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OPENSEQ.org
gyrA-CnpA
Genes: A B A+B
Length: 89 919 840
Sequences: 331 2339 120
Seq/Len: 3.72 2.55 0.14
MirrorTree (Pazo et al. 2001) 0.36
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.01 0.00
2 0.07 0.01 0.00
5 0.07 0.01 0.00
10 0.07 0.01 0.00
20 0.07 0.01 0.01
100 0.07 0.02 0.02
∞ 0.14 0.07 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
61_V 249_V 1.59 0.29 0.00
27_V 93_S 1.51 0.26 0.00
61_V 401_F 1.38 0.21 0.00
81_L 339_G 1.33 0.19 0.00
81_L 336_S 1.23 0.16 0.00
23_I 110_V 1.22 0.15 0.00
44_V 281_L 1.18 0.14 0.00
42_K 701_T 1.17 0.14 0.00
78_I 803_E 1.14 0.13 0.00
37_I 282_V 1.12 0.13 0.00
76_D 510_R 1.11 0.12 0.00
19_Q 650_M 1.07 0.12 0.00
50_G 902_D 1.05 0.11 0.00
19_Q 284_H 1.04 0.11 0.00
22_S 884_T 1.04 0.11 0.00
43_E 398_I 1.04 0.11 0.00
67_Q 844_L 1.03 0.11 0.00
76_D 879_N 1.03 0.11 0.00
71_K 109_L 1.03 0.11 0.00
24_I 598_K 1.03 0.11 0.00
67_Q 705_R 1.03 0.11 0.00
21_K 832_L 1.02 0.11 0.00
43_E 109_L 1.02 0.11 0.00
60_K 27_R 1.01 0.10 0.00
43_E 107_M 1.01 0.10 0.00
43_E 78_V 1.01 0.10 0.00
55_V 339_G 1.00 0.10 0.00
50_G 451_T 1.00 0.10 0.00
75_E 555_A 1.00 0.10 0.00
18_G 511_E 0.99 0.10 0.00
15_T 207_I 0.99 0.10 0.00
50_G 147_L 0.99 0.10 0.00
44_V 889_A 0.99 0.10 0.00
19_Q 572_T 0.99 0.10 0.00
65_R 275_Q 0.98 0.10 0.00
22_S 340_V 0.98 0.10 0.00
24_I 842_G 0.97 0.10 0.00
21_K 590_L 0.97 0.10 0.00
38_M 46_A 0.97 0.10 0.00
37_I 902_D 0.97 0.10 0.00
21_K 317_R 0.97 0.10 0.00
83_L 620_V 0.96 0.10 0.00
53_F 175_L 0.96 0.09 0.00
78_I 147_L 0.96 0.09 0.00
63_R 702_A 0.96 0.09 0.00
83_L 809_S 0.95 0.09 0.00
27_V 385_G 0.95 0.09 0.00
58_L 288_L 0.95 0.09 0.00
24_I 408_S 0.95 0.09 0.00
76_D 824_R 0.94 0.09 0.00
76_D 360_Q 0.94 0.09 0.00
68_D 92_A 0.94 0.09 0.00
16_A 328_L 0.94 0.09 0.00
50_G 819_A 0.94 0.09 0.00
50_G 359_I 0.94 0.09 0.00
53_F 409_K 0.94 0.09 0.00
72_R 411_P 0.94 0.09 0.00
23_I 716_V 0.94 0.09 0.00
80_D 479_A 0.94 0.09 0.00
33_E 77_R 0.93 0.09 0.00
66_K 813_F 0.93 0.09 0.00
24_I 332_T 0.93 0.09 0.00
58_L 309_M 0.93 0.09 0.00
16_A 406_R 0.93 0.09 0.00
86_I 57_V 0.93 0.09 0.00
35_A 148_D 0.93 0.09 0.00
83_L 448_I 0.93 0.09 0.00
58_L 685_I 0.92 0.09 0.00
70_A 622_L 0.92 0.09 0.00
21_K 389_V 0.91 0.09 0.00
21_K 609_L 0.91 0.09 0.00
88_E 701_T 0.91 0.09 0.00
62_V 229_G 0.91 0.09 0.00
61_V 324_I 0.91 0.08 0.00
43_E 257_V 0.91 0.08 0.00
67_Q 685_I 0.90 0.08 0.00
17_Q 510_R 0.90 0.08 0.00
37_I 479_A 0.90 0.08 0.00
68_D 203_C 0.90 0.08 0.00
53_F 274_Y 0.90 0.08 0.00
45_Y 406_R 0.90 0.08 0.00
68_D 24_D 0.90 0.08 0.00
40_Q 408_S 0.90 0.08 0.00
43_E 311_I 0.89 0.08 0.00
81_L 657_S 0.89 0.08 0.00
53_F 604_V 0.89 0.08 0.00
27_V 500_A 0.89 0.08 0.00
21_K 298_A 0.89 0.08 0.00
67_Q 813_F 0.89 0.08 0.00
60_K 634_I 0.88 0.08 0.00
53_F 334_L 0.88 0.08 0.00
33_E 535_V 0.88 0.08 0.00
60_K 311_I 0.88 0.08 0.00
71_K 404_I 0.88 0.08 0.00
43_E 349_R 0.88 0.08 0.00
75_E 370_V 0.88 0.08 0.00
66_K 297_V 0.87 0.08 0.00
53_F 595_S 0.87 0.08 0.00
64_I 65_G 0.87 0.08 0.00
27_V 313_V 0.87 0.08 0.00
29_R 388_L 0.87 0.08 0.00
43_E 601_K 0.87 0.08 0.00
40_Q 108_G 0.87 0.08 0.00
62_V 646_G 0.86 0.08 0.00
39_E 254_V 0.86 0.08 0.00
80_D 243_L 0.86 0.08 0.00
78_I 470_G 0.86 0.08 0.00
88_E 209_Q 0.86 0.08 0.00
29_R 384_R 0.86 0.08 0.00
62_V 488_Y 0.86 0.08 0.00
34_K 565_K 0.86 0.08 0.00
59_K 559_T 0.86 0.08 0.00
60_K 609_L 0.86 0.08 0.00
14_S 404_I 0.86 0.08 0.00
37_I 324_I 0.86 0.08 0.00
64_I 43_L 0.86 0.08 0.00
67_Q 121_V 0.85 0.08 0.00
55_V 483_D 0.85 0.07 0.00
84_S 221_V 0.85 0.07 0.00
23_I 610_G 0.85 0.07 0.00
41_I 46_A 0.85 0.07 0.00
43_E 617_K 0.85 0.07 0.00
81_L 503_R 0.84 0.07 0.00
33_E 578_V 0.84 0.07 0.00
71_K 494_D 0.84 0.07 0.00
62_V 685_I 0.84 0.07 0.00
76_D 21_N 0.84 0.07 0.00
60_K 213_T 0.84 0.07 0.00
60_K 728_V 0.84 0.07 0.00
69_R 221_V 0.84 0.07 0.00
43_E 281_L 0.84 0.07 0.00
18_G 231_E 0.84 0.07 0.00
53_F 880_T 0.84 0.07 0.00
71_K 737_I 0.84 0.07 0.00
69_R 204_L 0.83 0.07 0.00
33_E 647_L 0.83 0.07 0.00
80_D 614_S 0.83 0.07 0.00
35_A 253_G 0.83 0.07 0.00
71_K 685_I 0.83 0.07 0.00
43_E 861_D 0.83 0.07 0.00
23_I 873_I 0.83 0.07 0.00
50_G 520_Q 0.83 0.07 0.00
44_V 615_R 0.83 0.07 0.00
46_A 86_Y 0.82 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
6501 0 gyrA-CnpA Δgene:(0, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
6500 0.14 gyrA-CnpA Δgene:(0, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6499 0.14 gyrA-CnpA Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
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