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OPENSEQ.org
cI_Ld500_560_cIII_cytc1_Pdenitr
Genes: A B A+B
Length: 642 263 872
Sequences: 6833 954 347
Seq/Len: 10.64 3.63 0.4
MirrorTree (Pazo et al. 2001) 0.21
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 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.02 0.01 0.01
100 0.03 0.01 0.06
∞ 0.07 0.01 0.38
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
39_S 63_G 1.62 0.58 0.00
330_V 124_S 1.37 0.41 0.00
483_V 44_Q 1.37 0.40 0.00
242_L 215_F 1.34 0.38 0.00
379_K 81_P 1.29 0.35 0.00
135_A 241_L 1.26 0.33 0.00
175_V 43_D 1.18 0.28 0.00
80_T 130_R 1.11 0.24 0.00
204_R 45_H 1.11 0.24 0.00
230_L 49_R 1.11 0.24 0.00
82_I 216_L 1.08 0.23 0.00
548_A 240_V 1.07 0.22 0.00
50_F 229_Q 1.04 0.21 0.00
479_A 180_A 1.03 0.20 0.00
14_L 201_T 1.01 0.19 0.00
135_A 167_E 1.01 0.19 0.00
185_L 59_S 1.01 0.19 0.00
272_V 125_L 1.00 0.19 0.00
430_L 154_I 1.00 0.19 0.00
483_V 199_D 1.00 0.19 0.00
340_A 158_L 1.00 0.19 0.00
276_C 234_S 0.97 0.18 0.00
42_I 242_A 0.97 0.17 0.00
345_L 59_S 0.96 0.17 0.00
235_A 47_L 0.96 0.17 0.00
201_E 187_A 0.95 0.17 0.00
298_T 131_A 0.95 0.17 0.00
502_P 252_L 0.95 0.17 0.00
5_V 213_A 0.95 0.17 0.00
306_V 236_I 0.94 0.16 0.00
196_S 236_I 0.93 0.16 0.00
205_Q 224_M 0.93 0.16 0.00
488_V 42_F 0.93 0.16 0.00
231_L 241_L 0.93 0.16 0.00
394_A 201_T 0.93 0.16 0.00
308_L 75_E 0.92 0.16 0.00
408_A 256_I 0.92 0.16 0.00
55_R 220_A 0.92 0.16 0.00
394_A 86_R 0.92 0.15 0.00
599_A 250_K 0.92 0.15 0.00
525_M 46_Q 0.92 0.15 0.00
497_H 215_F 0.92 0.15 0.00
44_W 109_D 0.92 0.15 0.00
11_I 182_N 0.91 0.15 0.00
150_V 63_G 0.91 0.15 0.00
570_I 151_P 0.91 0.15 0.00
392_T 216_L 0.90 0.15 0.00
322_C 96_D 0.90 0.15 0.00
531_T 216_L 0.90 0.15 0.00
196_S 38_P 0.90 0.14 0.00
291_F 254_Q 0.90 0.14 0.00
298_T 74_D 0.89 0.14 0.00
13_S 28_I 0.89 0.14 0.00
275_V 206_D 0.89 0.14 0.00
57_I 243_A 0.89 0.14 0.00
162_K 43_D 0.88 0.14 0.00
59_V 84_Q 0.88 0.14 0.00
483_V 220_A 0.88 0.14 0.00
12_A 81_P 0.88 0.14 0.00
449_T 213_A 0.88 0.14 0.00
580_R 202_P 0.88 0.14 0.00
545_R 240_V 0.88 0.14 0.00
371_M 250_K 0.87 0.14 0.00
202_I 110_H 0.87 0.14 0.00
66_G 47_L 0.87 0.14 0.00
484_F 216_L 0.87 0.14 0.00
278_M 130_R 0.87 0.14 0.00
128_A 175_H 0.86 0.13 0.00
483_V 230_V 0.85 0.13 0.00
28_A 215_F 0.85 0.13 0.00
340_A 240_V 0.85 0.13 0.00
11_I 87_A 0.85 0.13 0.00
103_A 124_S 0.85 0.13 0.00
627_L 249_N 0.85 0.13 0.00
276_C 141_L 0.85 0.13 0.00
87_V 81_P 0.85 0.13 0.00
15_I 74_D 0.84 0.13 0.00
50_F 220_A 0.84 0.13 0.00
5_V 240_V 0.84 0.12 0.00
426_Y 74_D 0.84 0.12 0.00
618_L 125_L 0.84 0.12 0.00
630_V 46_Q 0.83 0.12 0.00
193_L 242_A 0.83 0.12 0.00
63_V 86_R 0.83 0.12 0.00
227_L 141_L 0.83 0.12 0.00
460_A 256_I 0.82 0.12 0.00
295_I 82_E 0.82 0.12 0.00
6_L 200_G 0.82 0.12 0.00
135_A 64_L 0.82 0.12 0.00
141_M 214_A 0.82 0.12 0.00
18_L 242_A 0.81 0.12 0.00
571_F 241_L 0.81 0.12 0.00
617_Y 241_L 0.81 0.12 0.00
530_I 91_N 0.81 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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