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OPENSEQ.org
cI_B_cIII_isp
Genes: A B A+B
Length: 613 190 795
Sequences: 2476 1442 360
Seq/Len: 4.04 7.59 0.45
MirrorTree (Pazo et al. 2001) 0.41
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.01 0.04
∞ 0.01 0.02 0.45
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
85_S 67_L 1.21 0.32 0.00
358_H 45_S 1.13 0.27 0.00
362_I 39_V 1.11 0.26 0.00
416_V 78_I 1.06 0.23 0.00
435_I 189_L 1.06 0.23 0.00
40_L 187_I 1.03 0.22 0.00
152_L 64_G 1.02 0.21 0.00
194_T 32_G 1.00 0.20 0.00
160_D 181_F 0.98 0.19 0.00
41_A 60_G 0.98 0.19 0.00
208_F 39_V 0.98 0.19 0.00
17_L 78_I 0.98 0.19 0.00
480_P 33_A 0.95 0.18 0.00
465_T 83_E 0.91 0.16 0.00
306_R 19_L 0.91 0.16 0.00
56_G 68_T 0.89 0.15 0.00
440_K 188_K 0.88 0.15 0.00
15_F 183_D 0.88 0.15 0.00
115_R 165_I 0.88 0.15 0.00
403_L 188_K 0.87 0.15 0.00
369_R 175_H 0.87 0.15 0.00
138_L 37_T 0.87 0.15 0.00
7_T 131_V 0.86 0.14 0.00
364_K 40_N 0.86 0.14 0.00
87_T 12_G 0.86 0.14 0.00
282_L 29_V 0.85 0.14 0.00
217_W 15_R 0.85 0.14 0.00
234_P 138_V 0.84 0.14 0.00
225_G 5_D 0.84 0.13 0.00
85_S 98_I 0.83 0.13 0.00
41_A 78_I 0.83 0.13 0.00
77_F 150_W 0.82 0.13 0.00
434_F 26_A 0.82 0.13 0.00
223_L 159_Y 0.82 0.13 0.00
200_M 159_Y 0.82 0.13 0.00
326_Q 22_A 0.82 0.13 0.00
79_L 144_A 0.81 0.13 0.00
182_A 29_V 0.81 0.13 0.00
79_L 175_H 0.81 0.13 0.00
87_T 189_L 0.81 0.12 0.00
370_K 39_V 0.81 0.12 0.00
390_P 21_Y 0.81 0.12 0.00
160_D 125_W 0.81 0.12 0.00
120_T 145_G 0.81 0.12 0.00
195_L 150_W 0.81 0.12 0.00
453_H 32_G 0.80 0.12 0.00
194_T 75_P 0.80 0.12 0.00
419_L 131_V 0.80 0.12 0.00
68_M 168_G 0.80 0.12 0.00
598_M 24_A 0.80 0.12 0.00
135_N 79_R 0.80 0.12 0.00
137_L 79_R 0.80 0.12 0.00
133_A 93_D 0.79 0.12 0.00
80_V 159_Y 0.79 0.12 0.00
231_A 162_S 0.79 0.12 0.00
508_A 112_A 0.79 0.12 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
2412 0.45 cI_B_cIII_isp Δgene:(1, ∞) A:(1E-40, 1) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2411 0.22 cI_B_cIII_isp Δgene:(1, ∞) A:(1E-60, 1) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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