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OPENSEQ.org
cI_Ld500_560_40_8_cIII_cytc1_Pdenitr
Genes: A B A+B
Length: 642 263 870
Sequences: 7701 954 360
Seq/Len: 12 3.63 0.41
MirrorTree (Pazo et al. 2001) 0.18
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 0.03 0.01 0.00
2 0.03 0.01 0.00
5 0.04 0.01 0.00
10 0.05 0.01 0.01
20 0.05 0.01 0.01
100 0.06 0.01 0.06
∞ 0.10 0.01 0.40
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
330_V 124_S 1.57 0.56 0.00
242_L 215_F 1.55 0.54 0.00
135_A 241_L 1.33 0.38 0.00
514_P 52_Q 1.21 0.30 0.00
204_R 45_H 1.20 0.29 0.00
618_L 125_L 1.14 0.26 0.00
175_V 43_D 1.11 0.25 0.00
196_S 54_Y 1.10 0.24 0.00
82_I 216_L 1.10 0.24 0.00
590_V 240_V 1.10 0.24 0.00
341_M 187_A 1.10 0.24 0.00
410_F 156_A 1.09 0.23 0.00
57_I 243_A 1.09 0.23 0.00
80_T 130_R 1.07 0.23 0.00
18_L 243_A 1.06 0.22 0.00
135_A 167_E 1.06 0.22 0.00
39_S 63_G 1.04 0.21 0.00
392_T 213_A 1.01 0.20 0.00
85_I 105_R 1.01 0.20 0.00
11_I 241_L 1.01 0.20 0.00
47_F 213_A 1.00 0.19 0.00
602_L 82_E 0.99 0.18 0.00
13_S 243_A 0.98 0.18 0.00
394_A 201_T 0.98 0.18 0.00
408_A 256_I 0.98 0.18 0.00
483_V 44_Q 0.97 0.17 0.00
291_F 254_Q 0.97 0.17 0.00
570_I 96_D 0.94 0.17 0.00
542_L 100_E 0.94 0.17 0.00
308_L 75_E 0.94 0.17 0.00
298_T 131_A 0.94 0.16 0.00
16_A 242_A 0.93 0.16 0.00
607_T 67_V 0.92 0.16 0.00
508_D 81_P 0.92 0.16 0.00
14_L 201_T 0.92 0.15 0.00
306_V 236_I 0.92 0.15 0.00
519_V 187_A 0.91 0.15 0.00
184_L 82_E 0.90 0.15 0.00
12_A 241_L 0.90 0.15 0.00
529_L 235_V 0.90 0.15 0.00
419_S 213_A 0.89 0.15 0.00
4_F 230_V 0.89 0.15 0.00
35_V 235_V 0.89 0.15 0.00
617_Y 241_L 0.89 0.14 0.00
408_A 46_Q 0.89 0.14 0.00
74_I 104_P 0.89 0.14 0.00
330_V 122_D 0.89 0.14 0.00
54_P 81_P 0.88 0.14 0.00
384_T 221_E 0.88 0.14 0.00
8_A 53_V 0.88 0.14 0.00
316_V 47_L 0.88 0.14 0.00
231_L 241_L 0.87 0.14 0.00
209_L 81_P 0.87 0.14 0.00
484_F 216_L 0.87 0.14 0.00
502_P 216_L 0.87 0.14 0.00
607_T 69_L 0.87 0.14 0.00
139_L 182_N 0.86 0.14 0.00
632_L 245_L 0.86 0.14 0.00
547_A 84_Q 0.86 0.14 0.00
446_I 213_A 0.86 0.13 0.00
473_I 96_D 0.85 0.13 0.00
584_K 213_A 0.85 0.13 0.00
162_K 149_G 0.85 0.13 0.00
196_S 236_I 0.85 0.13 0.00
285_A 93_D 0.85 0.13 0.00
39_S 185_Q 0.85 0.13 0.00
15_I 74_D 0.84 0.13 0.00
394_A 86_R 0.84 0.13 0.00
546_L 63_G 0.84 0.13 0.00
201_E 187_A 0.84 0.13 0.00
423_G 54_Y 0.84 0.13 0.00
407_F 195_V 0.84 0.13 0.00
479_A 180_A 0.83 0.13 0.00
408_A 94_I 0.83 0.12 0.00
186_G 42_F 0.83 0.12 0.00
189_G 64_L 0.83 0.12 0.00
565_E 103_R 0.83 0.12 0.00
6_L 200_G 0.83 0.12 0.00
31_L 203_A 0.83 0.12 0.00
631_G 102_D 0.82 0.12 0.00
371_M 250_K 0.82 0.12 0.00
50_F 205_V 0.82 0.12 0.00
483_V 230_V 0.82 0.12 0.00
2_E 246_Y 0.82 0.12 0.00
141_M 230_V 0.82 0.12 0.00
13_S 97_P 0.81 0.12 0.00
291_F 93_D 0.81 0.12 0.00
162_K 43_D 0.81 0.12 0.00
445_L 195_V 0.81 0.12 0.00
533_W 215_F 0.81 0.12 0.00
275_V 52_Q 0.81 0.12 0.00
301_F 81_P 0.81 0.12 0.00
41_L 137_Y 0.81 0.12 0.00
230_L 246_Y 0.81 0.12 0.00
292_I 201_T 0.80 0.12 0.00
371_M 190_L 0.80 0.12 0.00
510_A 201_T 0.80 0.12 0.00
339_A 216_L 0.80 0.12 0.00
5_V 219_T 0.80 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
2990 0.41 cI_Ld500_560_40_8_cIII_cytc1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2896 0.26 cI_Ld500_560_40_cIII_cytc1_Pdenitr Δgene:(1, ∞) A:(1E-40, 1) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2895 0.4 cI_Ld500_560_cIII_cytc1_Pdenitr Δgene:(1, ∞) A:(1E-04, 2) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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