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OPENSEQ.org
FliI_FliJ_first_attempt
Genes: A B A+B
Length: 456 147 568
Sequences: 5188 474 333
Seq/Len: 11.38 3.22 0.59
MirrorTree (Pazo et al. 2001) 0.83
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 0.14 0.00 0.55
2 0.43 0.00 0.55
5 0.44 0.00 0.55
10 0.45 0.00 0.55
20 0.46 0.00 0.55
100 0.47 0.00 0.55
∞ 0.51 0.01 0.56
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
407_V 140_R 1.78 0.80 0.04
342_S 13_L 1.64 0.71 0.03
418_L 10_L 1.59 0.68 0.02
163_V 75_T 1.49 0.61 0.02
48_L 98_L 1.47 0.59 0.02
48_L 90_W 1.41 0.54 0.01
35_T 18_V 1.37 0.51 0.01
159_L 83_H 1.36 0.50 0.01
54_I 38_Q 1.30 0.45 0.01
218_D 57_M 1.28 0.44 0.01
351_I 74_Q 1.27 0.43 0.01
248_Q 68_N 1.23 0.40 0.01
157_H 121_A 1.23 0.40 0.01
161_T 49_Y 1.22 0.39 0.01
220_I 111_W 1.20 0.37 0.01
34_A 75_T 1.19 0.37 0.01
67_S 21_A 1.19 0.37 0.01
379_L 97_A 1.18 0.36 0.01
42_T 75_T 1.18 0.36 0.01
447_Q 142_A 1.17 0.35 0.01
204_I 10_L 1.17 0.35 0.01
229_R 138_A 1.16 0.35 0.01
362_H 77_E 1.16 0.34 0.01
149_P 101_W 1.15 0.34 0.01
274_L 45_Y 1.14 0.33 0.01
196_A 5_G 1.14 0.33 0.01
368_I 39_L 1.13 0.33 0.01
196_A 111_W 1.13 0.33 0.01
369_E 72_F 1.12 0.32 0.01
54_I 87_L 1.11 0.31 0.01
242_S 114_L 1.11 0.31 0.01
295_K 110_A 1.09 0.30 0.01
277_Y 138_A 1.08 0.29 0.01
48_L 22_A 1.07 0.28 0.01
123_G 128_R 1.07 0.28 0.01
223_I 27_E 1.06 0.28 0.01
238_P 72_F 1.05 0.27 0.01
330_T 45_Y 1.04 0.27 0.01
379_L 82_Q 1.04 0.27 0.01
412_K 91_T 1.04 0.27 0.01
235_I 21_A 1.04 0.26 0.01
372_I 101_W 1.03 0.26 0.00
438_E 92_Q 1.03 0.26 0.00
270_I 111_W 1.03 0.26 0.00
357_L 77_E 1.03 0.26 0.00
178_M 54_N 1.02 0.25 0.00
449_L 10_L 1.02 0.25 0.00
221_E 132_K 1.02 0.25 0.00
90_P 101_W 1.02 0.25 0.00
235_I 46_Q 1.01 0.25 0.00
260_F 48_E 1.01 0.25 0.00
230_A 36_E 1.01 0.25 0.00
169_L 99_K 1.00 0.24 0.00
237_A 10_L 1.00 0.24 0.00
254_T 25_L 1.00 0.24 0.00
110_L 48_E 1.00 0.24 0.00
239_A 72_F 0.99 0.24 0.00
387_R 27_E 0.99 0.24 0.00
39_L 38_Q 0.99 0.23 0.00
368_I 60_G 0.99 0.23 0.00
407_V 26_G 0.99 0.23 0.00
453_F 140_R 0.99 0.23 0.00
399_Q 73_I 0.98 0.23 0.00
94_V 72_F 0.98 0.23 0.00
75_Q 126_E 0.98 0.23 0.00
266_H 107_R 0.98 0.23 0.00
407_V 108_L 0.97 0.22 0.00
301_V 49_Y 0.97 0.22 0.00
205_V 117_R 0.96 0.22 0.00
405_V 134_M 0.96 0.22 0.00
111_P 114_L 0.96 0.22 0.00
163_V 29_R 0.96 0.22 0.00
343_A 117_R 0.96 0.22 0.00
178_M 46_Q 0.96 0.21 0.00
38_V 18_V 0.95 0.21 0.00
270_I 5_G 0.95 0.21 0.00
230_A 98_L 0.94 0.21 0.00
270_I 113_T 0.94 0.21 0.00
39_L 144_R 0.94 0.21 0.00
220_I 114_L 0.94 0.21 0.00
226_P 85_L 0.94 0.21 0.00
337_D 42_L 0.94 0.21 0.00
372_I 136_E 0.94 0.21 0.00
28_Y 7_L 0.94 0.21 0.00
196_A 18_V 0.94 0.21 0.00
370_A 34_Q 0.94 0.21 0.00
39_L 5_G 0.94 0.20 0.00
392_K 77_E 0.94 0.20 0.00
204_I 6_A 0.93 0.20 0.00
218_D 109_Q 0.92 0.20 0.00
232_S 30_R 0.92 0.20 0.00
337_D 45_Y 0.92 0.20 0.00
133_A 120_A 0.91 0.19 0.00
73_N 48_E 0.91 0.19 0.00
232_S 136_E 0.90 0.19 0.00
351_I 20_D 0.90 0.19 0.00
238_P 42_L 0.89 0.18 0.00
400_R 113_T 0.89 0.18 0.00
203_V 87_L 0.89 0.18 0.00
54_I 99_K 0.89 0.18 0.00
196_A 75_T 0.89 0.18 0.00
166_I 72_F 0.89 0.18 0.00
174_R 117_R 0.89 0.18 0.00
46_L 41_M 0.89 0.18 0.00
164_R 117_R 0.88 0.18 0.00
293_A 110_A 0.88 0.18 0.00
217_K 83_H 0.88 0.18 0.00
110_L 28_M 0.88 0.17 0.00
239_A 49_Y 0.88 0.17 0.00
126_K 140_R 0.88 0.17 0.00
48_L 142_A 0.88 0.17 0.00
206_V 72_F 0.87 0.17 0.00
114_P 73_I 0.87 0.17 0.00
402_R 69_Y 0.87 0.17 0.00
411_A 35_A 0.87 0.17 0.00
336_Q 132_K 0.87 0.17 0.00
254_T 21_A 0.87 0.17 0.00
243_P 113_T 0.87 0.17 0.00
196_A 113_T 0.87 0.17 0.00
52_C 72_F 0.87 0.17 0.00
270_I 41_M 0.87 0.17 0.00
368_I 132_K 0.87 0.17 0.00
402_R 63_S 0.86 0.17 0.00
309_V 42_L 0.86 0.17 0.00
439_R 140_R 0.86 0.17 0.00
400_R 111_W 0.86 0.17 0.00
148_N 72_F 0.86 0.17 0.00
126_K 26_G 0.86 0.17 0.00
133_A 80_I 0.86 0.17 0.00
245_L 75_T 0.86 0.17 0.00
42_T 20_D 0.86 0.17 0.00
303_A 35_A 0.86 0.17 0.00
270_I 68_N 0.86 0.17 0.00
176_Q 135_D 0.85 0.16 0.00
297_Y 135_D 0.85 0.16 0.00
174_R 26_G 0.85 0.16 0.00
342_S 100_S 0.85 0.16 0.00
112_L 83_H 0.85 0.16 0.00
359_E 35_A 0.85 0.16 0.00
145_P 87_L 0.85 0.16 0.00
389_R 75_T 0.85 0.16 0.00
375_A 96_L 0.85 0.16 0.00
93_R 107_R 0.84 0.16 0.00
242_S 73_I 0.84 0.16 0.00
379_L 144_R 0.84 0.16 0.00
428_L 128_R 0.84 0.16 0.00
394_L 69_Y 0.84 0.16 0.00
32_T 77_E 0.84 0.16 0.00
400_R 10_L 0.84 0.16 0.00
424_L 19_D 0.84 0.16 0.00
337_D 72_F 0.84 0.16 0.00
196_A 6_A 0.84 0.16 0.00
270_I 57_M 0.84 0.16 0.00
168_A 138_A 0.84 0.16 0.00
384_H 18_V 0.84 0.16 0.00
295_K 30_R 0.84 0.16 0.00
239_A 42_L 0.84 0.16 0.00
279_M 5_G 0.84 0.16 0.00
315_G 20_D 0.83 0.16 0.00
375_A 11_K 0.83 0.16 0.00
288_I 117_R 0.83 0.15 0.00
266_H 106_Q 0.83 0.15 0.00
262_D 73_I 0.83 0.15 0.00
50_A 46_Q 0.83 0.15 0.00
330_T 116_D 0.83 0.15 0.00
293_A 17_E 0.83 0.15 0.00
277_Y 110_A 0.82 0.15 0.00
158_V 63_S 0.82 0.15 0.00
389_R 79_A 0.82 0.15 0.00
375_A 69_Y 0.82 0.15 0.00
256_I 65_R 0.82 0.15 0.00
154_P 42_L 0.82 0.15 0.00
218_D 10_L 0.82 0.15 0.00
191_L 79_A 0.82 0.15 0.00
312_A 39_L 0.82 0.15 0.00
32_T 16_K 0.82 0.15 0.00
331_E 72_F 0.81 0.15 0.00
133_A 11_K 0.81 0.15 0.00
281_Q 72_F 0.81 0.15 0.00
381_T 107_R 0.81 0.15 0.00
149_P 49_Y 0.81 0.15 0.00
232_S 130_D 0.81 0.15 0.00
440_A 109_Q 0.81 0.15 0.00
392_K 73_I 0.81 0.15 0.00
325_F 49_Y 0.81 0.14 0.00
30_R 120_A 0.81 0.14 0.00
414_S 48_E 0.81 0.14 0.00
78_F 67_I 0.80 0.14 0.00
238_P 49_Y 0.80 0.14 0.00
55_E 145_K 0.80 0.14 0.00
312_A 105_K 0.80 0.14 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.46 > 0.4) of paralogs.
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