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OPENSEQ.org
1bkd_A_B
Genes: A B A+B
Length: 463 166 588
Sequences: 1290 11837 197
Seq/Len: 2.79 71.31 0.34
MirrorTree (Pazo et al. 2001) 0.47
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 0.04 0.05 0.02
2 0.04 0.06 0.06
5 0.04 0.08 0.12
10 0.04 0.10 0.19
20 0.04 0.13 0.31
100 0.06 0.23 0.71
∞ 0.10 0.28 0.99
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
146_I 11_A 1.46 0.42 0.00
63_C 84_I 1.46 0.42 0.00
243_I 89_S 1.37 0.36 0.00
298_S 8_V 1.36 0.36 0.00
257_I 84_I 1.33 0.34 0.00
274_I 31_E 1.31 0.32 0.00
76_F 138_G 1.30 0.32 0.00
202_I 113_L 1.24 0.28 0.00
277_L 114_V 1.21 0.27 0.00
266_R 16_K 1.11 0.22 0.00
252_W 120_L 1.10 0.21 0.00
277_L 156_F 1.08 0.20 0.00
217_V 115_G 1.04 0.18 0.00
389_I 82_F 1.03 0.18 0.00
312_P 82_F 1.02 0.18 0.00
347_F 128_R 1.01 0.17 0.00
420_E 89_S 1.00 0.17 0.00
257_I 153_E 0.99 0.16 0.00
382_V 5_K 0.98 0.16 0.00
253_F 84_I 0.98 0.16 0.00
139_L 125_V 0.97 0.16 0.00
419_M 83_A 0.97 0.16 0.00
300_P 125_V 0.97 0.16 0.00
63_C 28_F 0.95 0.15 0.00
121_C 78_F 0.94 0.15 0.00
58_T 129_Q 0.94 0.15 0.00
76_F 55_I 0.93 0.14 0.00
42_T 114_V 0.93 0.14 0.00
392_Y 49_E 0.93 0.14 0.00
393_Q 17_S 0.93 0.14 0.00
126_E 17_S 0.93 0.14 0.00
386_T 100_I 0.92 0.14 0.00
343_P 146_A 0.92 0.14 0.00
64_K 125_V 0.92 0.14 0.00
436_P 82_F 0.91 0.14 0.00
227_W 156_F 0.91 0.14 0.00
266_R 15_G 0.91 0.14 0.00
301_V 89_S 0.90 0.13 0.00
269_V 112_V 0.90 0.13 0.00
138_L 54_D 0.89 0.13 0.00
195_L 156_F 0.88 0.13 0.00
300_P 80_C 0.88 0.13 0.00
29_I 146_A 0.88 0.13 0.00
428_F 162_E 0.88 0.13 0.00
288_G 61_Q 0.88 0.13 0.00
409_F 90_F 0.88 0.13 0.00
157_W 141_Y 0.87 0.12 0.00
145_F 34_P 0.87 0.12 0.00
346_P 15_G 0.86 0.12 0.00
32_G 149_R 0.86 0.12 0.00
286_F 29_V 0.85 0.12 0.00
317_K 128_R 0.85 0.12 0.00
433_E 23_L 0.85 0.12 0.00
358_T 128_R 0.85 0.12 0.00
272_R 112_V 0.84 0.12 0.00
223_V 28_F 0.84 0.12 0.00
360_E 130_A 0.84 0.12 0.00
346_P 119_D 0.84 0.11 0.00
396_P 120_L 0.84 0.11 0.00
434_I 163_I 0.84 0.11 0.00
161_I 81_V 0.83 0.11 0.00
274_I 82_F 0.83 0.11 0.00
194_L 76_E 0.83 0.11 0.00
325_L 80_C 0.83 0.11 0.00
101_E 151_G 0.83 0.11 0.00
280_F 76_E 0.83 0.11 0.00
309_E 11_A 0.83 0.11 0.00
48_D 26_N 0.82 0.11 0.00
76_F 82_F 0.82 0.11 0.00
309_E 19_L 0.82 0.11 0.00
399_L 77_G 0.82 0.11 0.00
409_F 100_I 0.82 0.11 0.00
206_L 135_R 0.82 0.11 0.00
294_S 79_L 0.82 0.11 0.00
304_L 16_K 0.81 0.11 0.00
38_I 88_K 0.81 0.11 0.00
286_F 162_E 0.81 0.11 0.00
304_L 10_G 0.81 0.11 0.00
33_T 154_D 0.81 0.11 0.00
321_E 65_S 0.81 0.11 0.00
186_P 112_V 0.81 0.11 0.00
296_M 51_C 0.81 0.11 0.00
145_F 113_L 0.81 0.11 0.00
222_L 82_F 0.80 0.10 0.00
121_C 24_I 0.80 0.10 0.00
269_V 135_R 0.80 0.10 0.00
209_L 87_T 0.80 0.10 0.00
172_F 113_L 0.80 0.10 0.00
397_Y 61_Q 0.80 0.10 0.00
249_L 9_V 0.80 0.10 0.00
253_F 138_G 0.80 0.10 0.00
311_I 125_V 0.80 0.10 0.00
366_L 120_L 0.79 0.10 0.00
266_R 10_G 0.79 0.10 0.00
272_R 100_I 0.79 0.10 0.00
214_Y 67_M 0.78 0.10 0.00
319_L 144_T 0.78 0.10 0.00
276_I 80_C 0.78 0.10 0.00
282_E 81_V 0.78 0.10 0.00
29_I 20_T 0.78 0.10 0.00
409_F 27_H 0.78 0.10 0.00
210_E 100_I 0.78 0.10 0.00
393_Q 55_I 0.78 0.10 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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