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OPENSEQ.org
RbcL-RbcS
Genes: A B A+B
Length: 473 110 579
Sequences: 477 346 105
Seq/Len: 1.01 3.15 0.18
MirrorTree (Pazo et al. 2001) 0.84
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 0.00 0.03 0.16
2 0.00 0.03 0.18
5 0.00 0.04 0.18
10 0.00 0.04 0.18
20 0.01 0.04 0.18
100 0.01 0.04 0.18
∞ 0.09 0.07 0.18
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
422_E 26_R 1.80 0.46 0.00
146_H 18_Y 1.56 0.33 0.00
175_A 18_Y 1.50 0.30 0.00
258_I 69_V 1.46 0.28 0.00
193_T 59_W 1.46 0.28 0.00
18_W 63_F 1.32 0.22 0.00
206_R 18_Y 1.31 0.21 0.00
167_I 59_W 1.30 0.21 0.00
111_T 18_Y 1.30 0.21 0.00
206_R 98_Q 1.27 0.20 0.00
77_A 63_F 1.26 0.19 0.00
365_P 98_Q 1.26 0.19 0.00
213_F 15_T 1.26 0.19 0.00
350_D 38_G 1.22 0.18 0.00
313_L 77_E 1.21 0.18 0.00
216_D 59_W 1.20 0.17 0.00
387_F 32_K 1.20 0.17 0.00
313_L 93_Y 1.19 0.17 0.00
462_F 92_A 1.17 0.17 0.00
193_T 61_L 1.16 0.16 0.00
364_M 66_E 1.14 0.16 0.00
18_W 43_I 1.14 0.16 0.00
36_T 22_M 1.14 0.15 0.00
302_I 21_P 1.11 0.15 0.00
449_K 92_A 1.11 0.15 0.00
364_M 22_M 1.11 0.14 0.00
338_W 69_V 1.10 0.14 0.00
216_D 82_A 1.10 0.14 0.00
447_E 90_L 1.09 0.14 0.00
92_A 31_I 1.08 0.14 0.00
313_L 89_K 1.07 0.14 0.00
430_I 69_V 1.06 0.13 0.00
365_P 18_Y 1.06 0.13 0.00
279_D 88_V 1.05 0.13 0.00
392_V 26_R 1.05 0.13 0.00
150_V 100_L 1.04 0.13 0.00
432_K 73_L 1.04 0.13 0.00
90_F 90_L 1.04 0.13 0.00
156_N 26_R 1.03 0.12 0.00
407_A 61_L 1.03 0.12 0.00
125_G 76_I 1.03 0.12 0.00
69_D 29_A 1.02 0.12 0.00
149_Q 99_S 1.02 0.12 0.00
111_T 26_R 1.02 0.12 0.00
281_G 98_Q 1.01 0.12 0.00
175_A 40_S 1.01 0.12 0.00
94_I 63_F 1.00 0.12 0.00
407_A 98_Q 1.00 0.12 0.00
392_V 73_L 1.00 0.12 0.00
411_A 80_R 0.99 0.11 0.00
419_A 36_A 0.99 0.11 0.00
338_W 35_I 0.99 0.11 0.00
366_G 18_Y 0.98 0.11 0.00
150_V 93_Y 0.98 0.11 0.00
206_R 93_Y 0.98 0.11 0.00
138_V 89_K 0.97 0.11 0.00
264_T 98_Q 0.97 0.11 0.00
220_T 88_V 0.97 0.11 0.00
176_K 96_Y 0.97 0.11 0.00
216_D 88_V 0.97 0.11 0.00
356_F 18_Y 0.97 0.11 0.00
135_L 22_M 0.97 0.11 0.00
214_V 89_K 0.96 0.11 0.00
258_I 25_E 0.96 0.11 0.00
8_A 72_V 0.96 0.11 0.00
462_F 71_N 0.96 0.11 0.00
258_I 71_N 0.96 0.11 0.00
445_S 98_Q 0.95 0.10 0.00
282_V 18_Y 0.94 0.10 0.00
224_Q 59_W 0.94 0.10 0.00
98_I 90_L 0.94 0.10 0.00
347_I 54_Q 0.93 0.10 0.00
213_F 74_A 0.93 0.10 0.00
150_V 101_G 0.93 0.10 0.00
281_G 18_Y 0.93 0.10 0.00
366_G 98_Q 0.93 0.10 0.00
145_P 22_M 0.93 0.10 0.00
338_W 104_F 0.93 0.10 0.00
93_F 92_A 0.92 0.10 0.00
30_L 40_S 0.92 0.10 0.00
358_D 73_L 0.92 0.10 0.00
31_A 41_P 0.92 0.10 0.00
154_K 18_Y 0.92 0.10 0.00
103_E 26_R 0.92 0.10 0.00
41_V 93_Y 0.92 0.10 0.00
98_I 88_V 0.91 0.10 0.00
308_T 38_G 0.91 0.10 0.00
124_R 21_P 0.91 0.10 0.00
366_G 40_S 0.91 0.10 0.00
153_D 52_M 0.91 0.10 0.00
74_K 18_Y 0.91 0.10 0.00
187_R 15_T 0.90 0.10 0.00
236_T 20_P 0.90 0.10 0.00
31_A 31_I 0.90 0.10 0.00
203_P 89_K 0.90 0.10 0.00
349_E 93_Y 0.90 0.10 0.00
81_E 34_A 0.90 0.09 0.00
93_F 34_A 0.90 0.09 0.00
438_L 108_R 0.90 0.09 0.00
135_L 93_Y 0.90 0.09 0.00
34_K 24_A 0.90 0.09 0.00
264_T 18_Y 0.89 0.09 0.00
167_I 61_L 0.89 0.09 0.00
458_I 69_V 0.89 0.09 0.00
122_A 92_A 0.89 0.09 0.00
158_Y 18_Y 0.88 0.09 0.00
335_T 74_A 0.88 0.09 0.00
319_L 73_L 0.88 0.09 0.00
125_G 22_M 0.88 0.09 0.00
60_T 17_S 0.88 0.09 0.00
437_I 12_K 0.87 0.09 0.00
235_V 55_Y 0.87 0.09 0.00
150_V 18_Y 0.87 0.09 0.00
224_Q 57_Y 0.87 0.09 0.00
443_Q 72_V 0.87 0.09 0.00
331_D 16_F 0.86 0.09 0.00
324_V 45_H 0.86 0.09 0.00
408_A 39_W 0.86 0.09 0.00
302_I 100_L 0.86 0.09 0.00
224_Q 72_V 0.86 0.09 0.00
71_D 26_R 0.86 0.09 0.00
438_L 39_W 0.85 0.09 0.00
220_T 99_S 0.85 0.09 0.00
158_Y 26_R 0.85 0.09 0.00
273_L 55_Y 0.85 0.09 0.00
37_P 17_S 0.85 0.09 0.00
348_P 83_Y 0.85 0.09 0.00
393_L 38_G 0.85 0.09 0.00
176_K 82_A 0.85 0.09 0.00
175_A 98_Q 0.85 0.08 0.00
80_I 70_D 0.85 0.08 0.00
431_E 45_H 0.84 0.08 0.00
222_E 59_W 0.84 0.08 0.00
277_C 34_A 0.84 0.08 0.00
74_K 93_Y 0.84 0.08 0.00
158_Y 98_Q 0.84 0.08 0.00
136_A 93_Y 0.83 0.08 0.00
135_L 90_L 0.83 0.08 0.00
279_D 76_I 0.83 0.08 0.00
34_K 87_Q 0.83 0.08 0.00
57_G 14_E 0.83 0.08 0.00
65_D 17_S 0.83 0.08 0.00
199_I 51_S 0.83 0.08 0.00
220_T 43_I 0.83 0.08 0.00
325_V 20_P 0.83 0.08 0.00
44_E 38_G 0.82 0.08 0.00
69_D 77_E 0.82 0.08 0.00
358_D 90_L 0.82 0.08 0.00
44_E 21_P 0.82 0.08 0.00
365_P 93_Y 0.82 0.08 0.00
70_M 100_L 0.82 0.08 0.00
10_V 72_V 0.82 0.08 0.00
220_T 59_W 0.82 0.08 0.00
98_I 109_G 0.82 0.08 0.00
16_T 98_Q 0.82 0.08 0.00
156_N 54_Q 0.82 0.08 0.00
36_T 76_I 0.82 0.08 0.00
263_I 98_Q 0.82 0.08 0.00
141_C 87_Q 0.82 0.08 0.00
85_G 26_R 0.81 0.08 0.00
146_H 98_Q 0.81 0.08 0.00
453_E 18_Y 0.81 0.08 0.00
18_W 18_Y 0.81 0.08 0.00
368_F 24_A 0.81 0.08 0.00
21_E 55_Y 0.81 0.08 0.00
222_E 35_I 0.81 0.08 0.00
358_D 88_V 0.81 0.08 0.00
74_K 100_L 0.81 0.08 0.00
193_T 82_A 0.80 0.08 0.00
156_N 57_Y 0.80 0.08 0.00
213_F 5_Q 0.80 0.08 0.00
445_S 18_Y 0.80 0.08 0.00
9_G 72_V 0.80 0.08 0.00
238_P 67_Q 0.80 0.08 0.00
274_A 97_A 0.80 0.08 0.00
39_P 100_L 0.80 0.08 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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