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OPENSEQ.org
3IP4_AC
Genes: A B A+B
Length: 485 92 560
Sequences: 9591 1894 1422
Seq/Len: 19.78 20.59 2.54
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 2.38
2 0.06 0.07 2.45
5 0.06 0.07 2.45
10 0.06 0.07 2.47
20 0.08 0.07 2.46
100 0.12 0.08 2.49
∞ 0.20 0.08 2.82
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 51_T 2.96 1.00 1.00
85_N 74_L 2.82 1.00 1.00
303_K 39_Q 2.25 1.00 0.99
377_K 45_T 2.03 0.99 0.98
345_M 17_Q 1.95 0.99 0.97
356_K 22_E 1.85 0.99 0.96
304_F 42_S 1.53 0.95 0.89
344_K 12_N 1.43 0.92 0.84
353_K 25_E 1.34 0.88 0.79
386_K 51_T 1.23 0.82 0.70
340_E 15_R 1.18 0.78 0.65
348_S 2_V 1.17 0.77 0.64
348_S 16_L 1.14 0.74 0.61
233_A 60_V 1.10 0.70 0.56
419_L 36_F 1.10 0.70 0.56
387_N 49_E 1.02 0.61 0.47
98_G 80_K 1.01 0.61 0.46
360_F 26_M 1.01 0.61 0.46
86_G 77_K 0.96 0.55 0.40
360_F 18_I 0.96 0.55 0.39
99_F 78_N 0.93 0.51 0.36
377_K 41_D 0.93 0.51 0.36
384_L 48_V 0.91 0.49 0.34
381_V 40_N 0.90 0.48 0.33
380_K 47_G 0.90 0.48 0.33
381_V 43_A 0.88 0.45 0.30
364_F 34_L 0.87 0.44 0.29
356_K 19_S 0.81 0.37 0.23
363_T 14_A 0.80 0.36 0.22
353_K 22_E 0.80 0.36 0.22
365_A 9_H 0.80 0.36 0.22
208_S 89_V 0.79 0.35 0.21
242_P 57_L 0.78 0.34 0.21
383_T 50_P 0.78 0.34 0.20
466_Y 92_I 0.77 0.33 0.20
360_F 16_L 0.76 0.32 0.19
303_K 42_S 0.76 0.32 0.19
380_K 44_D 0.76 0.32 0.19
380_K 46_E 0.75 0.31 0.18
304_F 43_A 0.73 0.29 0.16
306_I 36_F 0.72 0.28 0.15
311_V 37_A 0.71 0.27 0.15
344_K 17_Q 0.70 0.26 0.14
383_T 54_V 0.70 0.26 0.14
383_T 49_E 0.69 0.25 0.13
311_V 38_K 0.68 0.24 0.13
122_L 35_D 0.68 0.24 0.12
293_V 20_P 0.67 0.23 0.12
307_P 39_Q 0.67 0.23 0.12
327_I 55_L 0.67 0.23 0.12
459_P 54_V 0.67 0.23 0.12
383_T 88_K 0.66 0.22 0.11
455_F 4_R 0.66 0.22 0.11
369_G 13_L 0.64 0.21 0.10
338_S 91_T 0.64 0.21 0.10
376_K 50_P 0.64 0.21 0.10
260_K 73_E 0.63 0.20 0.10
314_S 34_L 0.62 0.20 0.09
332_H 80_K 0.62 0.20 0.09
348_S 18_I 0.62 0.20 0.09
365_A 32_S 0.62 0.19 0.09
247_D 34_L 0.61 0.19 0.09
416_D 14_A 0.60 0.18 0.08
134_E 2_V 0.60 0.18 0.08
443_C 86_Q 0.60 0.18 0.08
453_L 39_Q 0.60 0.18 0.08
383_T 9_H 0.59 0.17 0.08
238_S 60_V 0.59 0.17 0.08
472_Y 53_H 0.59 0.17 0.08
329_Y 25_E 0.59 0.17 0.08
43_F 19_S 0.59 0.17 0.08
91_C 36_F 0.59 0.17 0.07
462_E 10_I 0.58 0.17 0.07
108_M 17_Q 0.58 0.16 0.07
361_L 34_L 0.58 0.16 0.07
113_K 46_E 0.57 0.16 0.07
205_A 33_I 0.57 0.16 0.07
163_A 21_E 0.57 0.16 0.07
124_M 2_V 0.57 0.16 0.07
181_Q 89_V 0.57 0.16 0.07
300_P 11_A 0.57 0.16 0.07
26_V 43_A 0.57 0.16 0.07
384_L 45_T 0.57 0.16 0.07
211_D 89_V 0.57 0.16 0.07
373_A 13_L 0.56 0.16 0.07
324_F 65_K 0.56 0.16 0.07
86_G 20_P 0.56 0.15 0.07
426_L 50_P 0.56 0.15 0.07
389_F 80_K 0.56 0.15 0.07
423_A 92_I 0.56 0.15 0.06
308_S 49_E 0.56 0.15 0.06
135_T 16_L 0.55 0.15 0.06
86_G 39_Q 0.55 0.15 0.06
104_E 26_M 0.55 0.15 0.06
383_T 48_V 0.55 0.15 0.06
379_Q 52_Y 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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