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OPENSEQ.org
cI_3_4_cI_6_4_tt
Genes: A B A+B
Length: 783 181 901
Sequences: 1268 1709 704
Seq/Len: 1.62 9.44 0.78
MirrorTree (Pazo et al. 2001) 0.40
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 0.00
2 0.00 0.01 0.00
5 0.01 0.02 0.50
10 0.01 0.02 0.51
20 0.01 0.03 0.52
100 0.03 0.04 0.54
∞ 0.09 0.10 0.73
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
219_P 31_G 1.13 0.39 0.00
89_D 156_K 1.12 0.38 0.00
16_G 57_R 1.07 0.34 0.00
731_G 135_V 1.06 0.34 0.00
323_E 53_S 1.02 0.31 0.00
82_S 15_E 0.99 0.28 0.00
498_E 56_A 0.99 0.28 0.00
171_S 48_I 0.98 0.28 0.00
606_T 58_N 0.96 0.26 0.00
200_L 137_V 0.93 0.24 0.00
691_A 80_V 0.93 0.24 0.00
581_R 148_I 0.91 0.23 0.00
314_E 103_K 0.91 0.23 0.00
616_N 152_M 0.88 0.21 0.00
192_E 71_S 0.87 0.21 0.00
340_E 24_L 0.87 0.20 0.00
618_E 31_G 0.87 0.20 0.00
407_P 77_V 0.85 0.20 0.00
79_L 67_V 0.84 0.19 0.00
1_M 122_A 0.84 0.19 0.00
125_G 90_P 0.84 0.19 0.00
626_P 81_A 0.84 0.19 0.00
683_L 135_V 0.84 0.19 0.00
290_I 36_L 0.84 0.19 0.00
201_D 29_A 0.83 0.18 0.00
730_E 122_A 0.83 0.18 0.00
293_A 150_A 0.82 0.18 0.00
747_V 26_K 0.82 0.18 0.00
550_L 23_T 0.81 0.17 0.00
226_I 85_S 0.81 0.17 0.00
270_R 83_R 0.81 0.17 0.00
724_R 84_L 0.80 0.17 0.00
583_V 27_L 0.80 0.17 0.00
449_A 17_E 0.80 0.17 0.00
552_G 67_V 0.80 0.17 0.00
493_A 56_A 0.80 0.17 0.00
11_V 16_R 0.79 0.17 0.00
486_G 100_P 0.78 0.16 0.00
285_V 67_V 0.78 0.16 0.00
563_A 135_V 0.78 0.16 0.00
355_L 151_V 0.78 0.16 0.00
592_P 56_A 0.78 0.16 0.00
26_A 148_I 0.77 0.16 0.00
479_A 53_S 0.77 0.15 0.00
177_D 24_L 0.77 0.15 0.00
21_D 21_F 0.77 0.15 0.00
188_V 81_A 0.77 0.15 0.00
311_V 156_K 0.77 0.15 0.00
386_S 70_A 0.76 0.15 0.00
727_A 15_E 0.76 0.15 0.00
167_H 24_L 0.76 0.15 0.00
260_P 161_Q 0.76 0.15 0.00
188_V 137_V 0.75 0.15 0.00
525_A 160_G 0.75 0.15 0.00
25_H 32_R 0.75 0.15 0.00
290_I 24_L 0.75 0.14 0.00
183_H 26_K 0.75 0.14 0.00
698_M 77_V 0.75 0.14 0.00
182_I 95_V 0.75 0.14 0.00
729_P 36_L 0.75 0.14 0.00
6_V 77_V 0.74 0.14 0.00
618_E 24_L 0.74 0.14 0.00
484_K 107_S 0.74 0.14 0.00
189_R 141_P 0.74 0.14 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
4961 0.72 cI_3_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4960 0.78 cI_3_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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