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OPENSEQ.org
1jw9
Genes: A B A+B
Length: 249 81 326
Sequences: 7913 3133 541
Seq/Len: 31.78 38.68 1.66
MirrorTree (Pazo et al. 2001) 0.46
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.00 0.63
2 0.04 0.01 0.88
5 0.05 0.01 1.28
10 0.05 0.01 1.51
20 0.07 0.02 1.64
100 0.09 0.03 2.21
∞ 0.16 0.09 4.80
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
118_L 14_V 1.14 0.62 0.00
237_K 58_T 1.13 0.61 0.00
92_D 72_V 1.09 0.56 0.00
200_I 57_Q 0.99 0.46 0.00
151_S 75_F 0.97 0.43 0.00
60_L 27_T 0.96 0.43 0.00
58_L 7_F 0.96 0.43 0.00
173_Y 72_V 0.95 0.41 0.00
10_L 4_V 0.93 0.39 0.00
34_V 55_V 0.91 0.38 0.00
58_L 31_L 0.91 0.38 0.00
178_R 1_M 0.89 0.35 0.00
29_L 27_T 0.88 0.34 0.00
80_A 24_D 0.85 0.32 0.00
95_T 35_M 0.83 0.30 0.00
153_A 9_Q 0.83 0.30 0.00
55_V 42_W 0.83 0.30 0.00
151_S 74_F 0.83 0.30 0.00
12_Y 70_D 0.81 0.28 0.00
95_T 33_Q 0.81 0.28 0.00
147_V 63_D 0.80 0.27 0.00
113_A 24_D 0.80 0.27 0.00
89_S 54_A 0.79 0.27 0.00
72_Q 75_F 0.78 0.26 0.00
128_C 39_S 0.78 0.26 0.00
175_C 70_D 0.77 0.25 0.00
102_A 28_V 0.77 0.25 0.00
125_V 65_P 0.77 0.25 0.00
47_S 64_H 0.77 0.24 0.00
151_S 54_A 0.75 0.24 0.00
170_E 53_A 0.74 0.23 0.00
154_A 79_T 0.74 0.23 0.00
153_A 50_K 0.74 0.22 0.00
150_V 4_V 0.73 0.22 0.00
197_I 1_M 0.73 0.22 0.00
57_N 3_K 0.73 0.22 0.00
102_A 4_V 0.73 0.22 0.00
248_G 69_G 0.73 0.22 0.00
150_V 54_A 0.72 0.21 0.00
101_I 55_V 0.71 0.21 0.00
162_T 8_A 0.70 0.20 0.00
20_G 66_L 0.70 0.20 0.00
173_Y 11_R 0.69 0.19 0.00
89_S 28_V 0.69 0.19 0.00
213_A 17_D 0.69 0.19 0.00
151_S 79_T 0.69 0.19 0.00
113_A 33_Q 0.69 0.19 0.00
164_F 31_L 0.69 0.19 0.00
45_A 40_D 0.68 0.19 0.00
158_E 11_R 0.68 0.18 0.00
244_C 78_V 0.67 0.18 0.00
58_L 38_Q 0.67 0.18 0.00
151_S 73_A 0.67 0.18 0.00
149_L 12_E 0.67 0.18 0.00
175_C 56_N 0.67 0.18 0.00
31_D 68_D 0.67 0.18 0.00
55_V 21_V 0.67 0.17 0.00
227_D 28_V 0.66 0.17 0.00
28_A 20_E 0.66 0.17 0.00
114_E 40_D 0.66 0.17 0.00
99_P 51_L 0.66 0.17 0.00
113_A 16_T 0.65 0.17 0.00
239_M 27_T 0.65 0.17 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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