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OPENSEQ.org
cIV_A_4_cI_A_20_1_Pdenitr
Genes: A B A+B
Length: 538 121 636
Sequences: 3263 493 333
Seq/Len: 6.07 4.07 0.52
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 0.00 0.00 0.01
2 0.00 0.00 0.03
5 0.01 0.00 0.05
10 0.01 0.00 0.08
20 0.01 0.00 0.12
100 0.02 0.00 0.17
∞ 0.06 0.00 0.51
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
405_V 15_L 1.29 0.41 0.00
217_L 63_F 1.23 0.37 0.00
337_I 22_A 1.22 0.36 0.00
519_P 17_M 1.20 0.35 0.00
76_T 114_K 1.12 0.29 0.00
527_F 109_F 1.11 0.29 0.00
355_T 20_A 1.11 0.28 0.00
49_M 87_F 1.10 0.28 0.00
123_V 67_S 1.09 0.27 0.00
429_G 24_V 1.07 0.26 0.00
472_I 119_E 1.07 0.26 0.00
7_F 90_L 1.06 0.25 0.00
317_S 29_A 1.05 0.25 0.00
472_I 50_N 1.05 0.25 0.00
333_V 90_L 1.03 0.24 0.00
79_G 78_A 1.02 0.23 0.00
313_T 33_A 1.00 0.22 0.00
155_S 25_L 1.00 0.22 0.00
203_L 11_I 0.99 0.21 0.00
411_G 17_M 0.99 0.21 0.00
250_L 100_V 0.98 0.21 0.00
86_V 9_L 0.96 0.20 0.00
392_V 107_V 0.95 0.19 0.00
20_L 22_A 0.95 0.19 0.00
8_M 26_I 0.94 0.19 0.00
98_Y 107_V 0.94 0.19 0.00
333_V 97_G 0.94 0.19 0.00
328_T 11_I 0.94 0.19 0.00
472_I 18_A 0.93 0.18 0.00
483_S 67_S 0.93 0.18 0.00
218_S 33_A 0.93 0.18 0.00
189_L 104_V 0.92 0.18 0.00
198_L 22_A 0.92 0.18 0.00
134_L 110_A 0.91 0.18 0.00
475_I 51_A 0.91 0.17 0.00
301_I 61_V 0.90 0.17 0.00
491_V 119_E 0.90 0.17 0.00
378_S 37_P 0.90 0.17 0.00
333_V 44_A 0.90 0.17 0.00
459_Y 51_A 0.89 0.17 0.00
90_A 18_A 0.88 0.17 0.00
382_L 23_I 0.88 0.16 0.00
196_M 10_P 0.88 0.16 0.00
344_A 80_L 0.88 0.16 0.00
49_M 21_L 0.87 0.16 0.00
435_M 72_I 0.87 0.16 0.00
238_Q 4_L 0.86 0.16 0.00
468_Y 18_A 0.86 0.16 0.00
182_I 77_V 0.86 0.15 0.00
86_V 61_V 0.85 0.15 0.00
317_S 51_A 0.85 0.15 0.00
354_K 77_V 0.85 0.15 0.00
198_L 114_K 0.84 0.15 0.00
499_K 24_V 0.84 0.15 0.00
130_V 17_M 0.83 0.14 0.00
347_W 58_K 0.83 0.14 0.00
411_G 36_N 0.82 0.14 0.00
37_M 114_K 0.82 0.14 0.00
80_V 78_A 0.82 0.14 0.00
408_I 33_A 0.82 0.14 0.00
117_L 25_L 0.82 0.14 0.00
23_A 35_R 0.82 0.14 0.00
455_M 64_Y 0.82 0.14 0.00
298_A 32_I 0.82 0.14 0.00
277_V 90_L 0.82 0.14 0.00
325_M 57_M 0.82 0.14 0.00
435_M 94_A 0.82 0.14 0.00
492_F 17_M 0.81 0.14 0.00
18_L 104_V 0.81 0.14 0.00
333_V 66_V 0.81 0.14 0.00
343_I 25_L 0.81 0.14 0.00
473_S 77_V 0.81 0.14 0.00
133_L 57_M 0.81 0.14 0.00
236_G 37_P 0.81 0.14 0.00
277_V 92_D 0.80 0.13 0.00
455_M 67_S 0.80 0.13 0.00
25_I 85_V 0.80 0.13 0.00
372_V 43_S 0.80 0.13 0.00
26_V 78_A 0.80 0.13 0.00
489_G 9_L 0.80 0.13 0.00
430_Q 98_L 0.80 0.13 0.00
323_Y 92_D 0.79 0.13 0.00
365_F 96_W 0.79 0.13 0.00
491_V 16_G 0.78 0.13 0.00
216_L 13_V 0.78 0.13 0.00
501_V 7_E 0.78 0.13 0.00
186_T 90_L 0.78 0.13 0.00
353_F 10_P 0.78 0.13 0.00
226_I 45_Y 0.78 0.13 0.00
435_M 9_L 0.78 0.12 0.00
393_V 27_L 0.78 0.12 0.00
523_P 10_P 0.78 0.12 0.00
165_L 66_V 0.78 0.12 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
3350 3.54 cIV_A_2_cI_A_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3349 3.53 cIV_A_6_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3346 3.5 cIV_A_4_cI_A_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3345 3.52 cIV_A_4_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3344 0.52 cIV_A_4_cI_A_20_1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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