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OPENSEQ.org
3ip4 A vs C
Genes: A B A+B
Length: 485 100 561
Sequences: 9591 1891 1415
Seq/Len: 19.78 18.91 2.52
MirrorTree (Pazo et al. 2001) 0.71
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 0.05 0.07 2.34
2 0.06 0.07 2.42
5 0.06 0.07 2.43
10 0.06 0.07 2.43
20 0.08 0.07 2.42
100 0.12 0.08 2.46
∞ 0.20 0.08 2.78
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
383_T 53_T 2.90 1.00 1.00
85_N 76_L 2.84 1.00 1.00
303_K 41_Q 2.26 1.00 0.99
377_K 47_T 2.04 0.99 0.98
345_M 19_Q 1.96 0.99 0.97
356_K 24_E 1.83 0.99 0.96
304_F 44_S 1.54 0.95 0.89
344_K 14_N 1.47 0.93 0.86
353_K 27_E 1.34 0.88 0.79
386_K 53_T 1.24 0.82 0.71
348_S 18_L 1.22 0.80 0.68
340_E 17_R 1.17 0.77 0.64
348_S 4_V 1.15 0.74 0.61
233_A 62_V 1.14 0.74 0.60
419_L 38_F 1.12 0.72 0.58
387_N 51_E 1.02 0.62 0.47
98_G 82_K 1.00 0.59 0.44
86_G 79_K 0.98 0.57 0.41
377_K 43_D 0.97 0.56 0.41
380_K 49_G 0.97 0.55 0.40
99_F 80_N 0.95 0.53 0.38
384_L 50_V 0.94 0.52 0.37
360_F 28_M 0.94 0.52 0.37
360_F 20_I 0.91 0.49 0.34
381_V 45_A 0.88 0.45 0.30
363_T 16_A 0.86 0.43 0.28
364_F 36_L 0.86 0.42 0.28
356_K 21_S 0.84 0.40 0.26
381_V 42_N 0.84 0.40 0.26
353_K 24_E 0.82 0.38 0.24
365_A 11_H 0.79 0.35 0.21
242_P 59_L 0.78 0.34 0.20
380_K 48_E 0.78 0.34 0.20
303_K 44_S 0.77 0.33 0.20
208_S 91_V 0.77 0.33 0.20
383_T 52_P 0.77 0.33 0.19
380_K 46_D 0.75 0.31 0.17
311_V 39_A 0.73 0.29 0.16
304_F 45_A 0.73 0.29 0.16
383_T 56_V 0.72 0.28 0.15
306_I 38_F 0.71 0.27 0.15
260_K 75_E 0.71 0.27 0.14
360_F 18_L 0.70 0.26 0.14
344_K 19_Q 0.69 0.25 0.13
307_P 41_Q 0.67 0.23 0.12
327_I 57_L 0.67 0.23 0.12
369_G 15_L 0.67 0.23 0.12
383_T 51_E 0.67 0.23 0.12
338_S 93_T 0.66 0.23 0.12
311_V 40_K 0.66 0.23 0.11
247_D 36_L 0.66 0.22 0.11
383_T 90_K 0.65 0.22 0.11
459_P 56_V 0.65 0.22 0.11
466_Y 94_I 0.65 0.21 0.10
314_S 36_L 0.63 0.20 0.10
332_H 82_K 0.62 0.19 0.09
376_K 52_P 0.62 0.19 0.09
238_S 62_V 0.62 0.19 0.09
122_L 37_D 0.61 0.19 0.09
315_S 95_M 0.61 0.19 0.09
293_V 22_P 0.61 0.19 0.09
134_E 4_V 0.61 0.19 0.09
443_C 88_Q 0.61 0.18 0.09
365_A 34_S 0.60 0.18 0.08
453_L 41_Q 0.60 0.18 0.08
113_K 48_E 0.60 0.18 0.08
416_D 16_A 0.60 0.18 0.08
383_T 11_H 0.60 0.18 0.08
52_I 49_G 0.59 0.17 0.08
272_V 31_T 0.59 0.17 0.08
26_V 45_A 0.59 0.17 0.08
373_A 15_L 0.59 0.17 0.08
108_M 19_Q 0.59 0.17 0.07
308_S 51_E 0.59 0.17 0.07
348_S 20_I 0.59 0.17 0.07
455_F 6_R 0.59 0.17 0.07
383_T 50_V 0.59 0.17 0.07
205_A 35_I 0.58 0.17 0.07
377_K 46_D 0.58 0.17 0.07
91_C 38_F 0.58 0.17 0.07
86_G 41_Q 0.58 0.17 0.07
300_P 13_A 0.58 0.16 0.07
472_Y 55_H 0.58 0.16 0.07
361_L 36_L 0.58 0.16 0.07
104_E 28_M 0.58 0.16 0.07
10_N 22_P 0.58 0.16 0.07
129_M 15_L 0.57 0.16 0.07
135_T 18_L 0.57 0.16 0.07
462_E 12_I 0.57 0.16 0.07
181_Q 91_V 0.56 0.15 0.06
18_K 65_E 0.56 0.15 0.06
124_M 4_V 0.56 0.15 0.06
384_L 47_T 0.56 0.15 0.06
324_F 67_K 0.56 0.15 0.06
163_A 23_E 0.56 0.15 0.06
426_L 52_P 0.56 0.15 0.06
211_D 91_V 0.56 0.15 0.06
389_F 82_K 0.55 0.15 0.06
257_K 7_E 0.55 0.15 0.06
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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