May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_E_cIII_cyt1_10
Genes: A B A+B
Length: 147 263 363
Sequences: 3696 884 269
Seq/Len: 25.14 3.36 0.74
MirrorTree (Pazo et al. 2001) 0.34
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 0.01
20 0.00 0.01 0.01
100 0.01 0.01 0.05
∞ 0.01 0.01 0.66
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
119_R 241_L 1.92 0.90 0.34
95_S 73_A 1.63 0.77 0.18
126_T 242_A 1.62 0.76 0.17
22_V 202_P 1.49 0.67 0.12
72_A 29_E 1.34 0.56 0.08
82_A 251_K 1.23 0.46 0.05
95_S 242_A 1.19 0.42 0.05
10_I 39_F 1.18 0.42 0.04
16_F 104_P 1.15 0.40 0.04
32_V 214_A 1.12 0.37 0.04
77_I 154_I 1.08 0.34 0.03
71_V 224_M 1.06 0.32 0.03
36_F 141_L 1.06 0.32 0.03
102_E 91_N 1.05 0.31 0.03
14_W 84_Q 1.03 0.30 0.03
38_G 245_L 1.03 0.30 0.03
30_M 124_S 1.02 0.29 0.02
115_V 105_R 1.02 0.29 0.02
99_G 44_Q 1.01 0.29 0.02
29_L 38_P 1.01 0.29 0.02
112_A 246_Y 1.00 0.28 0.02
16_F 229_Q 0.98 0.27 0.02
91_S 249_N 0.98 0.27 0.02
18_I 246_Y 0.98 0.26 0.02
98_V 243_A 0.97 0.26 0.02
103_A 246_Y 0.97 0.26 0.02
20_L 52_Q 0.96 0.25 0.02
112_A 215_F 0.96 0.25 0.02
99_G 220_A 0.95 0.25 0.02
33_G 131_A 0.94 0.24 0.02
20_L 201_T 0.94 0.24 0.02
38_G 216_L 0.93 0.23 0.02
112_A 19_A 0.93 0.23 0.02
108_F 87_A 0.93 0.23 0.02
45_S 228_K 0.92 0.23 0.02
24_I 63_G 0.92 0.23 0.02
124_D 257_K 0.92 0.23 0.02
21_I 54_Y 0.92 0.23 0.02
16_F 218_W 0.92 0.23 0.02
124_D 210_T 0.92 0.23 0.02
91_S 195_V 0.91 0.22 0.02
29_L 93_D 0.91 0.22 0.01
112_A 93_D 0.91 0.22 0.01
24_I 163_G 0.90 0.22 0.01
117_L 96_D 0.90 0.21 0.01
109_V 245_L 0.90 0.21 0.01
60_A 88_Y 0.89 0.21 0.01
29_L 90_A 0.89 0.21 0.01
21_I 202_P 0.89 0.21 0.01
21_I 209_A 0.89 0.21 0.01
37_L 240_V 0.88 0.21 0.01
92_I 133_F 0.88 0.20 0.01
36_F 193_D 0.88 0.20 0.01
40_R 216_L 0.88 0.20 0.01
24_I 224_M 0.87 0.20 0.01
98_V 216_L 0.87 0.20 0.01
114_L 96_D 0.87 0.20 0.01
67_K 237_F 0.87 0.20 0.01
57_V 47_L 0.86 0.20 0.01
31_L 48_Q 0.86 0.20 0.01
22_V 240_V 0.86 0.20 0.01
124_D 82_E 0.86 0.19 0.01
77_I 73_A 0.86 0.19 0.01
99_G 84_Q 0.86 0.19 0.01
60_A 239_I 0.85 0.19 0.01
124_D 218_W 0.85 0.19 0.01
38_G 250_K 0.85 0.19 0.01
99_G 182_N 0.85 0.19 0.01
38_G 35_F 0.84 0.18 0.01
109_V 124_S 0.84 0.18 0.01
104_A 94_I 0.84 0.18 0.01
47_N 28_I 0.84 0.18 0.01
111_L 71_T 0.84 0.18 0.01
25_G 17_Q 0.84 0.18 0.01
85_L 72_L 0.84 0.18 0.01
29_L 158_L 0.83 0.18 0.01
105_I 151_P 0.83 0.18 0.01
95_S 232_F 0.83 0.18 0.01
24_I 239_I 0.82 0.17 0.01
18_I 154_I 0.82 0.17 0.01
34_G 137_Y 0.82 0.17 0.01
92_I 88_Y 0.82 0.17 0.01
41_A 118_G 0.81 0.17 0.01
31_L 151_P 0.81 0.17 0.01
95_S 116_G 0.81 0.17 0.01
103_A 135_G 0.81 0.17 0.01
8_E 164_E 0.80 0.17 0.01
92_I 215_F 0.80 0.16 0.01
31_L 63_G 0.80 0.16 0.01
100_F 88_Y 0.80 0.16 0.01
28_C 81_P 0.80 0.16 0.01
72_A 255_P 0.80 0.16 0.01
22_V 155_H 0.80 0.16 0.01
72_A 241_L 0.80 0.16 0.01
20_L 96_D 0.79 0.16 0.01
17_A 164_E 0.79 0.16 0.01
29_L 250_K 0.79 0.16 0.01
91_S 219_T 0.79 0.16 0.01
68_F 100_E 0.79 0.16 0.01
14_W 177_A 0.79 0.16 0.01
44_R 81_P 0.78 0.16 0.01
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
2960 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2959 0.79 cI_A_10_cIII_cyt1_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
2958 0.52 cI_A_10_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2957 0.79 cI_A_20_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
2956 0.79 cI_A_10_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
2425 0.77 cI_E_cIII_cyt1_4 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.22 Done - Shared
2419 0.76 cI_E_cIII_cyt1_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.16 Done - Shared
2418 0.74 cI_E_cIII_cyt1_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.34 Done - Shared
2292 0.47 cI_E_cIII_cyt1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
Page generated in 1.936 seconds.