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OPENSEQ.org
cI_K_40_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 101 263 348
Sequences: 222 954 232
Seq/Len: 2.2 3.63 0.67
MirrorTree (Pazo et al. 2001) 0.84
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 0.00
100 0.00 0.01 0.03
∞ 0.00 0.01 0.64
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 2.22 0.95 0.80
5_T 240_V 1.35 0.53 0.17
16_V 131_A 1.31 0.50 0.15
17_T 236_I 1.30 0.49 0.15
36_I 16_A 1.28 0.48 0.14
90_T 33_F 1.22 0.42 0.11
57_L 108_T 1.20 0.41 0.10
10_V 67_V 1.17 0.39 0.09
36_I 12_P 1.17 0.38 0.09
35_S 72_L 1.17 0.38 0.09
99_M 112_P 1.15 0.36 0.08
84_F 55_T 1.14 0.36 0.08
61_V 84_Q 1.13 0.36 0.08
88_R 214_A 1.11 0.34 0.07
96_V 250_K 1.10 0.33 0.07
83_V 230_V 1.08 0.32 0.07
53_H 110_H 1.08 0.32 0.07
47_F 95_T 1.07 0.31 0.06
1_M 49_R 1.07 0.31 0.06
61_V 254_Q 1.07 0.31 0.06
81_L 112_P 1.06 0.30 0.06
94_E 101_E 1.06 0.30 0.06
2_I 214_A 1.06 0.30 0.06
81_L 241_L 1.05 0.30 0.06
19_I 239_I 1.04 0.29 0.06
84_F 42_F 1.04 0.29 0.05
29_V 180_A 1.03 0.28 0.05
11_G 205_V 1.02 0.28 0.05
39_M 151_P 1.02 0.28 0.05
5_T 250_K 1.01 0.27 0.05
17_T 196_T 1.01 0.27 0.05
99_M 254_Q 1.00 0.26 0.05
47_F 25_A 1.00 0.26 0.04
31_V 91_N 0.99 0.26 0.04
27_K 246_Y 0.99 0.26 0.04
18_G 178_A 0.98 0.25 0.04
85_F 253_W 0.98 0.25 0.04
16_V 76_G 0.98 0.25 0.04
29_V 59_S 0.98 0.25 0.04
94_E 52_Q 0.97 0.24 0.04
88_R 35_F 0.97 0.24 0.04
6_H 237_F 0.97 0.24 0.04
88_R 125_L 0.97 0.24 0.04
57_L 179_F 0.97 0.24 0.04
29_V 157_V 0.97 0.24 0.04
97_N 20_G 0.96 0.24 0.04
17_T 187_A 0.96 0.24 0.04
66_V 167_E 0.96 0.24 0.04
7_Y 88_Y 0.96 0.23 0.04
27_K 40_G 0.95 0.23 0.04
47_F 83_D 0.95 0.23 0.04
27_K 146_N 0.95 0.23 0.04
7_Y 196_T 0.95 0.23 0.04
87_N 96_D 0.95 0.23 0.04
13_I 206_D 0.95 0.23 0.04
35_S 228_K 0.94 0.23 0.04
24_V 79_Q 0.94 0.23 0.04
12_A 36_E 0.94 0.23 0.04
10_V 219_T 0.94 0.23 0.04
76_I 79_Q 0.94 0.22 0.04
31_V 157_V 0.94 0.22 0.04
31_V 177_A 0.94 0.22 0.04
7_Y 243_A 0.93 0.22 0.03
4_L 26_A 0.93 0.22 0.03
84_F 154_I 0.93 0.22 0.03
31_V 53_V 0.92 0.21 0.03
31_V 39_F 0.92 0.21 0.03
99_M 140_G 0.92 0.21 0.03
65_F 173_L 0.92 0.21 0.03
32_I 187_A 0.92 0.21 0.03
35_S 178_A 0.92 0.21 0.03
29_V 23_H 0.92 0.21 0.03
94_E 163_G 0.92 0.21 0.03
11_G 177_A 0.91 0.21 0.03
47_F 24_A 0.91 0.21 0.03
22_I 142_S 0.90 0.20 0.03
66_V 241_L 0.90 0.20 0.03
55_G 233_V 0.90 0.20 0.03
20_F 76_G 0.89 0.20 0.03
5_T 246_Y 0.89 0.20 0.03
10_V 193_D 0.89 0.20 0.03
17_T 154_I 0.88 0.19 0.03
3_G 72_L 0.88 0.19 0.03
7_Y 214_A 0.88 0.19 0.03
5_T 249_N 0.88 0.19 0.03
90_T 97_P 0.87 0.19 0.03
11_G 181_G 0.87 0.19 0.03
98_V 183_W 0.87 0.19 0.03
97_N 202_P 0.87 0.19 0.03
54_L 74_D 0.87 0.18 0.03
88_R 178_A 0.86 0.18 0.03
18_G 80_L 0.86 0.18 0.03
52_T 100_E 0.86 0.18 0.03
65_F 235_V 0.86 0.18 0.03
48_V 40_G 0.86 0.18 0.02
9_V 32_S 0.85 0.18 0.02
33_L 111_F 0.85 0.18 0.02
3_G 195_V 0.85 0.18 0.02
76_I 115_S 0.85 0.18 0.02
96_V 204_T 0.85 0.18 0.02
18_G 175_H 0.85 0.17 0.02
35_S 40_G 0.84 0.17 0.02
14_L 245_L 0.84 0.17 0.02
76_I 84_Q 0.84 0.17 0.02
9_V 33_F 0.84 0.17 0.02
7_Y 109_D 0.84 0.17 0.02
97_N 158_L 0.84 0.17 0.02
22_I 206_D 0.84 0.17 0.02
58_A 100_E 0.84 0.17 0.02
76_I 80_L 0.83 0.17 0.02
65_F 139_T 0.83 0.17 0.02
22_I 234_S 0.83 0.17 0.02
87_N 249_N 0.83 0.17 0.02
72_A 182_N 0.83 0.17 0.02
88_R 129_A 0.83 0.17 0.02
83_V 101_E 0.83 0.17 0.02
19_I 113_T 0.83 0.17 0.02
11_G 21_D 0.83 0.17 0.02
29_V 131_A 0.82 0.16 0.02
63_T 144_L 0.82 0.16 0.02
99_M 60_A 0.82 0.16 0.02
63_T 252_L 0.82 0.16 0.02
1_M 97_P 0.82 0.16 0.02
11_G 139_T 0.82 0.16 0.02
99_M 142_S 0.82 0.16 0.02
64_M 152_E 0.82 0.16 0.02
89_G 109_D 0.81 0.16 0.02
6_H 224_M 0.81 0.16 0.02
42_A 226_D 0.81 0.16 0.02
82_V 124_S 0.81 0.16 0.02
89_G 39_F 0.81 0.16 0.02
52_T 198_E 0.81 0.16 0.02
39_M 193_D 0.81 0.16 0.02
2_I 64_L 0.81 0.16 0.02
18_G 200_G 0.81 0.16 0.02
47_F 21_D 0.81 0.16 0.02
1_M 241_L 0.81 0.16 0.02
11_G 75_E 0.80 0.15 0.02
42_A 193_D 0.80 0.15 0.02
2_I 229_Q 0.80 0.15 0.02
63_T 80_L 0.80 0.15 0.02
6_H 74_D 0.80 0.15 0.02
55_G 226_D 0.80 0.15 0.02
88_R 37_G 0.80 0.15 0.02
49_A 206_D 0.80 0.15 0.02
61_V 162_D 0.80 0.15 0.02
11_G 184_I 0.80 0.15 0.02
83_V 90_A 0.80 0.15 0.02
11_G 30_D 0.79 0.15 0.02
61_V 216_L 0.79 0.15 0.02
48_V 157_V 0.79 0.15 0.02
12_A 73_A 0.79 0.15 0.02
97_N 177_A 0.79 0.15 0.02
47_F 254_Q 0.79 0.15 0.02
57_L 229_Q 0.79 0.15 0.02
57_L 257_K 0.79 0.15 0.02
24_V 100_E 0.79 0.15 0.02
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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