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OPENSEQ.org
cI_C_F
Genes: A B A+B
Length: 509 184 671
Sequences: 1997 2037 1586
Seq/Len: 3.92 11.07 2.36
MirrorTree (Pazo et al. 2001) 0.79
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.06
2 0.00 0.00 0.13
5 0.01 0.00 2.00
10 0.01 0.00 2.10
20 0.01 0.00 2.15
100 0.01 0.01 2.21
∞ 0.03 0.02 2.29
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
99_V 154_V 1.26 0.82 0.09
347_A 159_G 1.04 0.62 0.05
386_A 40_S 1.03 0.61 0.05
256_S 15_A 1.01 0.58 0.04
117_H 134_F 0.97 0.54 0.04
229_I 56_I 0.95 0.51 0.04
477_L 143_L 0.91 0.46 0.03
93_L 9_G 0.88 0.43 0.03
318_T 156_F 0.85 0.40 0.03
486_L 130_G 0.85 0.40 0.03
91_V 56_I 0.84 0.39 0.02
185_M 12_A 0.83 0.38 0.02
175_F 24_N 0.82 0.37 0.02
245_P 70_V 0.82 0.37 0.02
377_L 139_L 0.82 0.37 0.02
335_Q 14_L 0.81 0.36 0.02
143_W 68_V 0.81 0.36 0.02
350_L 167_V 0.81 0.35 0.02
90_M 147_L 0.81 0.35 0.02
88_L 13_I 0.81 0.35 0.02
432_A 19_V 0.80 0.34 0.02
104_C 24_N 0.80 0.34 0.02
321_S 130_G 0.80 0.34 0.02
177_Y 135_G 0.79 0.34 0.02
313_R 129_V 0.79 0.34 0.02
430_V 45_S 0.78 0.33 0.02
286_F 19_V 0.77 0.32 0.02
351_S 60_A 0.77 0.32 0.02
397_G 133_L 0.77 0.32 0.02
157_W 52_G 0.77 0.31 0.02
414_S 29_L 0.77 0.31 0.02
344_Q 75_N 0.77 0.31 0.02
469_L 10_L 0.77 0.31 0.02
323_M 152_L 0.77 0.31 0.02
252_P 33_I 0.76 0.31 0.02
341_A 125_S 0.76 0.30 0.02
100_L 7_I 0.75 0.29 0.02
276_L 144_A 0.75 0.29 0.02
289_I 155_A 0.75 0.29 0.02
421_I 153_V 0.75 0.29 0.02
130_V 143_L 0.75 0.29 0.02
177_Y 129_V 0.75 0.29 0.02
153_L 153_V 0.75 0.29 0.02
91_V 3_F 0.74 0.28 0.02
92_V 163_R 0.73 0.28 0.02
299_F 36_L 0.73 0.28 0.02
375_G 48_A 0.73 0.28 0.02
185_M 58_V 0.73 0.28 0.02
178_T 60_A 0.73 0.28 0.02
179_Q 38_A 0.73 0.28 0.02
442_R 66_L 0.73 0.28 0.02
274_F 158_V 0.73 0.27 0.02
422_T 98_I 0.73 0.27 0.01
251_A 158_V 0.72 0.27 0.01
296_I 128_A 0.72 0.27 0.01
59_G 97_A 0.72 0.27 0.01
133_A 138_V 0.72 0.27 0.01
351_S 150_A 0.72 0.27 0.01
18_W 11_I 0.72 0.27 0.01
381_M 129_V 0.72 0.27 0.01
267_A 52_G 0.72 0.26 0.01
318_T 149_L 0.72 0.26 0.01
289_I 97_A 0.72 0.26 0.01
362_L 27_H 0.71 0.26 0.01
207_Y 54_L 0.71 0.26 0.01
99_V 25_P 0.71 0.26 0.01
69_M 129_V 0.71 0.26 0.01
110_E 21_T 0.71 0.26 0.01
345_M 152_L 0.71 0.25 0.01
334_S 162_E 0.70 0.25 0.01
401_T 56_I 0.70 0.25 0.01
469_L 146_M 0.70 0.25 0.01
168_I 102_I 0.70 0.25 0.01
389_L 19_V 0.70 0.25 0.01
75_F 124_I 0.70 0.25 0.01
408_F 62_A 0.70 0.25 0.01
218_G 13_I 0.70 0.25 0.01
179_Q 8_C 0.70 0.24 0.01
374_M 20_I 0.69 0.24 0.01
100_L 94_I 0.69 0.24 0.01
374_M 145_S 0.69 0.24 0.01
146_M 64_M 0.69 0.24 0.01
476_V 96_P 0.69 0.24 0.01
301_G 43_F 0.69 0.24 0.01
350_L 30_L 0.69 0.24 0.01
316_A 130_G 0.69 0.24 0.01
367_H 155_A 0.69 0.24 0.01
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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