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OPENSEQ.org
MtbClpSClpC1_redo3
Genes: A B A+B
Length: 101 848 911
Sequences: 1441 2555 493
Seq/Len: 14.27 3.01 0.54
MirrorTree (Pazo et al. 2001) 0.34
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 0.01 0.01
2 0.00 0.01 0.01
5 0.00 0.01 0.01
10 0.00 0.02 0.01
20 0.01 0.02 0.02
100 0.01 0.04 0.07
∞ 0.03 0.10 0.52
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
44_T 731_V 1.48 0.57 0.00
28_W 293_V 1.32 0.44 0.00
31_I 456_T 1.15 0.32 0.00
79_E 729_R 1.09 0.28 0.00
31_I 742_L 1.08 0.28 0.00
47_F 532_I 1.07 0.27 0.00
90_A 400_I 1.06 0.27 0.00
47_F 516_K 1.00 0.23 0.00
31_I 543_K 0.98 0.22 0.00
50_L 400_I 0.98 0.22 0.00
47_F 777_I 0.96 0.21 0.00
72_V 345_V 0.96 0.20 0.00
68_E 272_V 0.96 0.20 0.00
45_Y 481_D 0.94 0.20 0.00
75_A 528_V 0.94 0.20 0.00
65_V 622_V 0.94 0.20 0.00
48_Q 641_V 0.94 0.20 0.00
85_V 733_L 0.94 0.20 0.00
56_P 658_K 0.94 0.19 0.00
54_S 577_L 0.93 0.19 0.00
68_E 112_L 0.93 0.19 0.00
41_S 175_G 0.93 0.19 0.00
44_T 750_V 0.92 0.18 0.00
54_S 377_A 0.91 0.18 0.00
46_V 488_L 0.89 0.17 0.00
23_V 487_V 0.87 0.17 0.00
79_E 496_V 0.87 0.16 0.00
80_S 87_V 0.86 0.16 0.00
67_N 749_L 0.84 0.15 0.00
87_K 627_I 0.84 0.15 0.00
93_L 537_A 0.84 0.15 0.00
59_T 622_V 0.83 0.15 0.00
64_Q 785_L 0.83 0.15 0.00
41_S 379_M 0.82 0.14 0.00
22_D 203_V 0.82 0.14 0.00
73_V 86_K 0.82 0.14 0.00
89_H 532_I 0.81 0.14 0.00
46_V 703_K 0.81 0.14 0.00
99_Q 578_I 0.81 0.14 0.00
14_W 244_D 0.80 0.14 0.00
61_L 10_R 0.80 0.14 0.00
46_V 725_E 0.80 0.14 0.00
15_Q 796_P 0.80 0.14 0.00
79_E 292_L 0.80 0.14 0.00
79_E 597_A 0.80 0.13 0.00
30_T 223_T 0.80 0.13 0.00
31_I 691_E 0.79 0.13 0.00
51_F 589_F 0.78 0.13 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
3402 0.54 MtbClpSClpC1_redo3 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done
3400 0 MtbClpSClpC1_redo3 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed
3399 0 MtbClpSClpC1_redo2 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed
3397 0 MtbClpSClpC1_redo2 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed
3395 0.03 MtbClpSClpC1_redo Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed
3393 0 MtbClpSClpC1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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