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OPENSEQ.org
iscsiscx
Genes: A B A+B
Length: 404 66 467
Sequences: 31466 324 153
Seq/Len: 77.89 4.91 0.33
MirrorTree (Pazo et al. 2001) 0.11
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 0.07 0.00 0.01
2 0.09 0.00 0.01
5 0.11 0.00 0.05
10 0.12 0.00 0.33
20 0.15 0.00 0.35
100 0.25 0.00 0.42
∞ 0.29 0.00 0.54
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
377_I 63_D 1.59 0.50 0.00
383_L 50_N 1.48 0.43 0.00
170_C 63_D 1.40 0.38 0.00
391_K 27_V 1.39 0.37 0.00
256_Y 58_L 1.36 0.35 0.00
71_F 30_T 1.30 0.32 0.00
307_Y 10_E 1.25 0.29 0.00
63_G 62_L 1.25 0.28 0.00
377_I 52_K 1.24 0.28 0.00
258_I 40_E 1.23 0.27 0.00
383_L 28_R 1.21 0.26 0.00
71_F 28_R 1.19 0.25 0.00
182_T 32_M 1.18 0.25 0.00
403_H 50_N 1.18 0.24 0.00
373_V 27_V 1.16 0.23 0.00
284_I 50_N 1.14 0.23 0.00
399_I 53_I 1.14 0.22 0.00
245_P 40_E 1.12 0.22 0.00
46_Q 36_I 1.11 0.21 0.00
169_M 52_K 1.08 0.20 0.00
383_L 30_T 1.05 0.19 0.00
86_A 38_D 1.05 0.19 0.00
126_P 19_Y 1.03 0.18 0.00
366_I 13_E 1.03 0.18 0.00
235_H 24_P 1.02 0.18 0.00
388_E 52_K 1.01 0.17 0.00
132_I 19_Y 1.00 0.17 0.00
267_M 62_L 1.00 0.17 0.00
374_R 28_R 1.00 0.17 0.00
258_I 62_L 0.99 0.16 0.00
98_I 14_A 0.99 0.16 0.00
7_L 53_I 0.99 0.16 0.00
396_L 6_T 0.98 0.16 0.00
26_F 28_R 0.96 0.15 0.00
284_I 49_S 0.96 0.15 0.00
182_T 62_L 0.96 0.15 0.00
245_P 38_D 0.96 0.15 0.00
275_N 33_H 0.94 0.15 0.00
58_I 30_T 0.94 0.15 0.00
281_I 41_D 0.93 0.14 0.00
279_N 30_T 0.93 0.14 0.00
61_L 24_P 0.93 0.14 0.00
283_D 50_N 0.92 0.14 0.00
394_V 19_Y 0.92 0.14 0.00
94_G 24_P 0.92 0.14 0.00
390_Y 48_A 0.92 0.14 0.00
63_G 17_D 0.91 0.14 0.00
58_I 58_L 0.91 0.13 0.00
392_Q 21_D 0.91 0.13 0.00
58_I 22_L 0.91 0.13 0.00
383_L 21_D 0.91 0.13 0.00
353_I 6_T 0.90 0.13 0.00
52_D 8_S 0.90 0.13 0.00
97_I 31_D 0.90 0.13 0.00
192_L 37_C 0.90 0.13 0.00
260_K 37_C 0.90 0.13 0.00
307_Y 35_W 0.89 0.13 0.00
370_I 35_W 0.89 0.13 0.00
164_A 36_I 0.89 0.13 0.00
277_L 8_S 0.89 0.13 0.00
383_L 63_D 0.88 0.13 0.00
143_D 3_L 0.88 0.13 0.00
137_L 52_K 0.88 0.12 0.00
174_G 40_E 0.87 0.12 0.00
348_L 49_S 0.87 0.12 0.00
398_S 3_L 0.86 0.12 0.00
119_F 4_K 0.86 0.12 0.00
182_T 58_L 0.86 0.12 0.00
169_M 19_Y 0.86 0.12 0.00
373_V 30_T 0.86 0.12 0.00
188_L 40_E 0.85 0.12 0.00
25_Q 25_K 0.85 0.12 0.00
306_N 65_A 0.85 0.12 0.00
284_I 28_R 0.84 0.11 0.00
180_D 44_D 0.84 0.11 0.00
206_K 44_D 0.84 0.11 0.00
314_I 50_N 0.83 0.11 0.00
390_Y 28_R 0.83 0.11 0.00
373_V 22_L 0.83 0.11 0.00
373_V 48_A 0.83 0.11 0.00
320_L 36_I 0.83 0.11 0.00
306_N 14_A 0.82 0.11 0.00
150_I 49_S 0.82 0.11 0.00
63_G 40_E 0.82 0.11 0.00
155_N 44_D 0.81 0.11 0.00
25_Q 40_E 0.81 0.11 0.00
165_A 41_D 0.81 0.10 0.00
71_F 50_N 0.80 0.10 0.00
62_V 53_I 0.80 0.10 0.00
270_L 12_G 0.80 0.10 0.00
284_I 33_H 0.80 0.10 0.00
200_M 60_V 0.80 0.10 0.00
283_D 28_R 0.79 0.10 0.00
58_I 28_R 0.79 0.10 0.00
377_I 59_L 0.79 0.10 0.00
259_A 32_M 0.78 0.10 0.00
256_Y 32_M 0.78 0.10 0.00
170_C 28_R 0.78 0.10 0.00
66_P 22_L 0.78 0.10 0.00
297_A 12_G 0.78 0.10 0.00
43_F 27_V 0.77 0.10 0.00
204_G 53_I 0.77 0.10 0.00
58_I 36_I 0.77 0.10 0.00
373_V 40_E 0.77 0.10 0.00
307_Y 27_V 0.77 0.10 0.00
402_A 36_I 0.76 0.09 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
2091 0.33 IscSIscX Δgene:(1, 10) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1542 0.33 iscsiscx Δgene:(1, 10) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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