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OPENSEQ.org
cI_B_cIII_cytb
Genes: A B A+B
Length: 613 440 980
Sequences: 11857 3168 3509
Seq/Len: 19.34 7.2 3.58
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 1.42
5 0.60 0.00 2.45
10 0.60 0.00 2.60
20 0.60 0.00 2.67
100 0.60 0.00 2.75
∞ 0.60 0.01 3.33
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 0.97 0.66 0.01
181_L 70_T 0.96 0.65 0.01
413_N 261_V 0.95 0.64 0.01
62_Q 197_L 0.92 0.61 0.01
556_I 60_A 0.90 0.57 0.01
415_M 364_K 0.89 0.56 0.01
464_S 364_K 0.87 0.54 0.01
600_I 260_L 0.83 0.48 0.01
464_S 176_I 0.82 0.48 0.01
571_I 207_A 0.80 0.45 0.01
602_A 259_V 0.80 0.45 0.01
591_L 211_V 0.79 0.44 0.01
462_I 248_F 0.79 0.43 0.01
217_W 137_L 0.78 0.42 0.01
216_M 211_V 0.76 0.40 0.01
603_V 402_A 0.76 0.40 0.00
180_F 383_M 0.76 0.39 0.00
606_L 110_I 0.75 0.39 0.00
606_L 395_A 0.75 0.39 0.00
295_G 41_L 0.75 0.39 0.00
130_L 94_R 0.75 0.39 0.00
201_V 206_A 0.75 0.38 0.00
565_L 103_L 0.74 0.38 0.00
89_L 69_Y 0.74 0.37 0.00
528_G 334_I 0.74 0.37 0.00
527_P 204_V 0.74 0.37 0.00
286_V 112_I 0.74 0.37 0.00
467_V 131_V 0.74 0.37 0.00
195_L 268_G 0.73 0.37 0.00
49_G 351_T 0.73 0.37 0.00
141_L 397_S 0.73 0.36 0.00
517_T 71_P 0.73 0.36 0.00
379_F 121_Y 0.73 0.36 0.00
294_A 357_G 0.73 0.36 0.00
197_F 92_M 0.73 0.36 0.00
406_A 172_V 0.73 0.36 0.00
13_I 169_I 0.72 0.35 0.00
514_G 116_L 0.72 0.35 0.00
488_G 137_L 0.72 0.35 0.00
430_F 359_Y 0.71 0.34 0.00
474_P 286_L 0.71 0.34 0.00
108_R 121_Y 0.71 0.34 0.00
584_L 169_I 0.71 0.34 0.00
182_A 127_V 0.71 0.34 0.00
490_M 207_A 0.71 0.34 0.00
125_A 22_R 0.71 0.34 0.00
467_V 119_G 0.71 0.34 0.00
551_K 112_I 0.71 0.33 0.00
355_A 96_L 0.71 0.33 0.00
181_L 356_S 0.70 0.33 0.00
489_S 66_V 0.70 0.33 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 (0.60 > 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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