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OPENSEQ.org
ccdb f plasmid, coli gyrase A - take 4
Genes: A B A+B
Length: 101 908 876
Sequences: 291 2439 79
Seq/Len: 2.88 2.69 0.09
MirrorTree (Pazo et al. 2001) 0.12
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 0.00 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.02 0.01
∞ 0.03 0.07 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
98_F 870_I 1.50 0.19 0.00
80_V 354_L 1.45 0.17 0.00
58_D 580_V 1.39 0.16 0.00
69_A 622_V 1.23 0.12 0.00
72_P 365_N 1.20 0.12 0.00
63_M 741_S 1.14 0.10 0.00
94_I 162_D 1.12 0.10 0.00
94_I 483_L 1.12 0.10 0.00
16_L 489_D 1.11 0.10 0.00
69_A 523_I 1.11 0.10 0.00
94_I 882_V 1.11 0.10 0.00
62_R 511_V 1.11 0.10 0.00
26_D 215_T 1.11 0.10 0.00
28_P 858_N 1.08 0.09 0.00
71_V 631_G 1.07 0.09 0.00
49_E 462_D 1.07 0.09 0.00
82_D 855_L 1.07 0.09 0.00
3_F 302_L 1.07 0.09 0.00
39_A 22_V 1.06 0.09 0.00
1_M 541_M 1.04 0.09 0.00
17_F 75_V 1.04 0.09 0.00
59_E 257_S 1.03 0.09 0.00
94_I 726_T 1.02 0.09 0.00
84_S 324_D 1.02 0.08 0.00
97_M 512_R 1.02 0.08 0.00
5_V 270_I 1.02 0.08 0.00
25_I 315_V 1.01 0.08 0.00
80_V 634_I 1.01 0.08 0.00
34_I 744_I 1.01 0.08 0.00
63_M 251_I 1.00 0.08 0.00
39_A 204_A 0.98 0.08 0.00
101_I 354_L 0.98 0.08 0.00
91_K 874_G 0.98 0.08 0.00
72_P 742_M 0.98 0.08 0.00
99_W 61_Y 0.97 0.08 0.00
89_D 512_R 0.97 0.08 0.00
63_M 509_A 0.96 0.08 0.00
98_F 253_M 0.96 0.08 0.00
25_I 419_A 0.96 0.08 0.00
38_S 580_V 0.95 0.07 0.00
63_M 149_I 0.95 0.07 0.00
26_D 378_F 0.95 0.07 0.00
4_K 612_A 0.95 0.07 0.00
96_L 123_V 0.94 0.07 0.00
78_E 385_E 0.94 0.07 0.00
83_L 515_F 0.94 0.07 0.00
99_W 563_K 0.94 0.07 0.00
2_Q 313_I 0.94 0.07 0.00
50_L 146_L 0.94 0.07 0.00
56_I 505_K 0.93 0.07 0.00
79_E 361_L 0.93 0.07 0.00
2_Q 616_A 0.93 0.07 0.00
18_V 29_R 0.92 0.07 0.00
70_S 616_A 0.92 0.07 0.00
16_L 26_D 0.91 0.07 0.00
81_A 744_I 0.91 0.07 0.00
16_L 101_V 0.91 0.07 0.00
56_I 360_L 0.91 0.07 0.00
20_V 806_S 0.90 0.07 0.00
7_T 872_I 0.90 0.07 0.00
54_V 355_M 0.90 0.07 0.00
53_V 857_T 0.90 0.07 0.00
26_D 742_M 0.88 0.07 0.00
56_I 515_F 0.88 0.07 0.00
101_I 541_M 0.88 0.07 0.00
96_L 533_E 0.88 0.07 0.00
89_D 218_A 0.88 0.07 0.00
63_M 174_F 0.87 0.07 0.00
73_V 379_L 0.87 0.07 0.00
12_S 362_L 0.87 0.06 0.00
3_F 234_I 0.87 0.06 0.00
75_V 94_Q 0.87 0.06 0.00
18_V 395_I 0.86 0.06 0.00
51_Y 99_A 0.86 0.06 0.00
18_V 650_L 0.86 0.06 0.00
27_T 411_P 0.86 0.06 0.00
94_I 80_I 0.86 0.06 0.00
23_D 529_S 0.86 0.06 0.00
20_V 347_L 0.84 0.06 0.00
22_S 857_T 0.84 0.06 0.00
18_V 199_G 0.84 0.06 0.00
27_T 573_S 0.84 0.06 0.00
49_E 398_A 0.84 0.06 0.00
28_P 100_L 0.84 0.06 0.00
6_Y 127_P 0.84 0.06 0.00
9_K 570_S 0.83 0.06 0.00
79_E 295_R 0.83 0.06 0.00
7_T 899_G 0.83 0.06 0.00
94_I 378_F 0.83 0.06 0.00
58_D 742_M 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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