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OPENSEQ.org
info 1JIW_PI E 1AKL_A Alkaline metalloproteinase 2RN4_A(1) Proteinase inhibitor
Genes: A B A+B
Length: 470 106 519
Sequences: 165 272 58
Seq/Len: 0.35 2.57 0.11
MirrorTree (Pazo et al. 2001) 0.62
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 0.06 0.01 0.10
2 0.06 0.01 0.10
5 0.07 0.01 0.10
10 0.08 0.01 0.10
20 0.09 0.02 0.10
100 0.10 0.02 0.10
∞ 0.13 0.07 0.12
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
424_A 87_G 1.49 0.21 0.00
237_D 89_Y 1.48 0.21 0.00
316_L 68_I 1.38 0.18 0.00
265_T 68_I 1.35 0.17 0.00
379_G 17_L 1.35 0.17 0.00
271_S 12_A 1.33 0.16 0.00
236_L 72_E 1.31 0.16 0.00
375_T 12_A 1.28 0.15 0.00
292_L 60_A 1.26 0.14 0.00
228_G 50_L 1.23 0.14 0.00
441_G 80_L 1.22 0.13 0.00
212_S 89_Y 1.22 0.13 0.00
233_A 74_G 1.17 0.12 0.00
388_A 54_L 1.16 0.12 0.00
254_T 62_R 1.15 0.12 0.00
307_E 8_A 1.12 0.11 0.00
378_Y 32_D 1.11 0.11 0.00
443_L 101_L 1.11 0.11 0.00
104_S 68_I 1.09 0.10 0.00
164_P 89_Y 1.07 0.10 0.00
364_A 50_L 1.07 0.10 0.00
383_E 32_D 1.07 0.10 0.00
148_G 89_Y 1.06 0.10 0.00
252_T 54_L 1.06 0.10 0.00
225_D 62_R 1.05 0.10 0.00
266_E 59_R 1.05 0.10 0.00
283_V 54_L 1.05 0.10 0.00
95_Q 89_Y 1.03 0.10 0.00
359_Y 19_Q 1.03 0.10 0.00
357_I 21_E 1.03 0.10 0.00
373_A 50_L 1.01 0.09 0.00
194_E 85_G 1.00 0.09 0.00
258_V 74_G 1.00 0.09 0.00
114_A 68_I 0.99 0.09 0.00
227_K 32_D 0.99 0.09 0.00
115_G 103_R 0.99 0.09 0.00
254_T 80_L 0.99 0.09 0.00
327_T 86_E 0.99 0.09 0.00
459_L 62_R 0.98 0.09 0.00
469_V 80_L 0.97 0.09 0.00
283_V 25_I 0.97 0.08 0.00
217_W 101_L 0.97 0.08 0.00
107_T 66_A 0.97 0.08 0.00
310_L 66_A 0.97 0.08 0.00
392_L 66_A 0.97 0.08 0.00
405_S 26_C 0.96 0.08 0.00
276_S 93_K 0.96 0.08 0.00
344_D 34_E 0.96 0.08 0.00
433_S 29_E 0.96 0.08 0.00
217_W 12_A 0.95 0.08 0.00
104_S 86_E 0.95 0.08 0.00
236_L 90_R 0.95 0.08 0.00
145_A 53_W 0.94 0.08 0.00
409_A 64_T 0.94 0.08 0.00
110_H 24_A 0.93 0.08 0.00
98_L 43_L 0.93 0.08 0.00
138_F 14_Q 0.93 0.08 0.00
346_A 28_L 0.93 0.08 0.00
444_A 4_I 0.93 0.08 0.00
226_F 96_G 0.93 0.08 0.00
340_L 99_L 0.92 0.08 0.00
217_W 89_Y 0.92 0.08 0.00
379_G 98_Q 0.92 0.08 0.00
442_S 79_M 0.91 0.08 0.00
328_V 24_A 0.91 0.08 0.00
371_A 100_V 0.91 0.08 0.00
93_Q 40_G 0.91 0.07 0.00
320_V 50_L 0.90 0.07 0.00
108_N 80_L 0.90 0.07 0.00
108_N 67_G 0.90 0.07 0.00
250_L 6_L 0.90 0.07 0.00
165_A 71_L 0.90 0.07 0.00
111_F 2_S 0.89 0.07 0.00
192_A 2_S 0.89 0.07 0.00
425_G 2_S 0.89 0.07 0.00
193_G 12_A 0.89 0.07 0.00
228_G 62_R 0.89 0.07 0.00
346_A 46_D 0.89 0.07 0.00
391_T 79_M 0.89 0.07 0.00
435_D 70_L 0.89 0.07 0.00
254_T 47_T 0.88 0.07 0.00
378_Y 95_D 0.88 0.07 0.00
364_A 54_L 0.88 0.07 0.00
446_D 19_Q 0.88 0.07 0.00
264_N 80_L 0.88 0.07 0.00
307_E 68_I 0.88 0.07 0.00
346_A 100_V 0.88 0.07 0.00
406_G 64_T 0.88 0.07 0.00
340_L 64_T 0.88 0.07 0.00
373_A 60_A 0.87 0.07 0.00
174_L 79_M 0.87 0.07 0.00
355_N 54_L 0.87 0.07 0.00
109_I 8_A 0.87 0.07 0.00
393_R 55_P 0.87 0.07 0.00
272_A 9_S 0.86 0.07 0.00
266_E 74_G 0.86 0.07 0.00
283_V 30_L 0.86 0.07 0.00
293_D 3_L 0.86 0.07 0.00
296_G 3_L 0.86 0.07 0.00
188_G 38_A 0.86 0.07 0.00
429_Q 78_L 0.86 0.07 0.00
213_V 90_R 0.85 0.07 0.00
104_S 76_L 0.85 0.07 0.00
327_T 14_Q 0.85 0.07 0.00
316_L 8_A 0.85 0.07 0.00
280_V 68_I 0.85 0.07 0.00
419_Y 81_L 0.85 0.07 0.00
408_D 80_L 0.85 0.07 0.00
236_L 78_L 0.85 0.07 0.00
218_E 55_P 0.84 0.07 0.00
210_A 78_L 0.84 0.07 0.00
88_F 42_D 0.84 0.07 0.00
428_G 103_R 0.84 0.07 0.00
378_Y 73_R 0.84 0.07 0.00
386_A 55_P 0.84 0.07 0.00
396_V 33_S 0.83 0.07 0.00
388_A 33_S 0.83 0.07 0.00
432_L 56_S 0.83 0.07 0.00
274_S 12_A 0.83 0.07 0.00
226_F 10_D 0.83 0.07 0.00
339_L 80_L 0.83 0.07 0.00
167_G 60_A 0.83 0.07 0.00
89_S 20_D 0.83 0.07 0.00
440_A 79_M 0.83 0.06 0.00
205_A 69_A 0.82 0.06 0.00
97_K 74_G 0.82 0.06 0.00
164_P 101_L 0.82 0.06 0.00
237_D 54_L 0.82 0.06 0.00
389_P 53_W 0.82 0.06 0.00
470_V 74_G 0.82 0.06 0.00
126_N 8_A 0.82 0.06 0.00
328_V 28_L 0.82 0.06 0.00
327_T 4_I 0.82 0.06 0.00
93_Q 41_Y 0.82 0.06 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
7386 0.1 1JIW_PI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4081 0.11 info 1JIW_PI E 1AKL_A Alkaline metalloproteinase 2RN4_A(1) Proteinase inhibitor Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4071 0 info 1JIW_PI E 1AKL_A Alkaline metalloproteinase 2RN4_A(1) Proteinase inhibitor Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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