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OPENSEQ.org
D3_GS2
Genes: A B A+B
Length: 400 394 750
Sequences: 324 2903 62
Seq/Len: 0.81 7.37 0.08
MirrorTree (Pazo et al. 2001) 0.14
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 0.08 0.01 0.00
2 0.08 0.01 0.00
5 0.10 0.01 0.00
10 0.11 0.01 0.00
20 0.12 0.01 0.01
100 0.12 0.02 0.02
∞ 0.16 0.02 0.08
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
193_S 77_P 1.33 0.14 0.00
51_C 158_G 1.01 0.08 0.00
105_V 180_D 0.99 0.07 0.00
117_S 204_T 0.98 0.07 0.00
165_S 22_A 0.95 0.07 0.00
132_V 306_S 0.95 0.07 0.00
117_S 113_L 0.94 0.07 0.00
128_R 113_L 0.92 0.07 0.00
68_V 376_F 0.92 0.07 0.00
391_R 340_F 0.91 0.07 0.00
276_L 61_R 0.90 0.07 0.00
61_Q 169_Y 0.88 0.06 0.00
244_S 30_L 0.87 0.06 0.00
75_D 393_L 0.87 0.06 0.00
275_E 341_I 0.87 0.06 0.00
181_C 223_D 0.86 0.06 0.00
181_C 226_G 0.86 0.06 0.00
181_C 295_D 0.86 0.06 0.00
117_S 375_V 0.86 0.06 0.00
215_L 240_D 0.86 0.06 0.00
343_L 165_R 0.85 0.06 0.00
295_S 15_E 0.85 0.06 0.00
338_F 314_E 0.85 0.06 0.00
83_M 289_L 0.84 0.06 0.00
206_L 71_E 0.83 0.06 0.00
344_P 204_T 0.83 0.06 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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