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OPENSEQ.org
SpB-C
Genes: A B A+B
Length: 414 79 426
Sequences: 2088 194 205
Seq/Len: 5.04 2.46 0.48
MirrorTree (Pazo et al. 2001) 0.81
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 0.40
2 0.02 0.08 0.40
5 0.03 0.08 0.42
10 0.03 0.08 0.42
20 0.04 0.08 0.42
100 0.06 0.08 0.42
∞ 0.11 0.09 0.42
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
310_R 11_I 1.58 0.61 0.00
301_F 52_R 1.55 0.59 0.00
283_E 10_I 1.41 0.48 0.00
347_L 71_A 1.27 0.38 0.00
286_N 39_V 1.27 0.38 0.00
195_V 68_K 1.27 0.38 0.00
361_R 17_E 1.23 0.35 0.00
270_I 36_M 1.23 0.35 0.00
326_I 30_A 1.21 0.34 0.00
302_M 63_W 1.21 0.33 0.00
314_F 29_D 1.18 0.32 0.00
202_F 58_F 1.18 0.31 0.00
179_Q 9_E 1.15 0.29 0.00
212_L 73_I 1.14 0.29 0.00
270_I 26_D 1.09 0.26 0.00
328_N 19_V 1.09 0.26 0.00
239_M 10_I 1.08 0.26 0.00
320_T 19_V 1.07 0.25 0.00
283_E 7_V 1.06 0.24 0.00
132_R 25_E 1.06 0.24 0.00
304_M 47_N 1.05 0.23 0.00
262_N 43_V 1.05 0.23 0.00
279_R 43_V 1.04 0.23 0.00
70_Y 39_V 1.04 0.23 0.00
135_G 50_D 1.03 0.23 0.00
387_L 74_V 1.02 0.22 0.00
306_M 11_I 1.01 0.22 0.00
299_F 32_V 1.01 0.21 0.00
301_F 17_E 1.00 0.21 0.00
236_L 26_D 0.99 0.21 0.00
157_L 43_V 0.99 0.21 0.00
410_L 73_I 0.99 0.21 0.00
405_G 60_R 0.99 0.20 0.00
314_F 36_M 0.98 0.20 0.00
209_A 45_I 0.98 0.20 0.00
110_V 9_E 0.98 0.20 0.00
266_I 17_E 0.97 0.20 0.00
334_F 21_D 0.97 0.20 0.00
93_V 19_V 0.96 0.19 0.00
141_R 63_W 0.96 0.19 0.00
309_T 42_I 0.96 0.19 0.00
264_M 63_W 0.95 0.19 0.00
191_L 64_N 0.95 0.18 0.00
132_R 18_D 0.94 0.18 0.00
145_I 19_V 0.94 0.18 0.00
209_A 5_S 0.94 0.18 0.00
316_N 50_D 0.94 0.18 0.00
86_K 7_V 0.94 0.18 0.00
107_F 9_E 0.94 0.18 0.00
331_I 44_E 0.94 0.18 0.00
122_G 62_D 0.94 0.18 0.00
270_I 55_V 0.94 0.18 0.00
301_F 46_E 0.94 0.18 0.00
353_L 40_E 0.93 0.18 0.00
198_I 44_E 0.93 0.18 0.00
69_I 23_M 0.93 0.18 0.00
348_F 14_L 0.92 0.17 0.00
388_G 36_M 0.91 0.17 0.00
256_F 63_W 0.91 0.17 0.00
308_L 47_N 0.91 0.17 0.00
71_L 70_I 0.91 0.17 0.00
150_L 11_I 0.91 0.17 0.00
78_L 73_I 0.91 0.17 0.00
76_L 22_M 0.90 0.17 0.00
352_G 17_E 0.90 0.17 0.00
340_W 15_F 0.90 0.17 0.00
209_A 27_L 0.90 0.17 0.00
136_I 44_E 0.89 0.16 0.00
254_S 18_D 0.89 0.16 0.00
385_Q 10_I 0.89 0.16 0.00
113_A 36_M 0.89 0.16 0.00
290_M 77_Q 0.89 0.16 0.00
155_R 39_V 0.89 0.16 0.00
153_F 37_G 0.88 0.16 0.00
341_Y 56_T 0.88 0.15 0.00
232_N 73_I 0.88 0.15 0.00
283_E 24_D 0.88 0.15 0.00
291_S 25_E 0.87 0.15 0.00
137_V 45_I 0.87 0.15 0.00
188_M 73_I 0.87 0.15 0.00
233_L 26_D 0.87 0.15 0.00
321_S 62_D 0.87 0.15 0.00
202_F 63_W 0.87 0.15 0.00
327_V 61_D 0.86 0.15 0.00
327_V 47_N 0.86 0.15 0.00
341_Y 15_F 0.86 0.15 0.00
178_Y 14_L 0.86 0.15 0.00
286_N 37_G 0.86 0.15 0.00
258_L 43_V 0.85 0.15 0.00
306_M 66_A 0.85 0.15 0.00
106_I 8_I 0.85 0.15 0.00
382_R 4_K 0.85 0.14 0.00
266_I 10_I 0.85 0.14 0.00
352_G 41_L 0.85 0.14 0.00
321_S 50_D 0.85 0.14 0.00
207_I 44_E 0.85 0.14 0.00
305_V 47_N 0.84 0.14 0.00
90_G 7_V 0.84 0.14 0.00
243_G 49_F 0.84 0.14 0.00
344_A 5_S 0.84 0.14 0.00
74_E 58_F 0.84 0.14 0.00
262_N 42_I 0.84 0.14 0.00
402_I 30_A 0.84 0.14 0.00
214_E 43_V 0.84 0.14 0.00
301_F 38_T 0.84 0.14 0.00
348_F 17_E 0.84 0.14 0.00
138_I 71_A 0.84 0.14 0.00
343_I 4_K 0.84 0.14 0.00
325_Y 54_P 0.84 0.14 0.00
408_N 56_T 0.83 0.14 0.00
266_I 74_V 0.83 0.14 0.00
286_N 31_G 0.83 0.14 0.00
297_R 69_I 0.83 0.14 0.00
280_D 63_W 0.83 0.14 0.00
158_L 13_E 0.83 0.14 0.00
135_G 30_A 0.82 0.14 0.00
70_Y 76_L 0.82 0.13 0.00
150_L 52_R 0.82 0.13 0.00
243_G 66_A 0.82 0.13 0.00
122_G 31_G 0.82 0.13 0.00
215_T 51_I 0.81 0.13 0.00
94_F 63_W 0.81 0.13 0.00
354_V 9_E 0.81 0.13 0.00
184_R 57_E 0.80 0.13 0.00
103_L 61_D 0.80 0.13 0.00
302_M 38_T 0.80 0.13 0.00
100_L 44_E 0.80 0.13 0.00
146_K 31_G 0.80 0.13 0.00
400_F 4_K 0.80 0.12 0.00
294_F 38_T 0.80 0.12 0.00
84_Y 54_P 0.80 0.12 0.00
260_I 49_F 0.79 0.12 0.00
199_M 37_G 0.79 0.12 0.00
209_A 51_I 0.79 0.12 0.00
310_R 58_F 0.79 0.12 0.00
122_G 55_V 0.79 0.12 0.00
351_L 22_M 0.78 0.12 0.00
363_K 56_T 0.78 0.12 0.00
73_W 22_M 0.78 0.12 0.00
359_W 16_M 0.78 0.12 0.00
406_F 56_T 0.78 0.12 0.00
57_V 59_G 0.78 0.12 0.00
402_I 61_D 0.78 0.12 0.00
154_L 22_M 0.78 0.12 0.00
302_M 58_F 0.78 0.12 0.00
338_V 46_E 0.78 0.12 0.00
194_S 32_V 0.77 0.12 0.00
79_L 14_L 0.77 0.12 0.00
277_L 46_E 0.77 0.12 0.00
384_I 16_M 0.77 0.12 0.00
63_Q 31_G 0.77 0.12 0.00
394_H 64_N 0.77 0.12 0.00
59_G 74_V 0.77 0.12 0.00
357_D 39_V 0.77 0.12 0.00
73_W 14_L 0.77 0.12 0.00
306_M 55_V 0.77 0.12 0.00
357_D 54_P 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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