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OPENSEQ.org
cI_E_cIII_isp
Genes: A B A+B
Length: 147 195 304
Sequences: 3696 974 288
Seq/Len: 25.14 4.99 0.95
MirrorTree (Pazo et al. 2001) 0.39
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.00 0.01 0.02
100 0.01 0.01 0.09
∞ 0.01 0.02 0.84
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
33_G 181_I 1.80 0.90 0.34
16_F 136_V 1.59 0.81 0.21
20_L 63_V 1.47 0.73 0.15
124_D 24_L 1.41 0.69 0.13
94_E 27_A 1.37 0.66 0.12
24_I 63_V 1.32 0.61 0.10
92_I 146_G 1.29 0.59 0.09
115_V 40_A 1.28 0.58 0.09
47_N 60_Q 1.28 0.58 0.09
108_F 37_G 1.27 0.57 0.08
90_T 164_Y 1.24 0.54 0.07
24_I 129_E 1.23 0.53 0.07
29_L 36_A 1.23 0.53 0.07
98_V 43_L 1.11 0.42 0.05
115_V 110_S 1.10 0.41 0.05
12_H 44_V 1.10 0.41 0.04
71_V 64_S 1.10 0.41 0.04
16_F 47_M 1.09 0.41 0.04
23_A 130_W 1.08 0.40 0.04
22_V 97_V 1.07 0.39 0.04
44_R 27_A 1.01 0.33 0.03
117_L 161_G 1.00 0.33 0.03
124_D 38_A 0.99 0.32 0.03
115_V 88_E 0.99 0.32 0.03
38_G 173_G 0.97 0.31 0.03
56_S 190_T 0.96 0.30 0.03
58_G 83_I 0.96 0.29 0.03
18_I 47_M 0.95 0.29 0.03
91_S 43_L 0.95 0.29 0.03
36_F 100_G 0.94 0.28 0.03
23_A 52_D 0.94 0.28 0.02
25_G 36_A 0.93 0.28 0.02
95_S 39_A 0.92 0.27 0.02
37_L 145_I 0.92 0.27 0.02
35_W 46_Q 0.92 0.27 0.02
77_I 35_A 0.92 0.27 0.02
124_D 67_E 0.91 0.26 0.02
95_S 36_A 0.91 0.26 0.02
99_G 183_V 0.91 0.26 0.02
33_G 41_W 0.91 0.26 0.02
108_F 53_V 0.90 0.25 0.02
92_I 172_R 0.89 0.25 0.02
80_V 184_A 0.89 0.24 0.02
34_G 52_D 0.89 0.24 0.02
117_L 55_A 0.88 0.24 0.02
47_N 177_Q 0.88 0.24 0.02
12_H 187_L 0.88 0.24 0.02
40_R 101_Q 0.88 0.24 0.02
96_G 35_A 0.88 0.24 0.02
29_L 46_Q 0.88 0.24 0.02
107_I 83_I 0.87 0.23 0.02
100_F 83_I 0.87 0.23 0.02
90_T 28_T 0.86 0.23 0.02
88_W 76_W 0.86 0.23 0.02
77_I 155_W 0.86 0.23 0.02
37_L 117_A 0.86 0.23 0.02
23_A 164_Y 0.85 0.22 0.02
23_A 28_T 0.84 0.21 0.02
85_L 92_Q 0.84 0.21 0.02
101_V 85_R 0.83 0.21 0.02
36_F 60_Q 0.83 0.21 0.02
16_F 156_F 0.83 0.21 0.02
30_M 46_Q 0.83 0.21 0.02
60_A 190_T 0.83 0.21 0.01
82_A 57_A 0.82 0.20 0.01
16_F 84_R 0.82 0.20 0.01
34_G 50_S 0.82 0.20 0.01
40_R 75_K 0.82 0.20 0.01
26_L 131_L 0.82 0.20 0.01
102_E 155_W 0.82 0.20 0.01
12_H 52_D 0.82 0.20 0.01
28_C 40_A 0.82 0.20 0.01
90_T 192_I 0.81 0.20 0.01
72_A 58_S 0.81 0.20 0.01
112_A 91_I 0.81 0.20 0.01
29_L 117_A 0.81 0.20 0.01
100_F 79_K 0.81 0.20 0.01
38_G 120_E 0.81 0.20 0.01
14_W 84_R 0.81 0.20 0.01
23_A 186_F 0.80 0.19 0.01
112_A 166_T 0.80 0.19 0.01
115_V 23_F 0.80 0.19 0.01
96_G 184_A 0.80 0.19 0.01
27_C 181_I 0.80 0.19 0.01
93_R 73_T 0.79 0.19 0.01
32_V 35_A 0.79 0.19 0.01
85_L 37_G 0.79 0.19 0.01
35_W 77_L 0.79 0.19 0.01
92_I 35_A 0.79 0.19 0.01
124_D 70_T 0.79 0.19 0.01
126_T 99_L 0.79 0.19 0.01
115_V 134_I 0.79 0.18 0.01
72_A 181_I 0.79 0.18 0.01
17_A 147_D 0.78 0.18 0.01
118_V 82_F 0.78 0.18 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
2415 1.44 cI_E_cIII_isp_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.94 Done - Shared
2287 0.95 cI_E_cIII_isp Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.34 Done - Shared
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