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OPENSEQ.org
Yo2
Genes: A B A+B
Length: 441 81 505
Sequences: 1922 153 62
Seq/Len: 4.36 1.89 0.12
MirrorTree (Pazo et al. 2001) 0.27
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 0.34 0.27 0.02
2 0.36 0.27 0.02
5 0.38 0.28 0.02
10 0.39 0.28 0.02
20 0.39 0.29 0.03
100 0.40 0.30 0.05
∞ 0.44 0.35 0.12
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
161_S 51_C 1.40 0.19 0.00
318_C 51_C 1.40 0.19 0.00
19_V 13_F 1.39 0.19 0.00
277_M 13_F 1.33 0.17 0.00
15_F 74_R 1.28 0.16 0.00
24_F 74_R 1.27 0.15 0.00
306_C 51_C 1.23 0.14 0.00
344_N 7_S 1.21 0.14 0.00
199_G 42_C 1.19 0.13 0.00
25_R 13_F 1.17 0.13 0.00
108_G 44_P 1.15 0.12 0.00
83_S 14_M 1.15 0.12 0.00
414_L 24_D 1.13 0.12 0.00
44_A 27_A 1.12 0.12 0.00
191_K 58_S 1.11 0.12 0.00
435_R 55_Y 1.11 0.12 0.00
202_S 44_P 1.09 0.11 0.00
116_Q 12_V 1.09 0.11 0.00
400_F 12_V 1.08 0.11 0.00
253_F 32_C 1.07 0.11 0.00
224_A 16_V 1.07 0.11 0.00
161_S 42_C 1.07 0.11 0.00
318_C 42_C 1.07 0.11 0.00
102_G 5_T 1.05 0.10 0.00
199_G 51_C 1.05 0.10 0.00
349_C 47_G 1.05 0.10 0.00
377_I 2_K 1.03 0.10 0.00
23_L 5_T 1.03 0.10 0.00
182_K 12_V 1.03 0.10 0.00
243_R 14_M 1.03 0.10 0.00
189_S 40_G 1.02 0.10 0.00
203_Y 13_F 1.02 0.10 0.00
154_K 6_L 1.01 0.10 0.00
60_F 42_C 1.00 0.09 0.00
113_L 4_A 1.00 0.09 0.00
349_C 40_G 1.00 0.09 0.00
393_E 4_A 1.00 0.09 0.00
56_F 51_C 0.99 0.09 0.00
46_N 26_E 0.99 0.09 0.00
122_W 47_G 0.98 0.09 0.00
394_N 14_M 0.97 0.09 0.00
89_W 67_C 0.97 0.09 0.00
142_G 67_C 0.97 0.09 0.00
159_W 67_C 0.97 0.09 0.00
281_G 67_C 0.97 0.09 0.00
60_F 78_C 0.95 0.09 0.00
182_K 25_L 0.94 0.08 0.00
253_F 42_C 0.94 0.08 0.00
120_T 27_A 0.94 0.08 0.00
348_E 44_P 0.94 0.08 0.00
394_N 74_R 0.93 0.08 0.00
148_D 74_R 0.93 0.08 0.00
85_R 12_V 0.92 0.08 0.00
439_V 22_F 0.92 0.08 0.00
85_R 74_R 0.92 0.08 0.00
277_M 80_F 0.92 0.08 0.00
180_K 49_L 0.91 0.08 0.00
192_N 14_M 0.91 0.08 0.00
175_L 26_E 0.91 0.08 0.00
50_V 74_R 0.90 0.08 0.00
121_V 9_V 0.90 0.08 0.00
52_L 72_D 0.90 0.08 0.00
117_S 26_E 0.90 0.08 0.00
227_S 4_A 0.90 0.08 0.00
89_W 76_C 0.90 0.08 0.00
142_G 76_C 0.90 0.08 0.00
159_W 76_C 0.90 0.08 0.00
281_G 76_C 0.90 0.08 0.00
115_N 10_V 0.90 0.08 0.00
166_T 40_G 0.89 0.08 0.00
63_P 2_K 0.89 0.08 0.00
48_T 32_C 0.88 0.07 0.00
104_F 76_C 0.88 0.07 0.00
89_W 51_C 0.88 0.07 0.00
142_G 51_C 0.88 0.07 0.00
159_W 51_C 0.88 0.07 0.00
281_G 51_C 0.88 0.07 0.00
306_C 42_C 0.88 0.07 0.00
77_I 78_C 0.88 0.07 0.00
191_K 24_D 0.88 0.07 0.00
92_N 67_C 0.87 0.07 0.00
387_C 67_C 0.87 0.07 0.00
391_C 67_C 0.87 0.07 0.00
397_C 67_C 0.87 0.07 0.00
412_C 67_C 0.87 0.07 0.00
60_F 51_C 0.87 0.07 0.00
89_W 78_C 0.87 0.07 0.00
142_G 78_C 0.87 0.07 0.00
159_W 78_C 0.87 0.07 0.00
281_G 78_C 0.87 0.07 0.00
418_E 8_V 0.87 0.07 0.00
376_A 8_V 0.87 0.07 0.00
79_Y 12_V 0.86 0.07 0.00
51_S 51_C 0.86 0.07 0.00
138_L 16_V 0.86 0.07 0.00
113_L 3_S 0.86 0.07 0.00
349_C 42_C 0.86 0.07 0.00
88_V 51_C 0.85 0.07 0.00
121_V 3_S 0.85 0.07 0.00
129_A 41_Q 0.85 0.07 0.00
128_G 2_K 0.85 0.07 0.00
435_R 1_M 0.85 0.07 0.00
168_T 67_C 0.85 0.07 0.00
347_T 4_A 0.84 0.07 0.00
194_Y 74_R 0.84 0.07 0.00
440_D 41_Q 0.84 0.07 0.00
23_L 69_N 0.83 0.07 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 (0.44 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
2982 0.12 Yo2 Δgene:(1, ∞) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2981 0.03 Maxime Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2015_06) Killed - Shared
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