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OPENSEQ.org
MP5 gyrase B
Genes: A B A+B
Length: 104 815 902
Sequences: 3660 1191 368
Seq/Len: 35.19 1.46 0.41
MirrorTree (Pazo et al. 2001) 0.07
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 0.02 0.01 0.00
2 0.02 0.01 0.00
5 0.04 0.01 0.00
10 0.05 0.01 0.01
20 0.06 0.01 0.01
100 0.08 0.01 0.06
∞ 0.14 0.01 0.40
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
82_F 176_V 1.42 0.44 0.00
45_L 372_W 1.37 0.41 0.00
18_L 532_F 1.15 0.26 0.00
84_V 149_H 0.95 0.17 0.00
45_L 578_V 0.94 0.16 0.00
87_I 588_G 0.93 0.16 0.00
84_V 73_A 0.93 0.16 0.00
85_V 455_V 0.92 0.16 0.00
47_A 727_F 0.92 0.16 0.00
67_P 63_H 0.91 0.15 0.00
87_I 171_R 0.90 0.15 0.00
23_R 322_L 0.89 0.15 0.00
58_D 540_E 0.88 0.14 0.00
91_R 425_R 0.88 0.14 0.00
49_P 383_V 0.88 0.14 0.00
89_H 89_D 0.88 0.14 0.00
17_I 566_E 0.88 0.14 0.00
61_P 78_T 0.88 0.14 0.00
45_L 63_H 0.87 0.14 0.00
17_I 402_E 0.86 0.13 0.00
73_I 214_T 0.86 0.13 0.00
41_Q 566_E 0.84 0.13 0.00
14_L 314_I 0.83 0.12 0.00
17_I 167_P 0.82 0.12 0.00
14_L 305_L 0.81 0.12 0.00
52_L 543_H 0.81 0.12 0.00
23_R 600_V 0.81 0.12 0.00
29_A 727_F 0.81 0.12 0.00
88_L 538_I 0.81 0.12 0.00
38_L 65_D 0.81 0.12 0.00
70_G 78_T 0.79 0.11 0.00
14_L 325_D 0.79 0.11 0.00
52_L 79_V 0.79 0.11 0.00
87_I 402_E 0.78 0.11 0.00
87_I 218_H 0.78 0.11 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
4199 0.41 MP5 gyrase B Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
4128 0 MP5 gyrase B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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