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OPENSEQ.org
cIV_A_4_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 538 263 759
Sequences: 4477 973 430
Seq/Len: 8.32 3.7 0.57
MirrorTree (Pazo et al. 2001) 0.06
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 0.01 0.01 0.00
2 0.01 0.01 0.00
5 0.02 0.01 0.00
10 0.03 0.01 0.01
20 0.03 0.01 0.02
100 0.05 0.01 0.10
∞ 0.08 0.01 0.54
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
533_R 46_Q 1.12 0.31 0.00
106_A 240_V 1.06 0.27 0.00
273_I 240_V 1.01 0.24 0.00
492_F 256_I 1.01 0.24 0.00
488_I 74_D 1.00 0.23 0.00
488_I 54_Y 0.97 0.22 0.00
415_W 124_S 0.97 0.22 0.00
175_A 217_M 0.96 0.21 0.00
333_V 240_V 0.96 0.21 0.00
71_W 240_V 0.93 0.20 0.00
28_L 236_I 0.90 0.18 0.00
130_V 237_F 0.89 0.18 0.00
376_V 241_L 0.88 0.17 0.00
185_I 52_Q 0.87 0.17 0.00
339_V 127_A 0.86 0.17 0.00
479_I 66_Y 0.86 0.16 0.00
7_F 241_L 0.86 0.16 0.00
438_I 83_D 0.85 0.16 0.00
393_V 240_V 0.85 0.16 0.00
502_N 244_L 0.84 0.16 0.00
472_I 18_E 0.84 0.15 0.00
165_L 125_L 0.83 0.15 0.00
479_I 240_V 0.83 0.15 0.00
121_M 241_L 0.82 0.15 0.00
339_V 220_A 0.82 0.15 0.00
278_I 194_Q 0.82 0.15 0.00
446_P 63_G 0.81 0.14 0.00
83_M 73_A 0.81 0.14 0.00
355_T 221_E 0.81 0.14 0.00
24_G 85_V 0.81 0.14 0.00
20_L 81_P 0.80 0.14 0.00
472_I 243_A 0.80 0.14 0.00
491_V 44_Q 0.80 0.14 0.00
89_P 241_L 0.80 0.14 0.00
175_A 52_Q 0.79 0.14 0.00
486_F 243_A 0.79 0.14 0.00
351_I 240_V 0.79 0.14 0.00
382_L 208_M 0.79 0.14 0.00
489_G 256_I 0.79 0.14 0.00
482_A 219_T 0.78 0.13 0.00
495_L 193_D 0.78 0.13 0.00
511_A 130_R 0.78 0.13 0.00
290_L 241_L 0.78 0.13 0.00
483_S 254_Q 0.78 0.13 0.00
485_L 181_G 0.78 0.13 0.00
502_N 83_D 0.78 0.13 0.00
438_I 180_A 0.77 0.13 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)
ID Seq/Len Name Options I_Prob Status
3080 0.57 cIV_A_4_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3079 0.43 cIV_A_40_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3078 0.55 cIV_A_20_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3077 0.31 cIV_A_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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