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OPENSEQ.org
cI_A_4_cyt1_4_human
Genes: A B A+B
Length: 115 325 367
Sequences: 6650 829 151
Seq/Len: 57.83 2.55 0.41
MirrorTree (Pazo et al. 2001) 0.49
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 0.03
∞ 0.01 0.02 0.34
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
21_T 255_F 1.64 0.60 0.00
34_S 184_A 1.41 0.43 0.00
100_L 292_M 1.35 0.40 0.00
7_L 306_I 1.34 0.39 0.00
100_L 107_H 1.34 0.39 0.00
8_M 312_S 1.30 0.36 0.00
100_L 259_T 1.29 0.36 0.00
83_N 104_S 1.28 0.34 0.00
5_L 182_S 1.24 0.32 0.00
49_V 138_V 1.22 0.31 0.00
112_D 271_C 1.21 0.30 0.00
80_Q 238_P 1.20 0.29 0.00
12_L 127_M 1.16 0.27 0.00
47_A 304_Y 1.15 0.27 0.00
88_V 307_K 1.15 0.27 0.00
59_A 92_P 1.15 0.27 0.00
53_M 122_A 1.14 0.26 0.00
17_L 307_K 1.13 0.26 0.00
53_M 242_I 1.13 0.25 0.00
30_Y 102_L 1.12 0.25 0.00
34_S 91_P 1.12 0.25 0.00
10_N 282_H 1.12 0.25 0.00
59_A 299_L 1.10 0.24 0.00
4_A 169_G 1.10 0.24 0.00
35_T 245_A 1.09 0.23 0.00
16_L 127_M 1.08 0.23 0.00
23_W 311_W 1.08 0.23 0.00
84_L 172_F 1.04 0.21 0.00
103_A 261_A 1.04 0.21 0.00
96_I 150_A 1.03 0.20 0.00
81_T 266_I 1.03 0.20 0.00
3_F 105_L 1.02 0.20 0.00
79_X 192_A 1.01 0.20 0.00
84_L 300_V 0.99 0.19 0.00
47_A 221_P 0.97 0.18 0.00
14_A 305_T 0.96 0.17 0.00
13_L 266_I 0.96 0.17 0.00
22_F 96_W 0.96 0.17 0.00
5_L 220_E 0.96 0.17 0.00
10_N 177_K 0.96 0.17 0.00
47_A 84_A 0.96 0.17 0.00
59_A 89_L 0.95 0.17 0.00
18_M 287_R 0.95 0.17 0.00
81_T 201_V 0.95 0.17 0.00
18_M 154_V 0.94 0.16 0.00
9_I 78_L 0.94 0.16 0.00
12_L 130_V 0.93 0.16 0.00
114_A 300_V 0.93 0.16 0.00
7_L 266_I 0.93 0.16 0.00
17_L 306_I 0.92 0.16 0.00
107_L 67_L 0.92 0.16 0.00
8_M 251_D 0.92 0.16 0.00
61_T 253_L 0.91 0.15 0.00
107_L 69_A 0.91 0.15 0.00
15_L 170_K 0.91 0.15 0.00
11_T 130_V 0.91 0.15 0.00
7_L 213_S 0.90 0.15 0.00
114_A 146_K 0.90 0.15 0.00
43_P 264_S 0.90 0.15 0.00
59_A 219_C 0.90 0.15 0.00
9_I 212_F 0.89 0.15 0.00
34_S 180_P 0.89 0.14 0.00
21_T 309_H 0.89 0.14 0.00
9_I 189_N 0.88 0.14 0.00
87_M 209_D 0.88 0.14 0.00
12_L 81_A 0.88 0.14 0.00
89_M 191_G 0.87 0.14 0.00
32_E 122_A 0.87 0.14 0.00
97_I 148_L 0.87 0.14 0.00
93_L 284_H 0.86 0.14 0.00
31_M 127_M 0.86 0.14 0.00
88_V 107_H 0.86 0.14 0.00
100_L 190_N 0.86 0.14 0.00
5_L 114_F 0.86 0.14 0.00
85_P 307_K 0.86 0.13 0.00
26_Q 266_I 0.85 0.13 0.00
16_L 281_E 0.85 0.13 0.00
84_L 138_V 0.85 0.13 0.00
16_L 200_I 0.84 0.13 0.00
16_L 197_L 0.84 0.13 0.00
23_W 298_L 0.84 0.13 0.00
18_M 197_L 0.84 0.13 0.00
59_A 313_V 0.84 0.13 0.00
4_A 171_L 0.84 0.13 0.00
23_W 122_A 0.83 0.13 0.00
112_D 151_E 0.83 0.12 0.00
59_A 79_H 0.83 0.12 0.00
24_L 240_Q 0.83 0.12 0.00
28_N 155_Q 0.82 0.12 0.00
100_L 82_V 0.82 0.12 0.00
100_L 170_K 0.82 0.12 0.00
53_M 303_V 0.82 0.12 0.00
100_L 304_Y 0.82 0.12 0.00
21_T 307_K 0.82 0.12 0.00
53_M 240_Q 0.82 0.12 0.00
36_P 240_Q 0.82 0.12 0.00
28_N 287_R 0.82 0.12 0.00
15_L 256_D 0.81 0.12 0.00
21_T 266_I 0.81 0.12 0.00
24_L 254_E 0.81 0.12 0.00
43_P 81_A 0.80 0.12 0.00
82_T 153_E 0.80 0.12 0.00
26_Q 306_I 0.80 0.12 0.00
11_T 84_A 0.80 0.12 0.00
34_S 115_Q 0.80 0.12 0.00
87_M 114_F 0.80 0.12 0.00
24_L 241_A 0.80 0.12 0.00
81_T 99_R 0.79 0.11 0.00
4_A 177_K 0.79 0.11 0.00
10_N 259_T 0.79 0.11 0.00
17_L 240_Q 0.79 0.11 0.00
96_I 102_L 0.79 0.11 0.00
88_V 157_G 0.79 0.11 0.00
107_L 215_L 0.79 0.11 0.00
96_I 69_A 0.79 0.11 0.00
42_D 179_Y 0.79 0.11 0.00
9_I 268_K 0.78 0.11 0.00
5_L 126_S 0.78 0.11 0.00
58_V 97_S 0.78 0.11 0.00
9_I 143_D 0.78 0.11 0.00
88_V 160_E 0.78 0.11 0.00
17_L 139_C 0.78 0.11 0.00
81_T 109_S 0.78 0.11 0.00
27_L 225_V 0.78 0.11 0.00
27_L 298_L 0.78 0.11 0.00
49_V 139_C 0.78 0.11 0.00
80_Q 107_H 0.78 0.11 0.00
31_M 229_E 0.77 0.11 0.00
12_L 107_H 0.77 0.11 0.00
23_W 74_L 0.77 0.11 0.00
81_T 248_I 0.77 0.10 0.00
80_Q 166_M 0.77 0.10 0.00
5_L 236_Y 0.76 0.10 0.00
27_L 122_A 0.76 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
5575 0 cI_A_40_cyt1_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5560 0.41 cI_A_4_cyt1_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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