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OPENSEQ.org
cIV_A_4_cI_N_20_1_Pdenitr
Genes: A B A+B
Length: 538 499 976
Sequences: 4477 2180 1039
Seq/Len: 8.32 4.37 1.06
MirrorTree (Pazo et al. 2001) 0.03
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 0.01
2 0.01 0.01 0.03
5 0.02 0.01 0.04
10 0.03 0.01 0.08
20 0.03 0.02 0.13
100 0.05 0.03 0.26
∞ 0.08 0.05 1.00
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
23_A 221_V 1.06 0.41 0.00
182_I 394_V 1.01 0.36 0.00
438_I 162_V 0.95 0.31 0.00
378_S 47_L 0.95 0.31 0.00
175_A 86_A 0.92 0.28 0.00
475_I 190_I 0.91 0.28 0.00
188_F 355_L 0.90 0.27 0.00
314_A 129_L 0.90 0.27 0.00
277_V 316_G 0.88 0.26 0.00
36_Y 390_A 0.86 0.24 0.00
483_S 399_V 0.85 0.23 0.00
25_I 89_L 0.84 0.23 0.00
378_S 40_W 0.83 0.22 0.00
405_V 113_A 0.82 0.22 0.00
91_L 156_A 0.82 0.22 0.00
479_I 234_S 0.82 0.21 0.00
414_Y 285_S 0.81 0.21 0.00
286_I 214_L 0.80 0.20 0.00
471_N 336_I 0.80 0.20 0.00
123_V 254_I 0.79 0.20 0.00
114_L 425_V 0.78 0.19 0.00
483_S 376_M 0.78 0.19 0.00
488_I 214_L 0.78 0.19 0.00
29_I 52_M 0.78 0.19 0.00
168_F 197_G 0.77 0.19 0.00
333_V 86_A 0.77 0.19 0.00
37_M 323_N 0.77 0.18 0.00
71_W 94_D 0.77 0.18 0.00
83_M 374_V 0.77 0.18 0.00
235_F 157_G 0.76 0.18 0.00
486_F 294_I 0.76 0.18 0.00
178_I 221_V 0.76 0.18 0.00
420_S 280_S 0.76 0.18 0.00
475_I 55_L 0.76 0.18 0.00
196_M 425_V 0.76 0.18 0.00
378_S 275_A 0.76 0.18 0.00
409_F 157_G 0.76 0.18 0.00
491_V 416_I 0.75 0.18 0.00
442_L 276_L 0.75 0.18 0.00
71_W 106_F 0.75 0.18 0.00
489_G 83_V 0.75 0.18 0.00
488_I 433_E 0.75 0.17 0.00
273_I 191_I 0.75 0.17 0.00
293_V 204_L 0.75 0.17 0.00
533_R 342_I 0.74 0.17 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
3326 1.5 cIV_A_4_cI_N_4_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3325 1.06 cIV_A_4_cI_N_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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