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OPENSEQ.org
ClpB ClpS
Genes: A B A+B
Length: 848 100 907
Sequences: 3943 1232 768
Seq/Len: 4.65 12.32 0.85
MirrorTree (Pazo et al. 2001) 0.15
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 0.01 0.06 0.02
2 0.01 0.06 0.02
5 0.01 0.06 0.02
10 0.01 0.06 0.03
20 0.02 0.06 0.03
100 0.03 0.06 0.14
∞ 0.13 0.09 0.81
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
676_I 64_V 1.80 0.88 0.23
541_V 22_S 1.42 0.66 0.08
543_E 96_M 1.22 0.49 0.04
763_Q 78_E 1.06 0.35 0.03
717_I 64_V 0.99 0.30 0.02
424_E 38_L 0.99 0.30 0.02
481_D 58_T 0.94 0.26 0.02
807_L 31_V 0.94 0.26 0.02
111_L 96_M 0.93 0.25 0.01
823_L 20_V 0.92 0.25 0.01
190_V 38_L 0.91 0.24 0.01
787_L 98_Q 0.91 0.24 0.01
271_G 75_G 0.90 0.24 0.01
583_S 66_N 0.90 0.24 0.01
243_G 93_W 0.90 0.23 0.01
537_D 78_E 0.89 0.23 0.01
87_S 69_K 0.89 0.23 0.01
786_S 32_W 0.88 0.22 0.01
712_R 64_V 0.87 0.21 0.01
341_E 50_F 0.86 0.21 0.01
162_E 60_L 0.86 0.21 0.01
597_N 53_S 0.85 0.21 0.01
552_R 78_E 0.85 0.20 0.01
126_L 30_I 0.84 0.20 0.01
166_T 40_S 0.84 0.20 0.01
216_V 40_S 0.84 0.20 0.01
789_A 31_V 0.84 0.20 0.01
838_V 76_S 0.83 0.19 0.01
631_M 17_V 0.83 0.19 0.01
646_A 67_E 0.82 0.19 0.01
598_R 40_S 0.82 0.19 0.01
536_D 40_S 0.81 0.19 0.01
401_R 98_Q 0.81 0.18 0.01
223_I 96_M 0.80 0.18 0.01
541_V 49_L 0.80 0.18 0.01
541_V 28_V 0.80 0.18 0.01
688_V 33_D 0.79 0.17 0.01
715_I 47_Q 0.79 0.17 0.01
274_I 21_E 0.79 0.17 0.01
125_L 78_E 0.79 0.17 0.01
722_L 45_V 0.78 0.17 0.01
720_S 43_T 0.78 0.17 0.01
175_G 81_E 0.78 0.17 0.01
371_L 40_S 0.78 0.17 0.01
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
9731 0.85 ClpB ClpS Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.23 Done
9719 0.04 ClpB ClpS Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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