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OPENSEQ.org
ccdb f plasmid, coli gyrase A - take 2
Genes: A B A+B
Length: 101 908 975
Sequences: 293 3491 81
Seq/Len: 2.9 3.84 0.08
MirrorTree (Pazo et al. 2001) 0.27
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 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.02 0.00
20 0.01 0.02 0.00
100 0.02 0.04 0.01
∞ 0.03 0.11 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
80_V 354_L 1.52 0.18 0.00
96_L 533_E 1.51 0.18 0.00
84_S 324_D 1.39 0.15 0.00
72_P 80_I 1.30 0.13 0.00
25_I 315_V 1.27 0.12 0.00
79_E 361_L 1.23 0.11 0.00
10_R 324_D 1.22 0.11 0.00
94_I 726_T 1.22 0.11 0.00
39_A 22_V 1.21 0.11 0.00
17_F 75_V 1.19 0.11 0.00
32_M 515_F 1.17 0.10 0.00
18_V 271_F 1.15 0.10 0.00
63_M 251_I 1.14 0.10 0.00
97_M 378_F 1.14 0.10 0.00
98_F 30_R 1.13 0.10 0.00
38_S 580_V 1.13 0.10 0.00
11_E 609_L 1.11 0.09 0.00
92_N 731_I 1.11 0.09 0.00
97_M 512_R 1.07 0.09 0.00
49_E 398_A 1.07 0.09 0.00
98_F 253_M 1.07 0.09 0.00
91_K 173_R 1.06 0.09 0.00
23_D 529_S 1.05 0.08 0.00
54_V 355_M 1.04 0.08 0.00
46_V 736_D 1.03 0.08 0.00
94_I 136_S 1.03 0.08 0.00
75_V 80_I 1.02 0.08 0.00
55_H 61_Y 1.02 0.08 0.00
82_D 706_L 1.02 0.08 0.00
51_Y 99_A 1.01 0.08 0.00
71_V 173_R 1.01 0.08 0.00
53_V 685_G 1.01 0.08 0.00
58_D 361_L 1.00 0.08 0.00
99_W 61_Y 1.00 0.08 0.00
72_P 206_V 1.00 0.08 0.00
62_R 587_N 0.99 0.08 0.00
70_S 635_T 0.99 0.08 0.00
80_V 634_I 0.99 0.07 0.00
2_Q 274_I 0.98 0.07 0.00
82_D 293_D 0.98 0.07 0.00
101_I 541_M 0.98 0.07 0.00
25_I 521_T 0.97 0.07 0.00
18_V 615_N 0.97 0.07 0.00
20_V 318_K 0.97 0.07 0.00
39_A 204_A 0.97 0.07 0.00
56_I 515_F 0.97 0.07 0.00
62_R 358_K 0.97 0.07 0.00
3_F 580_V 0.96 0.07 0.00
96_L 579_F 0.96 0.07 0.00
3_F 302_L 0.96 0.07 0.00
16_L 385_E 0.96 0.07 0.00
45_K 95_S 0.95 0.07 0.00
5_V 80_I 0.95 0.07 0.00
38_S 123_V 0.94 0.07 0.00
97_M 203_D 0.94 0.07 0.00
25_I 709_C 0.94 0.07 0.00
89_D 512_R 0.94 0.07 0.00
59_E 257_S 0.94 0.07 0.00
81_A 744_I 0.94 0.07 0.00
18_V 215_T 0.93 0.07 0.00
74_S 206_V 0.93 0.07 0.00
49_E 462_D 0.93 0.07 0.00
23_D 140_R 0.93 0.07 0.00
58_D 156_F 0.92 0.07 0.00
80_V 574_T 0.92 0.07 0.00
2_Q 179_V 0.92 0.07 0.00
56_I 505_K 0.92 0.07 0.00
20_V 378_F 0.91 0.07 0.00
90_I 504_V 0.91 0.07 0.00
25_I 735_K 0.91 0.07 0.00
3_F 474_D 0.91 0.07 0.00
18_V 400_I 0.91 0.07 0.00
25_I 587_N 0.90 0.06 0.00
34_I 515_F 0.90 0.06 0.00
19_D 742_M 0.90 0.06 0.00
26_D 742_M 0.90 0.06 0.00
81_A 732_N 0.90 0.06 0.00
101_I 585_V 0.89 0.06 0.00
87_E 515_F 0.89 0.06 0.00
73_V 379_L 0.89 0.06 0.00
41_L 652_V 0.89 0.06 0.00
59_E 512_R 0.89 0.06 0.00
58_D 580_V 0.89 0.06 0.00
99_W 217_E 0.89 0.06 0.00
63_M 741_S 0.88 0.06 0.00
94_I 483_L 0.88 0.06 0.00
101_I 22_V 0.88 0.06 0.00
18_V 453_S 0.88 0.06 0.00
34_I 211_D 0.88 0.06 0.00
75_V 94_Q 0.88 0.06 0.00
2_Q 313_I 0.87 0.06 0.00
96_L 691_V 0.87 0.06 0.00
63_M 509_A 0.87 0.06 0.00
25_I 495_R 0.86 0.06 0.00
63_M 149_I 0.86 0.06 0.00
34_I 496_S 0.85 0.06 0.00
73_V 149_I 0.85 0.06 0.00
45_K 385_E 0.85 0.06 0.00
38_S 300_S 0.84 0.06 0.00
80_V 740_I 0.84 0.06 0.00
5_V 570_S 0.84 0.06 0.00
17_F 271_F 0.84 0.06 0.00
56_I 168_T 0.84 0.06 0.00
26_D 215_T 0.84 0.06 0.00
62_R 448_G 0.84 0.06 0.00
47_S 300_S 0.84 0.06 0.00
98_F 140_R 0.84 0.06 0.00
79_E 80_I 0.84 0.06 0.00
54_V 668_D 0.84 0.06 0.00
21_Q 595_F 0.84 0.06 0.00
17_F 538_R 0.84 0.06 0.00
84_S 693_I 0.83 0.06 0.00
40_R 604_E 0.83 0.06 0.00
68_M 651_D 0.83 0.06 0.00
56_I 114_I 0.83 0.06 0.00
87_E 281_A 0.83 0.06 0.00
18_V 506_H 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)
ID Seq/Len Name Options I_Prob Status
9242 0.09 ccdb f plasmid, coli gyrase A - take 4 Δgene:(0, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done
4956 0.96 ccdb f plasmid, coli gyrase A - take 3 Δgene:(0, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4955 0.08 ccdb f plasmid, coli gyrase A - take 2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
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