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OPENSEQ.org
cI_E_6_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 239 440 662
Sequences: 740 3285 197
Seq/Len: 3.1 7.47 0.3
MirrorTree (Pazo et al. 2001) 0.48
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.00
100 0.01 0.00 0.01
∞ 0.04 0.01 0.29
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
23_A 395_A 1.67 0.53 0.00
54_S 15_F 1.41 0.36 0.00
53_L 328_A 1.32 0.30 0.00
97_G 58_Q 1.29 0.29 0.00
159_V 414_I 1.28 0.28 0.00
92_H 385_A 1.21 0.25 0.00
182_G 88_N 1.20 0.24 0.00
131_S 207_A 1.17 0.23 0.00
53_L 417_P 1.17 0.22 0.00
46_A 196_S 1.16 0.22 0.00
124_L 112_I 1.15 0.21 0.00
169_F 364_K 1.13 0.21 0.00
158_T 393_A 1.13 0.21 0.00
146_M 172_V 1.11 0.20 0.00
98_T 220_G 1.11 0.20 0.00
62_A 172_V 1.10 0.20 0.00
93_I 116_L 1.09 0.19 0.00
194_A 407_I 1.09 0.19 0.00
166_I 284_N 1.08 0.19 0.00
17_P 304_I 1.05 0.18 0.00
42_V 112_I 1.05 0.18 0.00
58_I 75_L 1.05 0.17 0.00
158_T 73_V 1.05 0.17 0.00
163_A 66_V 1.05 0.17 0.00
97_G 359_Y 1.04 0.17 0.00
27_M 136_Y 1.04 0.17 0.00
167_D 19_L 1.04 0.17 0.00
103_I 248_F 1.03 0.17 0.00
158_T 93_L 1.03 0.17 0.00
54_S 416_K 1.02 0.17 0.00
85_Q 373_D 1.02 0.16 0.00
163_A 372_V 1.02 0.16 0.00
125_S 116_L 1.02 0.16 0.00
75_V 63_I 1.01 0.16 0.00
85_Q 258_V 0.99 0.15 0.00
108_D 115_G 0.98 0.15 0.00
14_E 208_L 0.98 0.15 0.00
27_M 371_A 0.98 0.15 0.00
158_T 63_I 0.98 0.15 0.00
93_I 375_V 0.98 0.15 0.00
160_E 179_W 0.97 0.15 0.00
106_A 394_L 0.97 0.15 0.00
53_L 175_A 0.97 0.15 0.00
27_M 395_A 0.97 0.15 0.00
93_I 207_A 0.96 0.14 0.00
61_C 31_D 0.95 0.14 0.00
192_P 204_V 0.95 0.14 0.00
61_C 29_V 0.95 0.14 0.00
148_Q 45_W 0.95 0.14 0.00
125_S 207_A 0.95 0.14 0.00
61_C 410_L 0.94 0.14 0.00
124_L 128_T 0.94 0.14 0.00
11_D 221_N 0.94 0.14 0.00
175_P 28_L 0.93 0.13 0.00
59_E 219_T 0.93 0.13 0.00
122_H 58_Q 0.93 0.13 0.00
68_P 398_A 0.93 0.13 0.00
93_I 68_H 0.93 0.13 0.00
39_I 134_L 0.92 0.13 0.00
93_I 254_F 0.92 0.13 0.00
35_Q 53_F 0.92 0.13 0.00
77_T 128_T 0.92 0.13 0.00
117_I 51_L 0.92 0.13 0.00
51_G 117_Y 0.92 0.13 0.00
115_E 393_A 0.91 0.13 0.00
16_T 156_F 0.91 0.13 0.00
20_L 374_F 0.91 0.13 0.00
108_D 213_I 0.91 0.13 0.00
234_A 344_A 0.91 0.13 0.00
166_I 342_V 0.90 0.12 0.00
165_L 16_E 0.89 0.12 0.00
119_P 410_L 0.88 0.12 0.00
11_D 238_K 0.88 0.12 0.00
27_M 341_L 0.88 0.12 0.00
65_L 56_V 0.87 0.12 0.00
24_R 106_L 0.87 0.12 0.00
147_A 402_A 0.87 0.12 0.00
132_W 49_I 0.87 0.12 0.00
53_L 338_G 0.87 0.12 0.00
166_I 376_V 0.87 0.12 0.00
109_L 107_A 0.87 0.12 0.00
117_I 49_I 0.87 0.12 0.00
61_C 39_K 0.87 0.12 0.00
148_Q 205_I 0.87 0.12 0.00
82_F 392_I 0.86 0.11 0.00
27_M 261_V 0.86 0.11 0.00
161_K 93_L 0.86 0.11 0.00
25_A 339_A 0.86 0.11 0.00
21_E 242_L 0.86 0.11 0.00
146_M 196_S 0.86 0.11 0.00
24_R 205_I 0.86 0.11 0.00
77_T 60_A 0.86 0.11 0.00
167_D 25_I 0.86 0.11 0.00
209_A 25_I 0.85 0.11 0.00
86_P 129_W 0.85 0.11 0.00
207_S 257_A 0.85 0.11 0.00
93_I 130_I 0.85 0.11 0.00
108_D 242_L 0.85 0.11 0.00
68_P 346_V 0.84 0.11 0.00
98_T 122_K 0.84 0.11 0.00
132_W 248_F 0.84 0.11 0.00
149_I 285_P 0.84 0.11 0.00
95_I 410_L 0.84 0.11 0.00
170_A 28_L 0.83 0.11 0.00
53_L 372_V 0.83 0.11 0.00
59_E 396_G 0.83 0.11 0.00
167_D 201_L 0.83 0.11 0.00
46_A 355_R 0.83 0.11 0.00
109_L 379_W 0.83 0.11 0.00
165_L 30_Y 0.83 0.10 0.00
23_A 393_A 0.83 0.10 0.00
171_A 213_I 0.83 0.10 0.00
113_C 180_L 0.83 0.10 0.00
26_Q 221_N 0.83 0.10 0.00
132_W 343_M 0.83 0.10 0.00
106_A 28_L 0.83 0.10 0.00
68_P 392_I 0.82 0.10 0.00
121_P 328_A 0.82 0.10 0.00
132_W 50_V 0.82 0.10 0.00
61_C 59_I 0.82 0.10 0.00
21_E 25_I 0.82 0.10 0.00
89_S 175_A 0.82 0.10 0.00
36_Q 17_R 0.81 0.10 0.00
167_D 253_L 0.81 0.10 0.00
109_L 413_I 0.81 0.10 0.00
59_E 355_R 0.81 0.10 0.00
133_E 72_H 0.81 0.10 0.00
202_E 232_G 0.81 0.10 0.00
82_F 117_Y 0.81 0.10 0.00
58_I 284_N 0.81 0.10 0.00
210_R 326_I 0.81 0.10 0.00
193_T 106_L 0.81 0.10 0.00
167_D 287_V 0.80 0.10 0.00
95_I 175_A 0.80 0.10 0.00
93_I 393_A 0.80 0.10 0.00
184_F 89_G 0.80 0.10 0.00
51_G 33_L 0.80 0.10 0.00
21_E 334_I 0.80 0.10 0.00
26_Q 248_F 0.80 0.10 0.00
72_A 346_V 0.80 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
3019 0.3 cI_E_6_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3018 0.31 cI_E_2_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2800 0.29 cI_E_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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