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OPENSEQ.org
cI_I_60_cIII_cytb_60_Pdenitr
Genes: A B A+B
Length: 163 263 406
Sequences: 329 561 141
Seq/Len: 2.02 2.13 0.35
MirrorTree (Pazo et al. 2001) 0.46
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.00
100 0.00 0.02 0.02
∞ 0.01 0.02 0.33
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
16_D 249_N 1.54 0.48 0.00
152_I 130_R 1.53 0.48 0.00
101_T 257_K 1.45 0.42 0.00
73_V 42_F 1.38 0.38 0.00
90_S 208_M 1.36 0.36 0.00
42_G 99_T 1.33 0.34 0.00
77_Q 228_K 1.32 0.34 0.00
28_F 64_L 1.31 0.33 0.00
87_E 208_M 1.30 0.33 0.00
73_V 170_G 1.30 0.33 0.00
13_L 237_F 1.26 0.30 0.00
26_R 166_K 1.25 0.29 0.00
35_L 178_A 1.24 0.29 0.00
19_K 101_E 1.23 0.28 0.00
159_D 47_L 1.20 0.27 0.00
21_F 69_L 1.19 0.26 0.00
7_R 185_Q 1.17 0.25 0.00
90_S 36_E 1.15 0.24 0.00
11_Y 249_N 1.14 0.24 0.00
127_A 230_V 1.14 0.23 0.00
143_A 91_N 1.14 0.23 0.00
44_L 85_V 1.11 0.22 0.00
13_L 164_E 1.09 0.21 0.00
35_L 132_G 1.08 0.21 0.00
73_V 247_L 1.08 0.20 0.00
147_R 110_H 1.07 0.20 0.00
84_E 203_A 1.07 0.20 0.00
23_L 46_Q 1.07 0.20 0.00
58_P 87_A 1.06 0.20 0.00
10_K 130_R 1.05 0.19 0.00
108_F 173_L 1.05 0.19 0.00
143_A 95_T 1.04 0.19 0.00
90_S 203_A 1.04 0.19 0.00
108_F 17_Q 1.03 0.19 0.00
155_N 130_R 1.03 0.18 0.00
156_L 191_S 1.03 0.18 0.00
101_T 203_A 1.02 0.18 0.00
12_F 36_E 1.01 0.18 0.00
131_R 244_L 1.01 0.17 0.00
17_F 224_M 1.01 0.17 0.00
157_Q 101_E 1.00 0.17 0.00
21_F 191_S 1.00 0.17 0.00
7_R 69_L 0.97 0.16 0.00
73_V 92_F 0.97 0.16 0.00
33_P 223_K 0.96 0.16 0.00
25_M 154_I 0.95 0.15 0.00
108_F 237_F 0.95 0.15 0.00
84_E 208_M 0.95 0.15 0.00
23_L 214_A 0.95 0.15 0.00
135_F 217_M 0.94 0.15 0.00
24_G 232_F 0.94 0.15 0.00
143_A 250_K 0.94 0.15 0.00
15_W 107_P 0.94 0.15 0.00
116_D 131_A 0.94 0.15 0.00
151_E 181_G 0.93 0.15 0.00
24_G 78_P 0.93 0.14 0.00
151_E 228_K 0.92 0.14 0.00
127_A 201_T 0.92 0.14 0.00
44_L 241_L 0.92 0.14 0.00
90_S 156_A 0.92 0.14 0.00
28_F 254_Q 0.91 0.14 0.00
90_S 233_V 0.91 0.14 0.00
101_T 208_M 0.90 0.14 0.00
44_L 247_L 0.90 0.14 0.00
24_G 74_D 0.90 0.14 0.00
12_F 191_S 0.90 0.14 0.00
124_F 179_F 0.90 0.14 0.00
130_T 56_E 0.90 0.13 0.00
135_F 130_R 0.90 0.13 0.00
42_G 168_E 0.90 0.13 0.00
124_F 242_A 0.89 0.13 0.00
153_A 47_L 0.89 0.13 0.00
135_F 228_K 0.89 0.13 0.00
33_P 27_H 0.88 0.13 0.00
19_K 164_E 0.88 0.13 0.00
154_R 236_I 0.88 0.13 0.00
39_H 85_V 0.88 0.13 0.00
137_D 194_Q 0.88 0.13 0.00
140_K 239_I 0.88 0.13 0.00
127_A 143_Q 0.88 0.13 0.00
35_L 151_P 0.88 0.13 0.00
9_T 164_E 0.88 0.13 0.00
25_M 141_L 0.88 0.13 0.00
32_K 40_G 0.87 0.13 0.00
28_F 163_G 0.87 0.12 0.00
110_Q 130_R 0.87 0.12 0.00
25_M 173_L 0.86 0.12 0.00
140_K 88_Y 0.86 0.12 0.00
12_F 102_D 0.86 0.12 0.00
146_E 100_E 0.85 0.12 0.00
140_K 193_D 0.85 0.12 0.00
155_N 85_V 0.85 0.12 0.00
82_D 140_G 0.85 0.12 0.00
94_T 256_I 0.84 0.12 0.00
156_L 192_D 0.84 0.12 0.00
85_R 102_D 0.84 0.12 0.00
82_D 234_S 0.84 0.12 0.00
159_D 214_A 0.84 0.12 0.00
127_A 56_E 0.84 0.12 0.00
143_A 137_Y 0.83 0.12 0.00
21_F 96_D 0.83 0.12 0.00
126_Y 148_I 0.83 0.11 0.00
58_P 195_V 0.83 0.11 0.00
147_R 64_L 0.83 0.11 0.00
152_I 85_V 0.82 0.11 0.00
127_A 98_E 0.82 0.11 0.00
5_F 45_H 0.82 0.11 0.00
10_K 56_E 0.82 0.11 0.00
147_R 19_A 0.82 0.11 0.00
156_L 106_V 0.82 0.11 0.00
42_G 247_L 0.82 0.11 0.00
44_L 39_F 0.81 0.11 0.00
10_K 98_E 0.81 0.11 0.00
44_L 154_I 0.81 0.11 0.00
95_R 47_L 0.81 0.11 0.00
77_Q 132_G 0.81 0.11 0.00
23_L 238_L 0.81 0.11 0.00
157_Q 52_Q 0.81 0.11 0.00
73_V 48_Q 0.81 0.11 0.00
156_L 99_T 0.81 0.11 0.00
5_F 16_A 0.81 0.11 0.00
11_Y 115_S 0.81 0.11 0.00
94_T 183_W 0.80 0.11 0.00
41_K 16_A 0.80 0.11 0.00
53_A 96_D 0.80 0.11 0.00
108_F 38_P 0.80 0.11 0.00
160_A 245_L 0.80 0.11 0.00
135_F 39_F 0.80 0.11 0.00
140_K 223_K 0.80 0.10 0.00
126_Y 52_Q 0.80 0.10 0.00
101_T 154_I 0.79 0.10 0.00
139_Q 237_F 0.79 0.10 0.00
45_S 200_G 0.79 0.10 0.00
20_G 83_D 0.79 0.10 0.00
137_D 66_Y 0.79 0.10 0.00
143_A 10_T 0.79 0.10 0.00
137_D 46_Q 0.78 0.10 0.00
131_R 39_F 0.78 0.10 0.00
82_D 147_G 0.78 0.10 0.00
124_F 174_Y 0.78 0.10 0.00
156_L 202_P 0.77 0.10 0.00
147_R 238_L 0.77 0.10 0.00
28_F 252_L 0.77 0.10 0.00
82_D 138_G 0.77 0.10 0.00
158_L 137_Y 0.77 0.10 0.00
24_G 143_Q 0.77 0.10 0.00
18_I 10_T 0.77 0.10 0.00
85_R 210_T 0.77 0.10 0.00
85_R 233_V 0.77 0.10 0.00
85_R 208_M 0.77 0.10 0.00
18_I 108_T 0.77 0.10 0.00
101_T 230_V 0.77 0.10 0.00
20_G 25_A 0.77 0.10 0.00
13_L 19_A 0.77 0.10 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
3057 0.35 cI_I_60_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3056 1.02 cI_I_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3055 0.36 cI_I_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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