.16 0.00
229_D 46_E 0.95 0.16 0.00
257_L 63_W 0.94 0.16 0.00
206_V 66_A 0.94 0.16 0.00
421_V 61_D 0.94 0.15 0.00
488_S 15_F 0.94 0.15 0.00
74_F 57_E 0.94 0.15 0.00
421_V 36_M 0.93 0.15 0.00
371_K 56_T 0.93 0.15 0.00
200_Y 14_L 0.93 0.15 0.00
212_T 43_V 0.92 0.15 0.00
28_V 70_I 0.92 0.15 0.00
419_E 14_L 0.92 0.15 0.00
273_Y 50_D 0.92 0.15 0.00
366_M 63_W 0.92 0.15 0.00
449_L 33_L 0.92 0.15 0.00
471_K 74_V 0.92 0.15 0.00
431_I 71_A 0.91 0.14 0.00
375_A 64_N 0.91 0.14 0.00
336_T 29_D 0.91 0.14 0.00
255_A 49_F 0.91 0.14 0.00
311_A 59_G 0.91 0.14 0.00
142_T 10_I 0.90 0.14 0.00
309_L 11_I 0.90 0.14 0.00
319_L 4_K 0.90 0.14 0.00
354_I 49_F 0.90 0.14 0.00
124_I 71_A 0.90 0.14 0.00
412_N 66_A 0.90 0.14 0.00
186_F 54_P 0.90 0.14 0.00
506_I 17_E 0.90 0.14 0.00
42_S 49_F 0.90 0.14 0.00
57_K 75_E 0.90 0.14 0.00
431_I 9_E 0.89 0.14 0.00
419_E 38_T 0.88 0.14 0.00
8_D 29_D 0.88 0.13 0.00
342_E 3_I 0.88 0.13 0.00
149_D 49_F 0.88 0.13 0.00
28_V 26_D 0.88 0.13 0.00
208_Y 66_A 0.88 0.13 0.00
258_S 57_E 0.88 0.13 0.00
355_I 25_E 0.88 0.13 0.00
453_V 70_I 0.87 0.13 0.00
331_K 54_P 0.87 0.13 0.00
252_A 49_F 0.87 0.13 0.00
194_M 13_E 0.87 0.13 0.00
61_V 48_R 0.87 0.13 0.00
82_H 57_E 0.87 0.13 0.00
474_K 7_V 0.87 0.13 0.00
407_F 11_I 0.87 0.13 0.00
428_S 17_E 0.87 0.13 0.00
386_H 32_V 0.86 0.13 0.00
420_D 19_V 0.86 0.13 0.00
82_H 37_G 0.86 0.13 0.00
445_K 28_F 0.86 0.13 0.00
354_I 37_G 0.86 0.13 0.00
247_S 67_N 0.86 0.13 0.00
482_M 45_I 0.86 0.13 0.00
414_Y 8_I 0.86 0.13 0.00
294_A 50_D 0.85 0.12 0.00
374_E 12_D 0.85 0.12 0.00
443_D 36_M 0.85 0.12 0.00
445_K 14_L 0.85 0.12 0.00
270_T 36_M 0.85 0.12 0.00
55_P 36_M 0.85 0.12 0.00
489_K 16_M 0.85 0.12 0.00
207_M 38_T 0.84 0.12 0.00
405_M 7_V 0.84 0.12 0.00
414_Y 64_N 0.84 0.12 0.00
272_F 65_T 0.84 0.12 0.00
280_T 37_G 0.84 0.12 0.00
474_K 6_E 0.84 0.12 0.00
26_Y 54_P 0.84 0.12 0.00
440_Y 7_V 0.83 0.12 0.00
34_T 71_A 0.83 0.12 0.00
15_H 18_D 0.83 0.12 0.00
338_I 52_R 0.83 0.12 0.00
109_I 13_E 0.83 0.12 0.00
313_A 64_N 0.83 0.12 0.00
26_Y 55_V 0.83 0.12 0.00
245_W 65_T 0.83 0.12 0.00
257_L 36_M 0.83 0.12 0.00
434_A 59_G 0.83 0.12 0.00
25_V 18_D 0.83 0.12 0.00
230_F 73_I 0.83 0.12 0.00
446_V 68_K 0.82 0.12 0.00
18_Q 29_D 0.82 0.12 0.00
96_V 21_D 0.82 0.12 0.00
310_S 9_E 0.82 0.11 0.00
509_L 26_D 0.82 0.11 0.00
440_Y 45_I 0.82 0.11 0.00
412_N 32_V 0.82 0.11 0.00
418_L 54_P 0.82 0.11 0.00
468_D 25_E 0.81 0.11 0.00
222_L 51_I 0.81 0.11 0.00
125_N 44_E 0.81 0.11 0.00
85_I 48_R 0.81 0.11 0.00
409_I 10_I 0.81 0.11 0.00
7_A 6_E 0.81 0.11 0.00
486_M 53_V 0.81 0.11 0.00
198_P 61_D 0.81 0.11 0.00
308_A 60_R 0.81 0.11 0.00
467_I 43_V 0.81 0.11 0.00
456_K 5_S 0.80 0.11 0.00
313_A 11_I 0.80 0.11 0.00
79_K 38_T 0.80 0.11 0.00
85_I 63_W 0.80 0.11 0.00
444_H 14_L 0.80 0.11 0.00
256_M 41_L 0.80 0.11 0.00
194_M 61_D 0.80 0.11 0.00
44_S 49_F 0.80 0.11 0.00
420_D 76_L 0.79 0.11 0.00
314_V 43_V 0.79 0.11 0.00
499_T 43_V 0.79 0.11 0.00
514_N 55_V 0.79 0.11 0.00
270_T 71_A 0.79 0.11 0.00
221_T 30_A 0.79 0.11 0.00
452_Y 27_L 0.79 0.11 0.00
72_A 66_A 0.79 0.11 0.00
318_M 74_V 0.79 0.11 0.00
224_S 66_A 0.79 0.11 0.00
318_M 30_A 0.79 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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