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OPENSEQ.org
cI_B_cIII_cytb
Genes: A B A+B
Length: 613 440 983
Sequences: 12095 3168 3573
Seq/Len: 19.73 7.2 3.63
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 0.39 0.00 0.26
2 0.43 0.00 1.44
5 0.59 0.00 2.49
10 0.60 0.00 2.65
20 0.60 0.00 2.71
100 0.60 0.00 2.80
∞ 0.60 0.01 3.39
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 0.98 0.68 0.01
13_I 169_I 0.93 0.62 0.01
181_L 70_T 0.89 0.57 0.01
529_R 176_I 0.87 0.55 0.01
216_M 211_V 0.86 0.53 0.01
464_S 176_I 0.86 0.53 0.01
602_A 338_G 0.86 0.53 0.01
464_S 364_K 0.85 0.51 0.01
89_L 69_Y 0.83 0.49 0.01
48_I 365_W 0.82 0.48 0.01
273_F 131_V 0.80 0.45 0.01
413_N 261_V 0.79 0.44 0.01
379_F 121_Y 0.79 0.44 0.01
591_L 211_V 0.79 0.44 0.01
420_V 345_L 0.78 0.43 0.01
184_A 259_V 0.77 0.41 0.01
357_H 349_L 0.77 0.41 0.01
40_L 410_L 0.76 0.40 0.01
571_I 207_A 0.76 0.40 0.01
467_V 131_V 0.76 0.40 0.01
421_G 334_I 0.76 0.40 0.01
286_V 112_I 0.75 0.39 0.01
180_F 383_M 0.75 0.39 0.01
343_A 189_P 0.74 0.38 0.01
458_I 61_T 0.74 0.38 0.01
294_A 357_G 0.74 0.38 0.01
596_A 169_I 0.74 0.37 0.01
41_A 37_T 0.73 0.37 0.01
544_L 207_A 0.73 0.37 0.01
553_F 261_V 0.73 0.36 0.01
604_V 116_L 0.72 0.36 0.01
600_I 260_L 0.72 0.36 0.01
189_Y 356_S 0.72 0.35 0.01
125_A 22_R 0.72 0.35 0.01
556_I 60_A 0.72 0.35 0.01
362_I 83_I 0.72 0.35 0.01
415_M 364_K 0.72 0.35 0.01
606_L 110_I 0.72 0.35 0.01
355_A 96_L 0.71 0.34 0.01
502_V 112_I 0.71 0.34 0.01
565_L 103_L 0.71 0.34 0.01
272_L 56_V 0.71 0.34 0.01
490_M 207_A 0.70 0.34 0.01
607_A 375_V 0.70 0.34 0.01
606_L 395_A 0.70 0.33 0.01
201_V 206_A 0.70 0.33 0.01
603_V 370_L 0.70 0.33 0.01
182_A 127_V 0.70 0.33 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 (0.60 > 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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