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OPENSEQ.org
cI_K_cIII_cyt1_20_Pdenitr
Genes: A B A+B
Length: 101 263 349
Sequences: 1319 651 185
Seq/Len: 13.06 2.48 0.53
MirrorTree (Pazo et al. 2001) 0.40
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 0.01 0.02 0.00
20 0.01 0.02 0.00
100 0.02 0.02 0.04
∞ 0.03 0.02 0.51
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
42_A 82_E 1.84 0.80 0.05
17_T 187_A 1.39 0.50 0.02
61_V 84_Q 1.32 0.44 0.01
31_V 144_L 1.24 0.38 0.01
96_V 44_Q 1.21 0.36 0.01
90_T 33_F 1.21 0.36 0.01
66_V 241_L 1.20 0.35 0.01
11_G 205_V 1.19 0.34 0.01
69_V 141_L 1.13 0.30 0.01
36_I 180_A 1.11 0.29 0.01
62_F 221_E 1.10 0.28 0.01
85_F 224_M 1.08 0.27 0.01
13_I 220_A 1.06 0.26 0.01
49_A 206_D 1.05 0.26 0.01
72_A 135_G 1.05 0.26 0.01
90_T 113_T 1.05 0.26 0.01
19_I 63_G 1.05 0.25 0.01
76_I 249_N 1.05 0.25 0.01
84_F 42_F 1.05 0.25 0.01
5_T 240_V 1.03 0.24 0.01
19_I 167_E 1.03 0.24 0.01
11_G 184_I 1.03 0.24 0.01
81_L 111_F 1.03 0.24 0.01
11_G 30_D 1.02 0.24 0.01
81_L 112_P 1.02 0.23 0.01
12_A 73_A 1.01 0.23 0.01
24_V 38_P 1.01 0.23 0.01
84_F 154_I 1.00 0.23 0.01
94_E 101_E 1.00 0.22 0.00
18_G 190_L 1.00 0.22 0.00
36_I 16_A 0.99 0.22 0.00
19_I 130_R 0.99 0.22 0.00
66_V 59_S 0.98 0.21 0.00
36_I 12_P 0.98 0.21 0.00
96_V 67_V 0.97 0.21 0.00
65_F 235_V 0.96 0.20 0.00
17_T 83_D 0.96 0.20 0.00
66_V 226_D 0.95 0.20 0.00
97_N 173_L 0.95 0.20 0.00
87_N 181_G 0.95 0.20 0.00
83_V 99_T 0.95 0.20 0.00
97_N 226_D 0.94 0.20 0.00
62_F 143_Q 0.94 0.19 0.00
64_M 223_K 0.94 0.19 0.00
29_V 23_H 0.94 0.19 0.00
87_N 36_E 0.94 0.19 0.00
42_A 166_K 0.94 0.19 0.00
43_V 246_Y 0.94 0.19 0.00
54_L 134_H 0.93 0.19 0.00
76_I 84_Q 0.93 0.19 0.00
58_A 256_I 0.93 0.19 0.00
3_G 166_K 0.93 0.19 0.00
76_I 79_Q 0.92 0.18 0.00
11_G 75_E 0.92 0.18 0.00
5_T 151_P 0.92 0.18 0.00
24_V 79_Q 0.92 0.18 0.00
57_L 49_R 0.92 0.18 0.00
90_T 60_A 0.91 0.18 0.00
85_F 147_G 0.91 0.18 0.00
53_H 26_A 0.91 0.18 0.00
47_F 20_G 0.91 0.18 0.00
85_F 141_L 0.91 0.18 0.00
47_F 59_S 0.90 0.18 0.00
29_V 59_S 0.90 0.17 0.00
9_V 33_F 0.90 0.17 0.00
22_I 142_S 0.90 0.17 0.00
17_T 196_T 0.90 0.17 0.00
18_G 197_Y 0.90 0.17 0.00
63_T 230_V 0.90 0.17 0.00
47_F 11_A 0.89 0.17 0.00
87_N 249_N 0.89 0.17 0.00
90_T 102_D 0.89 0.17 0.00
96_V 51_L 0.88 0.17 0.00
66_V 167_E 0.88 0.17 0.00
31_V 161_Y 0.88 0.16 0.00
47_F 237_F 0.88 0.16 0.00
57_L 108_T 0.88 0.16 0.00
65_F 85_V 0.87 0.16 0.00
42_A 229_Q 0.87 0.16 0.00
92_A 184_I 0.87 0.16 0.00
45_I 42_F 0.87 0.16 0.00
14_L 245_L 0.87 0.16 0.00
47_F 25_A 0.87 0.16 0.00
7_Y 196_T 0.86 0.16 0.00
58_A 100_E 0.86 0.16 0.00
20_F 149_G 0.86 0.16 0.00
42_A 193_D 0.86 0.16 0.00
97_N 20_G 0.86 0.16 0.00
90_T 249_N 0.86 0.15 0.00
80_I 152_E 0.85 0.15 0.00
57_L 197_Y 0.85 0.15 0.00
90_T 182_N 0.85 0.15 0.00
9_V 82_E 0.85 0.15 0.00
27_K 46_Q 0.85 0.15 0.00
99_M 60_A 0.85 0.15 0.00
28_N 238_L 0.85 0.15 0.00
74_A 250_K 0.84 0.15 0.00
12_A 36_E 0.84 0.15 0.00
47_F 83_D 0.84 0.15 0.00
49_A 85_V 0.84 0.15 0.00
23_F 59_S 0.84 0.15 0.00
24_V 229_Q 0.84 0.15 0.00
42_A 129_A 0.83 0.15 0.00
35_S 181_G 0.83 0.15 0.00
74_A 151_P 0.83 0.15 0.00
1_M 169_A 0.83 0.15 0.00
29_V 163_G 0.83 0.14 0.00
97_N 188_A 0.83 0.14 0.00
34_M 207_Q 0.83 0.14 0.00
47_F 163_G 0.83 0.14 0.00
84_F 55_T 0.83 0.14 0.00
24_V 195_V 0.82 0.14 0.00
11_G 77_G 0.82 0.14 0.00
17_T 236_I 0.82 0.14 0.00
96_V 159_T 0.82 0.14 0.00
4_L 26_A 0.82 0.14 0.00
10_V 67_V 0.82 0.14 0.00
42_A 226_D 0.82 0.14 0.00
47_F 24_A 0.82 0.14 0.00
58_A 42_F 0.82 0.14 0.00
35_S 161_Y 0.82 0.14 0.00
36_I 159_T 0.81 0.14 0.00
39_M 191_S 0.81 0.14 0.00
98_V 33_F 0.81 0.14 0.00
94_E 225_M 0.81 0.14 0.00
99_M 158_L 0.81 0.14 0.00
53_H 95_T 0.81 0.14 0.00
96_V 69_L 0.81 0.14 0.00
17_T 173_L 0.81 0.14 0.00
18_G 40_G 0.81 0.14 0.00
32_I 146_N 0.81 0.14 0.00
89_G 199_D 0.80 0.14 0.00
11_G 161_Y 0.80 0.13 0.00
35_S 169_A 0.80 0.13 0.00
36_I 30_D 0.80 0.13 0.00
61_V 52_Q 0.80 0.13 0.00
29_V 25_A 0.80 0.13 0.00
97_N 190_L 0.80 0.13 0.00
42_A 54_Y 0.80 0.13 0.00
42_A 16_A 0.80 0.13 0.00
85_F 144_L 0.79 0.13 0.00
96_V 250_K 0.79 0.13 0.00
88_R 214_A 0.79 0.13 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
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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