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OPENSEQ.org
cIV_A_20_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 538 263 760
Sequences: 4187 973 417
Seq/Len: 7.78 3.7 0.55
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 0.02 0.01 0.01
20 0.03 0.01 0.02
100 0.04 0.01 0.09
∞ 0.08 0.01 0.52
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
273_I 240_V 1.41 0.52 0.00
71_W 240_V 1.26 0.40 0.00
479_I 66_Y 1.22 0.38 0.00
472_I 247_L 1.04 0.25 0.00
165_L 125_L 1.03 0.25 0.00
492_F 256_I 1.03 0.25 0.00
333_V 240_V 1.01 0.24 0.00
286_I 220_A 0.99 0.22 0.00
489_G 256_I 0.95 0.20 0.00
438_I 235_V 0.95 0.20 0.00
99_F 99_T 0.94 0.20 0.00
438_I 83_D 0.92 0.19 0.00
488_I 74_D 0.92 0.19 0.00
121_M 241_L 0.90 0.18 0.00
486_F 243_A 0.90 0.18 0.00
278_I 194_Q 0.90 0.18 0.00
351_I 240_V 0.88 0.17 0.00
184_I 240_V 0.87 0.17 0.00
7_F 241_L 0.87 0.16 0.00
415_W 124_S 0.86 0.16 0.00
446_P 63_G 0.86 0.16 0.00
290_L 241_L 0.85 0.16 0.00
533_R 46_Q 0.85 0.16 0.00
355_T 221_E 0.85 0.15 0.00
466_F 81_P 0.84 0.15 0.00
462_Y 109_D 0.84 0.15 0.00
428_A 46_Q 0.84 0.15 0.00
48_Y 220_A 0.84 0.15 0.00
175_A 217_M 0.84 0.15 0.00
519_P 241_L 0.84 0.15 0.00
185_I 52_Q 0.84 0.15 0.00
499_K 195_V 0.83 0.15 0.00
472_I 18_E 0.83 0.15 0.00
533_R 54_Y 0.83 0.15 0.00
277_V 130_R 0.82 0.14 0.00
376_V 241_L 0.82 0.14 0.00
190_N 201_T 0.81 0.14 0.00
480_S 244_L 0.81 0.14 0.00
68_G 249_N 0.80 0.14 0.00
480_S 127_A 0.80 0.14 0.00
28_L 236_I 0.80 0.14 0.00
511_A 130_R 0.80 0.14 0.00
74_M 59_S 0.80 0.14 0.00
190_N 209_A 0.80 0.14 0.00
428_A 52_Q 0.79 0.13 0.00
172_V 195_V 0.79 0.13 0.00
488_I 54_Y 0.79 0.13 0.00
185_I 244_L 0.79 0.13 0.00
450_L 81_P 0.79 0.13 0.00
298_A 161_Y 0.79 0.13 0.00
489_G 242_A 0.78 0.13 0.00
425_P 59_S 0.78 0.13 0.00
25_I 149_G 0.78 0.13 0.00
409_F 160_G 0.78 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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