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OPENSEQ.org
cI_B_cIII_cytb
Genes: A B A+B
Length: 613 440 980
Sequences: 10093 3168 3408
Seq/Len: 16.46 7.2 3.48
MirrorTree (Pazo et al. 2001) 0.71
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 0.37 0.00 0.24
2 0.38 0.00 1.39
5 0.55 0.00 2.41
10 0.56 0.00 2.53
20 0.56 0.00 2.60
100 0.56 0.00 2.68
∞ 0.56 0.01 3.24
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
465_T 60_A 1.04 0.73 0.02
462_I 248_F 1.03 0.72 0.02
181_L 70_T 0.99 0.68 0.02
415_M 364_K 0.99 0.68 0.02
464_S 364_K 0.96 0.65 0.02
49_G 351_T 0.96 0.64 0.02
527_P 204_V 0.88 0.54 0.01
571_I 207_A 0.87 0.53 0.01
600_I 260_L 0.84 0.50 0.01
556_I 60_A 0.83 0.48 0.01
448_V 286_L 0.82 0.47 0.01
344_L 185_A 0.81 0.46 0.01
488_G 137_L 0.81 0.45 0.01
197_F 89_G 0.80 0.45 0.01
603_V 402_A 0.80 0.44 0.01
604_V 204_V 0.80 0.44 0.01
180_F 383_M 0.79 0.43 0.01
489_S 66_V 0.79 0.43 0.01
108_R 121_Y 0.78 0.42 0.01
602_A 338_G 0.78 0.42 0.01
500_V 209_V 0.78 0.41 0.01
606_L 110_I 0.78 0.41 0.01
125_A 22_R 0.77 0.41 0.01
490_M 207_A 0.77 0.41 0.01
180_F 341_L 0.77 0.41 0.01
79_L 410_L 0.77 0.40 0.01
413_N 261_V 0.77 0.40 0.01
540_G 364_K 0.77 0.40 0.01
264_Y 23_L 0.77 0.40 0.01
602_A 259_V 0.77 0.40 0.01
549_F 369_L 0.77 0.40 0.01
529_R 261_V 0.76 0.40 0.01
33_V 389_Y 0.76 0.39 0.01
464_S 176_I 0.75 0.39 0.01
325_V 270_M 0.75 0.38 0.01
216_M 211_V 0.75 0.38 0.01
556_I 78_A 0.75 0.38 0.01
379_F 121_Y 0.75 0.38 0.01
381_V 353_R 0.74 0.37 0.01
565_L 103_L 0.74 0.37 0.01
467_V 119_G 0.74 0.37 0.01
528_G 222_N 0.74 0.37 0.01
562_R 116_L 0.74 0.37 0.01
343_A 263_F 0.74 0.36 0.01
62_Q 197_L 0.74 0.36 0.01
273_F 136_Y 0.74 0.36 0.01
355_A 96_L 0.73 0.36 0.01
181_L 356_S 0.73 0.36 0.01
218_A 158_G 0.73 0.36 0.01
416_V 402_A 0.73 0.36 0.01
427_L 61_T 0.73 0.36 0.01
406_A 172_V 0.73 0.36 0.01
89_L 69_Y 0.73 0.36 0.01
430_F 359_Y 0.73 0.35 0.01
444_H 135_I 0.73 0.35 0.01
597_S 70_T 0.73 0.35 0.01
162_K 200_L 0.73 0.35 0.01
130_L 94_R 0.73 0.35 0.01
327_A 364_K 0.72 0.35 0.01
182_A 127_V 0.72 0.34 0.01
343_A 189_P 0.72 0.34 0.01
217_W 137_L 0.72 0.34 0.01
13_I 334_I 0.72 0.34 0.01
308_L 73_V 0.72 0.34 0.01
196_N 116_L 0.71 0.34 0.01
608_L 406_I 0.71 0.34 0.01
115_R 275_G 0.71 0.33 0.01
392_V 371_A 0.71 0.33 0.01
224_G 260_L 0.71 0.33 0.01
71_G 43_W 0.70 0.33 0.01
237_T 69_Y 0.70 0.33 0.01
215_L 59_I 0.70 0.32 0.01
514_G 116_L 0.70 0.32 0.01
506_L 211_V 0.70 0.32 0.01
86_L 80_V 0.70 0.32 0.01
472_V 246_P 0.70 0.32 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.56 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
2276 3.48 cI_B_cIII_cytb Δgene:(1, ∞) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.02 Done - Shared
2275 3.58 cI_B_cIII_cytb Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.01 Done - Shared
2270 3.61 cI_B_cIII_cytb Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.08 Done - Shared
2268 3.63 cI_B_cIII_cytb Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.01 Done - Shared
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