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OPENSEQ.org
cIV_A_40_cI_K_40_Pdenitr
Genes: A B A+B
Length: 538 101 622
Sequences: 3263 222 223
Seq/Len: 6.07 2.2 0.36
MirrorTree (Pazo et al. 2001) 0.05
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 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.01
100 0.02 0.00 0.03
∞ 0.06 0.00 0.35
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
297_A 47_F 1.42 0.41 0.00
278_I 53_H 1.41 0.41 0.00
212_A 42_A 1.41 0.40 0.00
378_S 61_V 1.32 0.34 0.00
369_V 94_E 1.32 0.34 0.00
36_Y 31_V 1.31 0.34 0.00
488_I 42_A 1.28 0.32 0.00
479_I 29_V 1.24 0.29 0.00
274_I 10_V 1.23 0.29 0.00
339_V 53_H 1.20 0.27 0.00
298_A 74_A 1.18 0.26 0.00
337_I 95_D 1.17 0.26 0.00
175_A 11_G 1.17 0.26 0.00
282_A 31_V 1.16 0.25 0.00
496_F 24_V 1.14 0.24 0.00
175_A 27_K 1.13 0.24 0.00
369_V 2_I 1.12 0.23 0.00
268_L 61_V 1.12 0.23 0.00
152_P 4_L 1.12 0.23 0.00
393_V 31_V 1.11 0.22 0.00
467_A 83_V 1.10 0.22 0.00
425_P 10_V 1.09 0.22 0.00
361_F 83_V 1.08 0.21 0.00
358_L 42_A 1.08 0.21 0.00
375_V 13_I 1.08 0.21 0.00
407_G 35_S 1.07 0.21 0.00
337_I 90_T 1.06 0.20 0.00
438_I 47_F 1.06 0.20 0.00
186_T 29_V 1.04 0.19 0.00
485_L 5_T 1.02 0.19 0.00
175_A 66_V 1.00 0.18 0.00
130_V 11_G 0.99 0.17 0.00
485_L 19_I 0.97 0.16 0.00
355_T 64_M 0.96 0.16 0.00
482_A 45_I 0.96 0.16 0.00
286_I 64_M 0.95 0.16 0.00
475_I 74_A 0.95 0.15 0.00
172_V 96_V 0.94 0.15 0.00
267_I 29_V 0.94 0.15 0.00
69_H 2_I 0.94 0.15 0.00
198_L 42_A 0.94 0.15 0.00
343_I 35_S 0.94 0.15 0.00
33_F 48_V 0.93 0.15 0.00
133_L 76_I 0.93 0.15 0.00
127_A 17_T 0.93 0.15 0.00
278_I 27_K 0.92 0.15 0.00
273_I 83_V 0.92 0.14 0.00
476_G 99_M 0.92 0.14 0.00
21_F 29_V 0.91 0.14 0.00
472_I 24_V 0.91 0.14 0.00
528_E 5_T 0.91 0.14 0.00
172_V 48_V 0.91 0.14 0.00
208_V 36_I 0.90 0.14 0.00
198_L 83_V 0.90 0.14 0.00
463_P 84_F 0.90 0.14 0.00
149_V 2_I 0.89 0.14 0.00
76_T 17_T 0.89 0.14 0.00
91_L 48_V 0.89 0.13 0.00
91_L 31_V 0.88 0.13 0.00
488_I 55_G 0.88 0.13 0.00
408_I 54_L 0.87 0.13 0.00
68_G 94_E 0.87 0.13 0.00
181_A 31_V 0.87 0.13 0.00
126_V 81_L 0.87 0.13 0.00
532_K 64_M 0.87 0.13 0.00
463_P 31_V 0.86 0.13 0.00
117_L 17_T 0.86 0.13 0.00
277_V 24_V 0.86 0.12 0.00
472_I 35_S 0.86 0.12 0.00
492_F 55_G 0.86 0.12 0.00
447_Q 35_S 0.86 0.12 0.00
488_I 35_S 0.86 0.12 0.00
439_G 30_I 0.85 0.12 0.00
48_Y 99_M 0.85 0.12 0.00
45_G 32_I 0.85 0.12 0.00
29_I 99_M 0.85 0.12 0.00
45_G 36_I 0.84 0.12 0.00
487_F 36_I 0.84 0.12 0.00
533_R 20_F 0.84 0.12 0.00
337_I 61_V 0.84 0.12 0.00
348_G 1_M 0.83 0.12 0.00
191_M 31_V 0.83 0.12 0.00
423_Q 76_I 0.83 0.12 0.00
124_C 29_V 0.83 0.12 0.00
70_L 27_K 0.83 0.12 0.00
312_Y 36_I 0.82 0.11 0.00
408_I 61_V 0.82 0.11 0.00
250_L 32_I 0.82 0.11 0.00
250_L 76_I 0.82 0.11 0.00
249_V 7_Y 0.82 0.11 0.00
28_L 27_K 0.82 0.11 0.00
106_A 66_V 0.81 0.11 0.00
407_G 18_G 0.81 0.11 0.00
325_M 39_M 0.81 0.11 0.00
379_Q 32_I 0.81 0.11 0.00
298_A 69_V 0.81 0.11 0.00
339_V 29_V 0.81 0.11 0.00
381_P 6_H 0.80 0.11 0.00
463_P 35_S 0.80 0.11 0.00
530_L 45_I 0.80 0.11 0.00
98_Y 83_V 0.80 0.11 0.00
24_G 61_V 0.80 0.11 0.00
333_V 66_V 0.80 0.11 0.00
216_L 61_V 0.80 0.11 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
3364 2.98 cIV_A_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3362 2.97 cIV_A_10_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3359 3.4 cIV_A_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3358 3.42 cIV_A_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3356 0.36 cIV_A_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3355 3.6 cIV_A_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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