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OPENSEQ.org
STE7-FUS3
Genes: A B A+B
Length: 515 353 777
Sequences: 2368 34302 164
Seq/Len: 4.6 97.17 0.21
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 0.04 0.06 0.02
2 0.05 0.08 0.03
5 0.05 0.09 0.05
10 0.05 0.12 0.11
20 0.06 0.15 0.19
100 0.10 0.22 0.39
∞ 0.19 0.24 0.48
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
437_K 159_A 1.36 0.26 0.00
397_L 94_E 1.29 0.23 0.00
218_A 152_K 1.25 0.21 0.00
460_L 133_V 1.21 0.20 0.00
319_D 134_I 1.12 0.16 0.00
317_G 69_E 1.12 0.16 0.00
349_D 42_K 1.03 0.14 0.00
349_D 137_D 1.03 0.14 0.00
349_D 142_N 1.03 0.14 0.00
349_D 155_D 1.03 0.14 0.00
349_D 297_R 1.03 0.14 0.00
386_D 42_K 1.03 0.14 0.00
386_D 137_D 1.03 0.14 0.00
386_D 142_N 1.03 0.14 0.00
386_D 155_D 1.03 0.14 0.00
386_D 297_R 1.03 0.14 0.00
167_S 138_L 1.03 0.14 0.00
454_R 42_K 1.01 0.13 0.00
454_R 137_D 1.01 0.13 0.00
454_R 142_N 1.01 0.13 0.00
454_R 155_D 1.01 0.13 0.00
454_R 297_R 1.01 0.13 0.00
168_P 216_L 1.00 0.13 0.00
389_S 27_V 1.00 0.13 0.00
442_F 25_G 1.00 0.13 0.00
76_D 216_L 0.98 0.12 0.00
346_K 135_H 0.97 0.12 0.00
267_I 127_V 0.95 0.11 0.00
185_Y 71_I 0.95 0.11 0.00
349_D 59_E 0.94 0.11 0.00
386_D 59_E 0.94 0.11 0.00
367_T 156_F 0.94 0.11 0.00
241_I 286_L 0.94 0.11 0.00
330_R 66_F 0.94 0.11 0.00
349_D 205_D 0.93 0.11 0.00
386_D 205_D 0.93 0.11 0.00
349_D 22_G 0.93 0.11 0.00
386_D 22_G 0.93 0.11 0.00
249_E 133_V 0.92 0.11 0.00
200_G 42_K 0.92 0.11 0.00
200_G 137_D 0.92 0.11 0.00
200_G 142_N 0.92 0.11 0.00
200_G 155_D 0.92 0.11 0.00
200_G 297_R 0.92 0.11 0.00
454_R 59_E 0.92 0.11 0.00
331_D 42_K 0.92 0.11 0.00
331_D 137_D 0.92 0.11 0.00
331_D 142_N 0.92 0.11 0.00
331_D 155_D 0.92 0.11 0.00
331_D 297_R 0.92 0.11 0.00
454_R 205_D 0.91 0.10 0.00
454_R 22_G 0.90 0.10 0.00
391_G 210_G 0.90 0.10 0.00
333_K 22_G 0.90 0.10 0.00
246_K 19_L 0.89 0.10 0.00
372_S 133_V 0.89 0.10 0.00
327_I 125_V 0.89 0.10 0.00
314_V 25_G 0.88 0.10 0.00
116_T 145_I 0.88 0.10 0.00
318_L 127_V 0.88 0.10 0.00
127_F 19_L 0.87 0.10 0.00
333_K 139_K 0.86 0.10 0.00
158_S 13_F 0.86 0.09 0.00
101_S 204_M 0.86 0.09 0.00
351_G 157_G 0.86 0.09 0.00
317_G 68_H 0.86 0.09 0.00
460_L 309_L 0.86 0.09 0.00
349_D 157_G 0.86 0.09 0.00
386_D 157_G 0.86 0.09 0.00
205_V 139_K 0.86 0.09 0.00
353_S 25_G 0.86 0.09 0.00
465_L 308_Y 0.86 0.09 0.00
332_I 145_I 0.85 0.09 0.00
372_S 68_H 0.85 0.09 0.00
283_L 196_T 0.85 0.09 0.00
161_P 293_D 0.85 0.09 0.00
246_K 159_A 0.85 0.09 0.00
328_I 118_I 0.84 0.09 0.00
195_G 134_I 0.84 0.09 0.00
445_R 185_T 0.84 0.09 0.00
389_S 293_D 0.84 0.09 0.00
251_I 25_G 0.83 0.09 0.00
200_G 59_E 0.83 0.09 0.00
93_N 133_V 0.83 0.09 0.00
454_R 157_G 0.83 0.09 0.00
327_I 138_L 0.83 0.09 0.00
331_D 59_E 0.83 0.09 0.00
394_I 13_F 0.82 0.09 0.00
456_S 92_I 0.82 0.09 0.00
352_V 25_G 0.82 0.09 0.00
115_S 56_T 0.82 0.09 0.00
34_E 19_L 0.82 0.09 0.00
349_D 135_H 0.82 0.09 0.00
386_D 135_H 0.82 0.09 0.00
200_G 205_D 0.82 0.09 0.00
395_I 211_C 0.82 0.09 0.00
270_L 71_I 0.82 0.09 0.00
219_K 217_F 0.82 0.09 0.00
200_G 22_G 0.81 0.09 0.00
258_Y 62_I 0.81 0.08 0.00
398_V 133_V 0.81 0.08 0.00
331_D 205_D 0.81 0.08 0.00
48_S 185_T 0.81 0.08 0.00
323_R 125_V 0.81 0.08 0.00
434_I 160_R 0.81 0.08 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!
  • Sequence A is very similar to Sequence B (HHΔ = 0.241), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
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