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OPENSEQ.org
cI_E_cIII_cyt1
Genes: A B A+B
Length: 147 263 369
Sequences: 3696 574 173
Seq/Len: 25.14 2.18 0.47
MirrorTree (Pazo et al. 2001) 0.35
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 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.05
∞ 0.01 0.02 0.42
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
22_V 202_P 1.69 0.68 0.00
126_T 242_A 1.62 0.63 0.00
95_S 242_A 1.35 0.43 0.00
82_A 105_R 1.35 0.43 0.00
99_G 44_Q 1.34 0.42 0.00
10_I 39_F 1.32 0.41 0.00
95_S 59_S 1.31 0.40 0.00
95_S 73_A 1.31 0.40 0.00
119_R 241_L 1.29 0.39 0.00
115_V 105_R 1.28 0.38 0.00
112_A 64_L 1.27 0.37 0.00
101_V 153_Y 1.26 0.37 0.00
35_W 33_F 1.25 0.36 0.00
40_R 240_V 1.23 0.34 0.00
25_G 17_Q 1.20 0.33 0.00
22_V 155_H 1.18 0.31 0.00
92_I 146_N 1.17 0.30 0.00
57_V 47_L 1.15 0.29 0.00
66_A 184_I 1.14 0.28 0.00
29_L 38_P 1.13 0.28 0.00
72_A 29_E 1.12 0.28 0.00
94_E 41_K 1.09 0.26 0.00
29_L 90_A 1.08 0.25 0.00
82_A 251_K 1.07 0.25 0.00
37_L 46_Q 1.07 0.24 0.00
26_L 130_R 1.07 0.24 0.00
30_M 249_N 1.05 0.24 0.00
47_N 128_K 1.05 0.23 0.00
95_S 6_A 1.05 0.23 0.00
96_G 142_S 1.05 0.23 0.00
47_N 28_I 1.02 0.22 0.00
92_I 147_G 1.02 0.22 0.00
21_I 53_V 1.02 0.22 0.00
16_F 67_V 1.00 0.21 0.00
100_F 135_G 1.00 0.21 0.00
18_I 63_G 1.00 0.21 0.00
99_G 84_Q 0.99 0.20 0.00
126_T 146_N 0.99 0.20 0.00
109_V 33_F 0.98 0.20 0.00
16_F 230_V 0.98 0.20 0.00
38_G 96_D 0.98 0.20 0.00
119_R 246_Y 0.97 0.19 0.00
20_L 85_V 0.97 0.19 0.00
91_S 91_N 0.97 0.19 0.00
20_L 180_A 0.96 0.19 0.00
55_D 69_L 0.96 0.19 0.00
20_L 145_F 0.95 0.18 0.00
112_A 13_A 0.95 0.18 0.00
115_V 137_Y 0.95 0.18 0.00
16_F 156_A 0.95 0.18 0.00
108_F 14_G 0.94 0.18 0.00
109_V 181_G 0.94 0.18 0.00
110_L 153_Y 0.94 0.18 0.00
38_G 245_L 0.94 0.18 0.00
34_G 191_S 0.94 0.18 0.00
90_T 141_L 0.94 0.18 0.00
20_L 52_Q 0.94 0.18 0.00
68_F 228_K 0.93 0.17 0.00
99_G 249_N 0.93 0.17 0.00
55_D 213_A 0.93 0.17 0.00
92_I 233_V 0.92 0.17 0.00
23_A 67_V 0.90 0.16 0.00
92_I 46_Q 0.90 0.16 0.00
95_S 8_G 0.90 0.16 0.00
22_V 100_E 0.89 0.16 0.00
108_F 87_A 0.89 0.16 0.00
34_G 234_S 0.89 0.16 0.00
91_S 60_A 0.89 0.16 0.00
23_A 229_Q 0.89 0.16 0.00
21_I 130_R 0.88 0.15 0.00
100_F 181_G 0.88 0.15 0.00
82_A 153_Y 0.88 0.15 0.00
111_L 71_T 0.88 0.15 0.00
18_I 178_A 0.88 0.15 0.00
117_L 153_Y 0.88 0.15 0.00
25_G 144_L 0.88 0.15 0.00
60_A 256_I 0.87 0.15 0.00
9_V 9_T 0.87 0.15 0.00
32_V 192_D 0.87 0.15 0.00
12_H 83_D 0.86 0.15 0.00
31_L 106_V 0.86 0.15 0.00
31_L 242_A 0.86 0.15 0.00
37_L 154_I 0.86 0.15 0.00
99_G 182_N 0.86 0.14 0.00
62_L 191_S 0.86 0.14 0.00
90_T 136_P 0.86 0.14 0.00
17_A 36_E 0.85 0.14 0.00
37_L 48_Q 0.85 0.14 0.00
25_G 11_A 0.85 0.14 0.00
95_S 18_E 0.85 0.14 0.00
29_L 145_F 0.85 0.14 0.00
98_V 91_N 0.84 0.14 0.00
95_S 134_H 0.84 0.14 0.00
93_R 163_G 0.84 0.14 0.00
14_W 82_E 0.84 0.14 0.00
91_S 219_T 0.83 0.14 0.00
80_V 253_W 0.83 0.14 0.00
91_S 205_V 0.83 0.14 0.00
34_G 197_Y 0.83 0.14 0.00
24_I 239_I 0.83 0.14 0.00
92_I 208_M 0.83 0.14 0.00
35_W 83_D 0.83 0.14 0.00
42_R 47_L 0.83 0.14 0.00
34_G 98_E 0.83 0.14 0.00
29_L 52_Q 0.83 0.14 0.00
72_A 241_L 0.83 0.13 0.00
66_A 245_L 0.83 0.13 0.00
94_E 151_P 0.83 0.13 0.00
109_V 153_Y 0.83 0.13 0.00
95_S 65_R 0.83 0.13 0.00
104_A 209_A 0.82 0.13 0.00
17_A 201_T 0.82 0.13 0.00
108_F 36_E 0.82 0.13 0.00
82_A 162_D 0.82 0.13 0.00
124_D 193_D 0.82 0.13 0.00
14_W 223_K 0.81 0.13 0.00
126_T 147_G 0.81 0.13 0.00
17_A 164_E 0.81 0.13 0.00
105_I 24_A 0.81 0.13 0.00
26_L 156_A 0.81 0.13 0.00
26_L 115_S 0.81 0.13 0.00
124_D 115_S 0.81 0.13 0.00
29_L 208_M 0.80 0.12 0.00
99_G 220_A 0.80 0.12 0.00
20_L 208_M 0.80 0.12 0.00
126_T 156_A 0.80 0.12 0.00
119_R 38_P 0.80 0.12 0.00
30_M 182_N 0.80 0.12 0.00
35_W 97_P 0.80 0.12 0.00
38_G 35_F 0.80 0.12 0.00
31_L 202_P 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
2960 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2959 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
2958 0.52 cI_A_10_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2957 0.79 cI_A_20_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2956 0.79 cI_A_10_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
2425 0.77 cI_E_cIII_cyt1_4 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.22 Done - Shared
2419 0.76 cI_E_cIII_cyt1_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.16 Done - Shared
2418 0.74 cI_E_cIII_cyt1_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.34 Done - Shared
2292 0.47 cI_E_cIII_cyt1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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