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OPENSEQ.org
Rpn12-6 wide open
Genes: A B A+B
Length: 434 274 691
Sequences: 991 1340 73
Seq/Len: 2.28 4.89 0.11
MirrorTree (Pazo et al. 2001) 0.11
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 0.05 0.06 0.01
2 0.05 0.06 0.01
5 0.06 0.10 0.01
10 0.07 0.10 0.01
20 0.07 0.11 0.01
100 0.08 0.13 0.03
∞ 0.11 0.17 0.10
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
391_D 111_L 1.77 0.33 0.00
391_D 197_Y 1.29 0.15 0.00
391_D 155_G 1.28 0.15 0.00
270_I 205_I 1.17 0.12 0.00
391_D 85_L 1.17 0.12 0.00
386_F 26_L 1.10 0.11 0.00
146_Y 13_I 1.05 0.10 0.00
176_D 185_I 1.03 0.10 0.00
266_L 126_L 1.03 0.09 0.00
386_F 19_D 1.01 0.09 0.00
70_A 219_K 1.00 0.09 0.00
153_D 111_L 0.99 0.09 0.00
232_Y 13_I 0.98 0.09 0.00
170_D 69_S 0.98 0.09 0.00
391_D 154_E 0.96 0.08 0.00
97_L 32_I 0.96 0.08 0.00
395_G 130_D 0.96 0.08 0.00
360_S 114_L 0.95 0.08 0.00
359_I 6_E 0.94 0.08 0.00
317_A 193_T 0.94 0.08 0.00
157_L 129_L 0.94 0.08 0.00
69_G 186_R 0.94 0.08 0.00
175_V 26_L 0.93 0.08 0.00
276_D 155_G 0.93 0.08 0.00
262_L 186_R 0.92 0.08 0.00
115_I 196_S 0.92 0.08 0.00
72_D 114_L 0.92 0.08 0.00
101_I 219_K 0.92 0.08 0.00
343_L 140_S 0.91 0.08 0.00
133_L 243_A 0.91 0.08 0.00
97_L 136_L 0.90 0.07 0.00
150_Q 111_L 0.89 0.07 0.00
105_E 90_F 0.88 0.07 0.00
350_I 72_T 0.88 0.07 0.00
257_K 69_S 0.88 0.07 0.00
318_L 126_L 0.88 0.07 0.00
426_L 113_L 0.88 0.07 0.00
240_F 36_K 0.88 0.07 0.00
72_D 184_A 0.87 0.07 0.00
133_L 220_F 0.86 0.07 0.00
231_D 230_N 0.86 0.07 0.00
384_K 157_Y 0.85 0.07 0.00
261_V 118_N 0.85 0.07 0.00
373_V 229_V 0.85 0.07 0.00
407_A 197_Y 0.85 0.07 0.00
63_Q 89_Y 0.84 0.07 0.00
350_I 21_A 0.84 0.07 0.00
69_G 162_D 0.84 0.07 0.00
346_N 48_N 0.83 0.07 0.00
117_V 216_E 0.83 0.07 0.00
216_A 10_S 0.83 0.07 0.00
395_G 217_T 0.83 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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