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OPENSEQ.org
cI_G_cIII_isp_Pdenitr
Genes: A B A+B
Length: 674 190 840
Sequences: 1936 1692 539
Seq/Len: 2.87 8.91 0.64
MirrorTree (Pazo et al. 2001) 0.25
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 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.03 0.01 0.07
∞ 0.09 0.05 0.62
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
406_V 31_A 1.28 0.47 0.00
289_I 30_A 1.17 0.37 0.00
378_I 32_G 1.11 0.33 0.00
160_S 176_I 1.09 0.32 0.00
575_K 31_A 1.01 0.26 0.00
193_N 98_I 0.99 0.25 0.00
312_K 28_T 0.98 0.24 0.00
525_I 183_D 0.95 0.23 0.00
540_I 55_Q 0.95 0.22 0.00
445_V 63_T 0.94 0.22 0.00
289_I 33_A 0.94 0.22 0.00
589_G 109_D 0.94 0.22 0.00
369_I 30_A 0.94 0.22 0.00
378_I 76_V 0.94 0.22 0.00
205_I 78_I 0.93 0.21 0.00
72_D 18_F 0.92 0.21 0.00
316_I 29_V 0.92 0.21 0.00
580_I 29_V 0.89 0.19 0.00
262_G 61_V 0.88 0.19 0.00
238_A 39_V 0.88 0.18 0.00
290_R 83_E 0.88 0.18 0.00
375_I 13_A 0.87 0.18 0.00
72_D 168_G 0.87 0.18 0.00
147_L 34_A 0.85 0.17 0.00
596_S 22_A 0.85 0.17 0.00
22_L 162_S 0.84 0.17 0.00
22_L 174_L 0.83 0.16 0.00
505_A 75_P 0.83 0.16 0.00
220_F 186_T 0.82 0.16 0.00
602_R 78_I 0.81 0.16 0.00
365_R 24_A 0.80 0.15 0.00
621_E 182_L 0.79 0.15 0.00
305_E 80_R 0.79 0.15 0.00
360_Y 53_S 0.79 0.15 0.00
373_E 133_T 0.79 0.15 0.00
207_L 126_L 0.79 0.15 0.00
98_V 68_T 0.79 0.14 0.00
28_M 59_S 0.79 0.14 0.00
30_G 131_V 0.78 0.14 0.00
22_L 35_A 0.78 0.14 0.00
600_L 28_T 0.78 0.14 0.00
286_R 115_E 0.78 0.14 0.00
661_M 131_V 0.78 0.14 0.00
17_D 74_K 0.77 0.14 0.00
171_V 79_R 0.77 0.14 0.00
339_L 187_I 0.77 0.14 0.00
467_L 129_I 0.77 0.14 0.00
374_M 78_I 0.77 0.14 0.00
397_W 131_V 0.77 0.14 0.00
311_M 80_R 0.77 0.14 0.00
393_I 111_P 0.77 0.14 0.00
598_A 123_G 0.77 0.14 0.00
378_I 85_E 0.77 0.14 0.00
269_S 187_I 0.76 0.13 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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