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OPENSEQ.org
10vs49_-06
Genes: A B A+B
Length: 86 420 463
Sequences: 196 1143 63
Seq/Len: 2.28 2.72 0.14
MirrorTree (Pazo et al. 2001) 0.24
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 0.00 0.03 0.00
2 0.01 0.04 0.00
5 0.01 0.04 0.01
10 0.01 0.05 0.01
20 0.01 0.05 0.01
100 0.01 0.07 0.03
∞ 0.01 0.10 0.12
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
84_E 324_A 1.45 0.23 0.00
58_N 17_V 1.35 0.20 0.00
40_Y 39_V 1.32 0.19 0.00
40_Y 154_A 1.15 0.14 0.00
34_N 70_A 1.13 0.13 0.00
51_N 104_I 1.12 0.13 0.00
35_Q 265_P 1.12 0.13 0.00
31_W 120_F 1.10 0.12 0.00
65_R 57_G 1.08 0.12 0.00
65_R 344_P 1.04 0.11 0.00
84_E 149_F 1.04 0.11 0.00
6_T 26_E 1.03 0.11 0.00
4_R 26_E 1.01 0.10 0.00
55_I 74_M 1.01 0.10 0.00
54_A 298_P 1.00 0.10 0.00
61_K 280_T 0.99 0.10 0.00
1_M 149_F 0.98 0.10 0.00
17_K 167_L 0.97 0.10 0.00
81_D 218_P 0.96 0.09 0.00
28_K 265_P 0.95 0.09 0.00
36_H 39_V 0.95 0.09 0.00
16_S 67_A 0.95 0.09 0.00
84_E 214_A 0.91 0.09 0.00
19_I 145_A 0.91 0.09 0.00
28_K 256_G 0.90 0.08 0.00
44_M 232_L 0.90 0.08 0.00
29_W 218_P 0.89 0.08 0.00
55_I 305_G 0.88 0.08 0.00
17_K 115_L 0.88 0.08 0.00
58_N 115_L 0.88 0.08 0.00
31_W 124_G 0.88 0.08 0.00
84_E 241_G 0.87 0.08 0.00
36_H 223_P 0.87 0.08 0.00
84_E 240_P 0.87 0.08 0.00
16_S 141_S 0.87 0.08 0.00
39_S 243_F 0.87 0.08 0.00
74_Q 209_Q 0.86 0.08 0.00
7_I 26_E 0.85 0.08 0.00
39_S 335_P 0.85 0.08 0.00
24_A 18_G 0.85 0.08 0.00
51_N 344_P 0.85 0.08 0.00
78_P 20_L 0.85 0.07 0.00
82_K 163_N 0.85 0.07 0.00
69_M 316_P 0.84 0.07 0.00
49_L 261_M 0.84 0.07 0.00
3_D 48_R 0.84 0.07 0.00
54_A 151_S 0.84 0.07 0.00
36_H 133_M 0.84 0.07 0.00
19_I 111_I 0.83 0.07 0.00
84_E 189_S 0.83 0.07 0.00
41_C 218_P 0.82 0.07 0.00
25_D 120_F 0.82 0.07 0.00
17_K 165_Q 0.81 0.07 0.00
69_M 61_F 0.81 0.07 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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