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OPENSEQ.org
cI_K_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 101 263 348
Sequences: 1319 954 282
Seq/Len: 13.06 3.63 0.81
MirrorTree (Pazo et al. 2001) 0.42
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.05
∞ 0.03 0.01 0.77
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
42_A 82_E 1.84 0.89 0.28
17_T 236_I 1.64 0.80 0.17
88_R 214_A 1.45 0.67 0.10
17_T 187_A 1.35 0.59 0.08
16_V 131_A 1.32 0.56 0.07
97_N 158_L 1.28 0.53 0.06
5_T 240_V 1.28 0.53 0.06
12_A 73_A 1.27 0.53 0.06
90_T 33_F 1.23 0.49 0.05
7_Y 214_A 1.14 0.41 0.04
66_V 81_P 1.14 0.40 0.04
90_T 249_N 1.12 0.40 0.04
99_M 254_Q 1.08 0.36 0.03
94_E 101_E 1.08 0.36 0.03
47_F 237_F 1.08 0.36 0.03
23_F 59_S 1.07 0.35 0.03
57_L 108_T 1.06 0.34 0.03
7_Y 243_A 1.06 0.34 0.03
11_G 205_V 1.03 0.32 0.03
42_A 54_Y 1.02 0.31 0.02
10_V 219_T 1.02 0.31 0.02
18_G 178_A 1.01 0.31 0.02
62_F 221_E 1.01 0.31 0.02
88_R 35_F 1.01 0.30 0.02
90_T 158_L 1.00 0.30 0.02
36_I 16_A 0.99 0.29 0.02
27_K 246_Y 0.99 0.29 0.02
1_M 49_R 0.98 0.28 0.02
96_V 250_K 0.98 0.28 0.02
13_I 243_A 0.97 0.27 0.02
47_F 25_A 0.95 0.26 0.02
10_V 73_A 0.95 0.26 0.02
39_M 213_A 0.95 0.26 0.02
39_M 151_P 0.94 0.26 0.02
97_N 188_A 0.94 0.25 0.02
84_F 55_T 0.94 0.25 0.02
47_F 24_A 0.93 0.25 0.02
81_L 45_H 0.93 0.25 0.02
58_A 100_E 0.93 0.25 0.02
81_L 84_Q 0.93 0.25 0.02
11_G 30_D 0.93 0.25 0.02
84_F 154_I 0.92 0.24 0.02
7_Y 126_M 0.92 0.24 0.02
66_V 59_S 0.92 0.24 0.02
36_I 12_P 0.91 0.23 0.01
97_N 20_G 0.91 0.23 0.01
99_M 60_A 0.90 0.23 0.01
61_V 216_L 0.90 0.23 0.01
57_L 179_F 0.90 0.23 0.01
29_V 131_A 0.90 0.23 0.01
19_I 239_I 0.89 0.23 0.01
16_V 76_G 0.89 0.22 0.01
99_M 140_G 0.89 0.22 0.01
1_M 241_L 0.89 0.22 0.01
14_L 141_L 0.88 0.22 0.01
31_V 157_V 0.88 0.21 0.01
81_L 241_L 0.87 0.21 0.01
47_F 95_T 0.87 0.21 0.01
24_V 104_P 0.87 0.21 0.01
34_M 256_I 0.87 0.21 0.01
53_H 206_D 0.87 0.21 0.01
61_V 254_Q 0.87 0.21 0.01
48_V 45_H 0.87 0.21 0.01
18_G 200_G 0.86 0.21 0.01
61_V 202_P 0.86 0.21 0.01
81_L 112_P 0.86 0.20 0.01
5_T 250_K 0.86 0.20 0.01
97_N 177_A 0.86 0.20 0.01
20_F 213_A 0.85 0.20 0.01
76_I 249_N 0.85 0.20 0.01
6_H 74_D 0.84 0.20 0.01
48_V 217_M 0.84 0.20 0.01
16_V 152_E 0.84 0.20 0.01
30_I 118_G 0.84 0.19 0.01
61_V 84_Q 0.84 0.19 0.01
27_K 146_N 0.84 0.19 0.01
4_L 26_A 0.83 0.19 0.01
35_S 86_R 0.83 0.19 0.01
66_V 194_Q 0.83 0.19 0.01
88_R 129_A 0.83 0.19 0.01
24_V 38_P 0.83 0.19 0.01
83_V 230_V 0.83 0.19 0.01
35_S 236_I 0.83 0.19 0.01
2_I 65_R 0.83 0.19 0.01
10_V 154_I 0.82 0.18 0.01
19_I 113_T 0.82 0.18 0.01
47_F 20_G 0.82 0.18 0.01
27_K 42_F 0.82 0.18 0.01
87_N 249_N 0.81 0.18 0.01
76_I 79_Q 0.81 0.18 0.01
9_V 33_F 0.81 0.18 0.01
27_K 196_T 0.81 0.17 0.01
88_R 49_R 0.80 0.17 0.01
88_R 37_G 0.80 0.17 0.01
53_H 256_I 0.80 0.17 0.01
13_I 247_L 0.80 0.17 0.01
47_F 163_G 0.80 0.17 0.01
5_T 151_P 0.79 0.17 0.01
29_V 157_V 0.79 0.17 0.01
36_I 168_E 0.79 0.17 0.01
2_I 214_A 0.79 0.17 0.01
97_N 226_D 0.79 0.17 0.01
42_A 226_D 0.79 0.17 0.01
42_A 74_D 0.78 0.16 0.01
47_F 21_D 0.78 0.16 0.01
12_A 36_E 0.78 0.16 0.01
100_K 237_F 0.78 0.16 0.01
10_V 67_V 0.78 0.16 0.01
6_H 224_M 0.77 0.16 0.01
99_M 112_P 0.77 0.16 0.01
8_L 240_V 0.77 0.16 0.01
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
2919 0 cI_K_60_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) Killed - Shared
2914 0.67 cI_K_40_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.80 Done - Shared
2913 1.01 cI_K_10_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2912 0.53 cI_K_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2911 0.82 cI_K_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
2910 0.81 cI_K_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
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