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OPENSEQ.org
carO-oxa23
Genes: A B A+B
Length: 273 247 513
Sequences: 11667 196 116
Seq/Len: 42.74 0.79 0.23
MirrorTree (Pazo et al. 2001) 0.33
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 0.03 0.01 0.00
2 0.03 0.01 0.01
5 0.04 0.01 0.01
10 0.05 0.01 0.01
20 0.06 0.01 0.01
100 0.15 0.01 0.06
∞ 0.23 0.02 0.22
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
262_L 145_G 1.40 0.30 0.00
101_F 243_V 1.40 0.29 0.00
173_T 114_Q 1.36 0.28 0.00
101_F 239_G 1.29 0.24 0.00
183_Q 168_A 1.17 0.19 0.00
29_P 67_L 1.16 0.19 0.00
16_S 243_V 1.15 0.18 0.00
218_G 174_G 1.12 0.17 0.00
218_G 190_G 1.12 0.17 0.00
52_V 245_F 1.12 0.17 0.00
133_E 131_L 1.11 0.17 0.00
55_I 220_L 1.09 0.16 0.00
192_S 102_I 1.09 0.16 0.00
134_L 197_P 1.09 0.16 0.00
259_R 168_A 1.05 0.15 0.00
52_V 189_V 1.05 0.15 0.00
143_M 63_V 1.04 0.15 0.00
172_V 191_A 1.03 0.14 0.00
173_T 218_Q 1.02 0.14 0.00
53_L 154_G 1.02 0.14 0.00
79_S 174_G 1.01 0.14 0.00
79_S 190_G 1.01 0.14 0.00
199_V 144_D 1.01 0.14 0.00
218_G 121_G 1.01 0.14 0.00
24_L 179_F 1.01 0.14 0.00
178_V 216_L 1.01 0.14 0.00
218_G 50_G 1.01 0.14 0.00
126_S 174_G 1.01 0.14 0.00
126_S 190_G 1.01 0.14 0.00
86_A 48_T 1.00 0.14 0.00
173_T 42_A 1.00 0.13 0.00
98_N 148_F 0.99 0.13 0.00
243_A 115_G 0.99 0.13 0.00
231_T 157_I 0.99 0.13 0.00
214_F 213_G 0.98 0.13 0.00
112_A 161_L 0.97 0.13 0.00
177_E 234_K 0.97 0.13 0.00
16_S 29_S 0.97 0.12 0.00
21_Q 104_P 0.97 0.12 0.00
217_T 66_A 0.96 0.12 0.00
109_S 53_G 0.96 0.12 0.00
209_N 243_V 0.96 0.12 0.00
101_F 171_I 0.96 0.12 0.00
62_N 143_I 0.95 0.12 0.00
217_T 174_G 0.95 0.12 0.00
217_T 190_G 0.95 0.12 0.00
184_L 56_L 0.95 0.12 0.00
48_N 120_A 0.95 0.12 0.00
218_G 169_P 0.95 0.12 0.00
12_S 171_I 0.94 0.12 0.00
60_K 102_I 0.94 0.12 0.00
56_Q 195_G 0.93 0.12 0.00
82_K 174_G 0.93 0.12 0.00
82_K 190_G 0.93 0.12 0.00
16_S 226_K 0.93 0.12 0.00
97_I 60_N 0.93 0.11 0.00
90_L 120_A 0.92 0.11 0.00
197_A 242_G 0.92 0.11 0.00
267_L 157_I 0.92 0.11 0.00
266_S 119_A 0.92 0.11 0.00
210_G 220_L 0.91 0.11 0.00
41_H 42_A 0.91 0.11 0.00
202_M 129_Y 0.91 0.11 0.00
45_D 247_W 0.90 0.11 0.00
182_S 160_N 0.90 0.11 0.00
176_Q 119_A 0.90 0.11 0.00
218_G 104_P 0.90 0.11 0.00
79_S 121_G 0.90 0.11 0.00
151_G 50_G 0.90 0.11 0.00
16_S 199_V 0.90 0.11 0.00
79_S 50_G 0.89 0.11 0.00
126_S 121_G 0.89 0.10 0.00
42_Q 193_Y 0.89 0.10 0.00
126_S 50_G 0.89 0.10 0.00
114_E 120_A 0.89 0.10 0.00
15_L 170_Y 0.88 0.10 0.00
100_I 122_A 0.88 0.10 0.00
42_Q 124_Y 0.88 0.10 0.00
213_I 193_Y 0.88 0.10 0.00
22_H 100_A 0.88 0.10 0.00
119_L 36_Q 0.87 0.10 0.00
15_L 172_G 0.87 0.10 0.00
224_K 47_G 0.87 0.10 0.00
43_Y 242_G 0.87 0.10 0.00
61_I 35_N 0.86 0.10 0.00
13_L 193_Y 0.86 0.10 0.00
233_W 157_I 0.86 0.10 0.00
22_H 92_D 0.86 0.10 0.00
228_G 118_V 0.86 0.10 0.00
54_V 130_D 0.86 0.10 0.00
118_T 179_F 0.86 0.10 0.00
91_E 95_L 0.86 0.10 0.00
216_K 174_G 0.86 0.10 0.00
216_K 190_G 0.86 0.10 0.00
99_E 143_I 0.85 0.10 0.00
66_N 47_G 0.85 0.10 0.00
203_L 122_A 0.85 0.10 0.00
81_F 128_Q 0.85 0.10 0.00
130_V 46_V 0.84 0.09 0.00
42_Q 183_W 0.84 0.09 0.00
96_D 5_R 0.84 0.09 0.00
243_A 44_A 0.84 0.09 0.00
155_A 142_E 0.84 0.09 0.00
47_K 79_D 0.84 0.09 0.00
45_D 141_V 0.84 0.09 0.00
232_G 188_E 0.83 0.09 0.00
24_L 7_L 0.83 0.09 0.00
99_E 228_A 0.83 0.09 0.00
267_L 59_A 0.83 0.09 0.00
140_L 65_L 0.83 0.09 0.00
16_S 120_A 0.83 0.09 0.00
173_T 176_A 0.83 0.09 0.00
79_S 169_P 0.83 0.09 0.00
44_F 161_L 0.83 0.09 0.00
54_V 14_L 0.83 0.09 0.00
150_I 41_G 0.83 0.09 0.00
244_F 145_G 0.82 0.09 0.00
52_V 244_N 0.82 0.09 0.00
128_V 174_G 0.82 0.09 0.00
128_V 190_G 0.82 0.09 0.00
82_K 121_G 0.81 0.09 0.00
143_M 120_A 0.81 0.09 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
1275 0.23 carO-oxa23 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1210 0 carO-oxa23 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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