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OPENSEQ.org
dltb-dltc_bs
Genes: A B A+B
Length: 395 78 424
Sequences: 2068 190 205
Seq/Len: 5.24 2.44 0.48
MirrorTree (Pazo et al. 2001) 0.80
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 0.08 0.42
2 0.02 0.08 0.41
5 0.03 0.08 0.43
10 0.03 0.08 0.43
20 0.04 0.08 0.43
100 0.06 0.08 0.43
∞ 0.11 0.09 0.44
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
302_K 11_L 1.57 0.60 0.00
293_F 53_L 1.49 0.55 0.00
275_D 10_V 1.37 0.45 0.00
347_C 20_V 1.36 0.45 0.00
262_E 37_F 1.27 0.38 0.00
278_N 40_V 1.27 0.38 0.00
353_K 17_D 1.24 0.36 0.00
175_Q 9_D 1.19 0.32 0.00
294_M 64_W 1.18 0.32 0.00
198_F 59_F 1.18 0.32 0.00
339_L 72_N 1.17 0.31 0.00
318_F 31_E 1.16 0.30 0.00
306_I 30_E 1.11 0.27 0.00
191_I 69_N 1.10 0.26 0.00
194_I 45_A 1.09 0.26 0.00
208_I 74_L 1.07 0.25 0.00
127_K 26_I 1.06 0.24 0.00
275_D 7_V 1.06 0.24 0.00
298_F 11_L 1.05 0.24 0.00
231_M 10_V 1.05 0.24 0.00
117_S 63_V 1.03 0.23 0.00
262_E 27_E 1.02 0.22 0.00
315_I 51_D 1.02 0.22 0.00
59_F 40_V 1.01 0.22 0.00
153_I 44_L 1.01 0.22 0.00
130_Q 51_D 1.01 0.21 0.00
293_F 17_D 1.00 0.21 0.00
174_E 14_V 0.99 0.21 0.00
371_A 37_F 0.99 0.20 0.00
301_T 43_L 0.99 0.20 0.00
306_I 37_F 0.98 0.20 0.00
146_L 11_L 0.98 0.20 0.00
99_I 9_D 0.97 0.19 0.00
258_I 17_D 0.97 0.19 0.00
388_G 61_R 0.96 0.19 0.00
205_G 46_I 0.95 0.18 0.00
67_I 74_L 0.95 0.18 0.00
177_A 43_L 0.94 0.18 0.00
136_R 64_W 0.94 0.18 0.00
293_F 47_E 0.94 0.18 0.00
96_L 9_D 0.94 0.18 0.00
205_G 5_Q 0.94 0.18 0.00
58_L 24_P 0.94 0.18 0.00
271_K 44_L 0.93 0.18 0.00
291_Y 33_L 0.93 0.18 0.00
293_F 39_T 0.93 0.18 0.00
131_L 45_A 0.93 0.18 0.00
256_M 64_W 0.93 0.18 0.00
323_L 45_A 0.93 0.18 0.00
340_Y 14_V 0.93 0.18 0.00
49_D 75_S 0.93 0.17 0.00
262_E 56_I 0.92 0.17 0.00
254_Y 44_L 0.92 0.17 0.00
345_M 41_E 0.92 0.17 0.00
248_F 64_W 0.91 0.17 0.00
326_V 20_V 0.91 0.17 0.00
344_L 17_D 0.91 0.17 0.00
178_W 18_D 0.90 0.16 0.00
326_V 22_E 0.90 0.16 0.00
102_F 37_F 0.90 0.16 0.00
79_S 7_V 0.90 0.16 0.00
187_L 65_N 0.89 0.16 0.00
300_M 48_N 0.89 0.16 0.00
356_K 10_V 0.89 0.16 0.00
132_I 69_N 0.89 0.16 0.00
393_H 74_L 0.89 0.16 0.00
235_S 50_F 0.88 0.15 0.00
383_F 4_K 0.88 0.15 0.00
283_S 26_I 0.87 0.15 0.00
151_Y 40_V 0.87 0.15 0.00
297_V 48_N 0.87 0.15 0.00
225_L 27_E 0.87 0.15 0.00
254_Y 43_L 0.87 0.15 0.00
198_F 64_W 0.86 0.15 0.00
203_I 45_A 0.86 0.15 0.00
95_F 8_L 0.86 0.15 0.00
332_P 15_C 0.86 0.15 0.00
333_Q 15_C 0.86 0.15 0.00
320_L 19_I 0.86 0.15 0.00
308_N 51_D 0.86 0.15 0.00
275_D 25_D 0.85 0.15 0.00
346_T 9_D 0.85 0.14 0.00
381_F 5_Q 0.85 0.14 0.00
385_I 62_D 0.85 0.14 0.00
298_F 67_P 0.84 0.14 0.00
132_I 46_I 0.84 0.14 0.00
335_I 4_K 0.84 0.14 0.00
250_V 44_L 0.84 0.14 0.00
63_Q 59_F 0.84 0.14 0.00
363_S 11_L 0.84 0.14 0.00
149_L 38_G 0.84 0.14 0.00
333_Q 57_T 0.84 0.14 0.00
340_Y 17_D 0.84 0.14 0.00
228_L 27_E 0.84 0.14 0.00
317_Y 55_P 0.83 0.14 0.00
319_L 5_Q 0.83 0.14 0.00
365_R 4_K 0.83 0.14 0.00
296_F 48_N 0.83 0.14 0.00
65_L 23_N 0.83 0.14 0.00
184_A 74_L 0.82 0.14 0.00
60_T 71_V 0.82 0.14 0.00
303_K 48_N 0.82 0.13 0.00
89_A 45_A 0.82 0.13 0.00
278_N 38_G 0.82 0.13 0.00
391_F 57_T 0.82 0.13 0.00
189_T 42_L 0.82 0.13 0.00
130_Q 31_E 0.82 0.13 0.00
370_L 75_S 0.82 0.13 0.00
313_S 51_D 0.82 0.13 0.00
278_N 32_G 0.81 0.13 0.00
180_K 48_N 0.81 0.13 0.00
193_K 37_F 0.81 0.13 0.00
313_S 63_V 0.81 0.13 0.00
252_V 50_F 0.81 0.13 0.00
100_W 28_I 0.81 0.13 0.00
233_G 44_L 0.81 0.13 0.00
272_N 64_W 0.81 0.13 0.00
371_A 9_D 0.81 0.13 0.00
195_F 38_G 0.81 0.13 0.00
351_F 46_I 0.81 0.13 0.00
66_L 4_K 0.81 0.13 0.00
235_S 67_P 0.81 0.13 0.00
154_L 13_E 0.81 0.13 0.00
369_I 13_E 0.81 0.13 0.00
269_I 5_Q 0.81 0.13 0.00
83_F 64_W 0.81 0.13 0.00
313_S 18_D 0.81 0.13 0.00
289_R 70_I 0.80 0.13 0.00
88_I 63_V 0.80 0.13 0.00
141_K 32_G 0.80 0.13 0.00
330_L 47_E 0.80 0.13 0.00
160_S 7_V 0.80 0.12 0.00
368_T 10_V 0.80 0.12 0.00
117_S 32_G 0.80 0.12 0.00
302_K 59_F 0.80 0.12 0.00
230_Y 67_P 0.80 0.12 0.00
294_M 39_T 0.79 0.12 0.00
297_V 34_L 0.79 0.12 0.00
207_A 71_V 0.79 0.12 0.00
146_L 53_L 0.79 0.12 0.00
282_M 78_K 0.79 0.12 0.00
355_N 57_T 0.78 0.12 0.00
205_G 52_I 0.78 0.12 0.00
313_S 53_L 0.78 0.12 0.00
367_T 16_Q 0.78 0.12 0.00
150_L 23_N 0.78 0.12 0.00
207_A 30_E 0.78 0.12 0.00
385_I 31_E 0.78 0.12 0.00
182_E 38_G 0.78 0.12 0.00
140_L 43_L 0.78 0.12 0.00
210_T 44_L 0.78 0.12 0.00
92_L 62_D 0.78 0.12 0.00
254_Y 10_V 0.78 0.12 0.00
356_K 31_E 0.77 0.12 0.00
75_Q 24_P 0.77 0.12 0.00
154_L 15_C 0.77 0.12 0.00
391_F 33_L 0.77 0.12 0.00
204_I 8_L 0.77 0.12 0.00
203_I 52_I 0.77 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)
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