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OPENSEQ.org
PcrA_RpoB (A, 650-724)
Genes: A B A+B
Length: 75 1048 1110
Sequences: 1454 438 117
Seq/Len: 19.39 0.42 0.11
MirrorTree (Pazo et al. 2001) 0.71
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 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.02
∞ 0.00 0.00 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
52_L 204_D 1.75 0.32 0.00
55_A 249_E 1.43 0.19 0.00
41_V 775_I 1.41 0.19 0.00
72_I 111_V 1.27 0.15 0.00
29_R 126_I 1.26 0.14 0.00
28_D 207_I 1.24 0.14 0.00
52_L 239_R 1.24 0.14 0.00
41_V 530_S 1.21 0.13 0.00
54_I 1015_T 1.19 0.13 0.00
64_R 497_E 1.17 0.12 0.00
49_D 819_D 1.15 0.12 0.00
24_W 641_A 1.15 0.12 0.00
54_I 978_M 1.13 0.12 0.00
51_E 268_A 1.11 0.11 0.00
71_P 111_V 1.10 0.11 0.00
26_V 17_Y 1.08 0.10 0.00
52_L 1041_A 1.08 0.10 0.00
67_A 765_T 1.08 0.10 0.00
35_W 186_R 1.07 0.10 0.00
35_W 268_A 1.06 0.10 0.00
64_R 239_R 1.06 0.10 0.00
41_V 323_E 1.06 0.10 0.00
45_G 657_F 1.06 0.10 0.00
35_W 911_V 1.05 0.10 0.00
41_V 617_Q 1.05 0.10 0.00
57_P 761_V 1.05 0.10 0.00
72_I 285_L 1.03 0.10 0.00
51_E 26_L 1.03 0.09 0.00
35_W 1037_M 1.02 0.09 0.00
53_D 535_A 1.02 0.09 0.00
30_A 1013_A 1.02 0.09 0.00
41_V 561_I 1.02 0.09 0.00
35_W 111_V 1.01 0.09 0.00
51_E 988_A 1.00 0.09 0.00
53_D 457_S 0.99 0.09 0.00
67_A 787_Y 0.99 0.09 0.00
29_R 651_M 0.98 0.09 0.00
64_R 46_R 0.97 0.09 0.00
53_D 172_Y 0.96 0.08 0.00
33_R 432_R 0.96 0.08 0.00
47_G 1017_L 0.96 0.08 0.00
72_I 379_A 0.96 0.08 0.00
40_V 112_F 0.94 0.08 0.00
35_W 12_R 0.94 0.08 0.00
40_V 539_R 0.94 0.08 0.00
34_K 187_T 0.94 0.08 0.00
39_T 179_V 0.93 0.08 0.00
53_D 978_M 0.93 0.08 0.00
51_E 19_R 0.93 0.08 0.00
45_G 126_I 0.93 0.08 0.00
66_L 529_N 0.92 0.08 0.00
35_W 988_A 0.91 0.08 0.00
48_D 775_I 0.91 0.08 0.00
49_D 409_L 0.91 0.08 0.00
71_P 452_R 0.91 0.07 0.00
53_D 762_G 0.91 0.07 0.00
40_V 358_E 0.91 0.07 0.00
49_D 202_G 0.90 0.07 0.00
45_G 986_H 0.90 0.07 0.00
75_V 747_S 0.90 0.07 0.00
48_D 742_L 0.90 0.07 0.00
42_S 281_I 0.90 0.07 0.00
41_V 662_M 0.90 0.07 0.00
57_P 126_I 0.90 0.07 0.00
63_K 869_A 0.89 0.07 0.00
65_L 867_E 0.89 0.07 0.00
66_L 303_L 0.89 0.07 0.00
16_Q 32_I 0.89 0.07 0.00
29_R 111_V 0.88 0.07 0.00
73_E 202_G 0.88 0.07 0.00
35_W 641_A 0.88 0.07 0.00
71_P 762_G 0.88 0.07 0.00
30_A 540_F 0.87 0.07 0.00
74_K 662_M 0.87 0.07 0.00
74_K 377_T 0.87 0.07 0.00
54_I 1000_V 0.87 0.07 0.00
28_D 23_V 0.87 0.07 0.00
35_W 668_K 0.86 0.07 0.00
24_W 203_S 0.86 0.07 0.00
72_I 249_E 0.86 0.07 0.00
55_A 946_Y 0.86 0.07 0.00
64_R 382_I 0.85 0.07 0.00
63_K 1026_F 0.85 0.07 0.00
53_D 431_V 0.85 0.07 0.00
67_A 570_D 0.85 0.07 0.00
74_K 287_N 0.85 0.07 0.00
69_F 304_A 0.85 0.07 0.00
65_L 232_A 0.84 0.07 0.00
54_I 444_T 0.84 0.07 0.00
72_I 12_R 0.84 0.07 0.00
52_L 452_R 0.84 0.07 0.00
64_R 437_I 0.84 0.07 0.00
41_V 187_T 0.84 0.07 0.00
67_A 602_V 0.84 0.07 0.00
54_I 458_I 0.84 0.07 0.00
43_V 173_E 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)
ID Seq/Len Name Options I_Prob Status
4326 0.11 PcrA_RpoB (A, 650-724) Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4325 0 PcrA_RpoB (A, 650-724) Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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