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OPENSEQ.org
SSPB-ClpXP
Genes: A B A+B
Length: 424 165 563
Sequences: 2192 536 164
Seq/Len: 5.17 3.25 0.29
MirrorTree (Pazo et al. 2001) 0.33
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 0.07 0.00 0.00
2 0.08 0.00 0.00
5 0.08 0.00 0.00
10 0.08 0.00 0.00
20 0.08 0.00 0.00
100 0.08 0.00 0.02
∞ 0.09 0.00 0.28
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
194_D 162_R 1.80 0.61 0.00
110_L 92_A 1.78 0.59 0.00
160_N 94_Y 1.48 0.39 0.00
76_D 14_L 1.34 0.31 0.00
111_G 50_Q 1.32 0.30 0.00
142_M 100_A 1.32 0.30 0.00
398_I 45_Y 1.32 0.30 0.00
376_V 68_D 1.31 0.29 0.00
334_T 102_T 1.31 0.29 0.00
100_R 50_Q 1.26 0.27 0.00
285_E 48_D 1.26 0.27 0.00
108_V 44_E 1.25 0.26 0.00
181_V 163_V 1.24 0.25 0.00
142_M 102_T 1.21 0.24 0.00
382_D 8_P 1.21 0.24 0.00
376_V 100_A 1.21 0.24 0.00
242_K 102_T 1.21 0.24 0.00
395_K 30_L 1.20 0.23 0.00
79_I 51_I 1.18 0.23 0.00
232_Q 21_L 1.18 0.22 0.00
337_Y 80_P 1.17 0.22 0.00
41_V 60_V 1.16 0.22 0.00
296_I 50_Q 1.16 0.22 0.00
130_E 21_L 1.15 0.21 0.00
142_M 158_R 1.15 0.21 0.00
305_I 62_N 1.14 0.21 0.00
304_F 57_P 1.14 0.21 0.00
118_I 92_A 1.11 0.20 0.00
305_I 61_G 1.10 0.19 0.00
410_L 96_R 1.10 0.19 0.00
324_Q 106_P 1.10 0.19 0.00
337_Y 65_L 1.10 0.19 0.00
284_G 17_F 1.09 0.19 0.00
296_I 34_V 1.09 0.19 0.00
236_L 9_R 1.08 0.18 0.00
142_M 61_G 1.08 0.18 0.00
232_Q 26_L 1.07 0.18 0.00
141_T 10_R 1.07 0.18 0.00
350_F 18_Y 1.07 0.18 0.00
298_F 22_L 1.06 0.18 0.00
296_I 25_Q 1.06 0.17 0.00
70_I 8_P 1.06 0.17 0.00
178_R 50_Q 1.05 0.17 0.00
252_A 21_L 1.05 0.17 0.00
358_I 10_R 1.05 0.17 0.00
141_T 21_L 1.03 0.17 0.00
339_A 100_A 1.03 0.17 0.00
50_E 60_V 1.03 0.17 0.00
305_I 102_T 1.03 0.17 0.00
232_Q 9_R 1.03 0.16 0.00
392_D 70_V 1.03 0.16 0.00
247_C 14_L 1.03 0.16 0.00
35_Y 110_Y 1.02 0.16 0.00
100_R 105_E 1.01 0.16 0.00
305_I 17_F 1.01 0.16 0.00
118_I 162_R 1.01 0.16 0.00
415_K 10_R 1.01 0.16 0.00
130_E 163_V 1.01 0.16 0.00
89_A 40_Q 1.01 0.16 0.00
333_L 30_L 1.01 0.16 0.00
296_I 87_L 1.00 0.15 0.00
379_A 6_L 1.00 0.15 0.00
297_K 147_D 1.00 0.15 0.00
361_K 94_Y 1.00 0.15 0.00
410_L 158_R 1.00 0.15 0.00
337_Y 45_Y 0.99 0.15 0.00
26_R 50_Q 0.99 0.15 0.00
110_L 17_F 0.98 0.15 0.00
26_R 158_R 0.98 0.15 0.00
339_A 102_T 0.98 0.15 0.00
352_D 80_P 0.98 0.15 0.00
50_E 10_R 0.98 0.14 0.00
398_I 77_G 0.97 0.14 0.00
280_K 45_Y 0.96 0.14 0.00
275_K 52_V 0.95 0.14 0.00
141_T 26_L 0.95 0.14 0.00
242_K 9_R 0.95 0.14 0.00
304_F 22_L 0.95 0.14 0.00
242_K 100_A 0.95 0.14 0.00
383_T 56_A 0.95 0.14 0.00
334_T 113_D 0.94 0.14 0.00
141_T 39_V 0.94 0.14 0.00
376_V 55_I 0.94 0.13 0.00
400_E 94_Y 0.94 0.13 0.00
387_L 9_R 0.94 0.13 0.00
337_Y 104_F 0.93 0.13 0.00
242_K 17_F 0.92 0.13 0.00
27_K 92_A 0.92 0.13 0.00
241_S 21_L 0.92 0.13 0.00
252_A 36_L 0.92 0.13 0.00
275_K 92_A 0.92 0.13 0.00
401_S 31_V 0.91 0.13 0.00
343_L 7_T 0.91 0.12 0.00
257_V 50_Q 0.91 0.12 0.00
353_E 48_D 0.91 0.12 0.00
130_E 6_L 0.91 0.12 0.00
141_T 89_A 0.91 0.12 0.00
363_M 73_N 0.91 0.12 0.00
281_A 96_R 0.91 0.12 0.00
234_E 36_L 0.90 0.12 0.00
374_S 51_I 0.90 0.12 0.00
323_I 143_D 0.90 0.12 0.00
35_Y 21_L 0.89 0.12 0.00
379_A 79_I 0.89 0.12 0.00
130_E 9_R 0.88 0.12 0.00
108_V 17_F 0.88 0.12 0.00
141_T 34_V 0.88 0.12 0.00
130_E 7_T 0.88 0.12 0.00
259_S 102_T 0.88 0.12 0.00
339_A 26_L 0.87 0.12 0.00
342_N 10_R 0.87 0.11 0.00
260_H 80_P 0.87 0.11 0.00
141_T 6_L 0.87 0.11 0.00
342_N 68_D 0.87 0.11 0.00
22_Q 49_G 0.86 0.11 0.00
130_E 34_V 0.86 0.11 0.00
364_A 85_V 0.86 0.11 0.00
387_L 74_A 0.86 0.11 0.00
41_V 21_L 0.86 0.11 0.00
73_H 29_H 0.85 0.11 0.00
376_V 29_H 0.85 0.11 0.00
247_C 109_A 0.85 0.11 0.00
398_I 37_P 0.85 0.11 0.00
404_D 44_E 0.85 0.11 0.00
130_E 10_R 0.85 0.11 0.00
363_M 64_E 0.85 0.11 0.00
53_K 100_A 0.84 0.11 0.00
297_K 62_N 0.84 0.11 0.00
49_R 67_N 0.84 0.11 0.00
241_S 26_L 0.84 0.11 0.00
387_L 77_G 0.84 0.10 0.00
364_A 31_V 0.84 0.10 0.00
298_F 108_A 0.84 0.10 0.00
274_V 33_D 0.84 0.10 0.00
72_N 66_A 0.84 0.10 0.00
262_V 58_R 0.84 0.10 0.00
160_N 92_A 0.83 0.10 0.00
340_L 94_Y 0.83 0.10 0.00
219_V 17_F 0.83 0.10 0.00
288_A 68_D 0.83 0.10 0.00
271_G 48_D 0.83 0.10 0.00
137_D 8_P 0.83 0.10 0.00
27_K 94_Y 0.83 0.10 0.00
374_S 68_D 0.82 0.10 0.00
62_S 80_P 0.82 0.10 0.00
411_L 29_H 0.82 0.10 0.00
100_R 100_A 0.82 0.10 0.00
36_I 33_D 0.82 0.10 0.00
252_A 33_D 0.82 0.10 0.00
141_T 36_L 0.81 0.10 0.00
173_V 50_Q 0.81 0.10 0.00
236_L 39_V 0.81 0.10 0.00
52_I 65_L 0.81 0.10 0.00
142_M 9_R 0.81 0.10 0.00
89_A 29_H 0.80 0.10 0.00
36_I 96_R 0.80 0.10 0.00
379_A 30_L 0.80 0.10 0.00
255_D 154_P 0.80 0.10 0.00
241_S 38_G 0.80 0.10 0.00
255_D 44_E 0.80 0.10 0.00
350_F 73_N 0.80 0.10 0.00
36_I 55_I 0.80 0.10 0.00
390_M 21_L 0.79 0.10 0.00
142_M 17_F 0.79 0.10 0.00
259_S 107_E 0.79 0.10 0.00
387_L 105_E 0.79 0.10 0.00
177_Q 47_R 0.79 0.09 0.00
327_K 48_D 0.79 0.09 0.00
247_C 47_R 0.79 0.09 0.00
232_Q 36_L 0.79 0.09 0.00
178_R 31_V 0.79 0.09 0.00
178_R 100_A 0.79 0.09 0.00
89_A 81_R 0.79 0.09 0.00
260_H 17_F 0.79 0.09 0.00
137_D 29_H 0.79 0.09 0.00
387_L 103_M 0.79 0.09 0.00
30_A 49_G 0.78 0.09 0.00
89_A 85_V 0.78 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)
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