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OPENSEQ.org
cI_E_cIII_isp_10
Genes: A B A+B
Length: 147 195 307
Sequences: 3696 1453 442
Seq/Len: 25.14 7.45 1.44
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.01
10 0.00 0.00 0.02
20 0.00 0.00 0.03
100 0.01 0.01 0.10
∞ 0.01 0.02 1.29
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
16_F 136_V 2.10 0.99 0.94
108_F 37_G 1.42 0.81 0.59
33_G 181_I 1.34 0.76 0.52
77_I 131_L 1.27 0.69 0.45
41_A 179_L 1.24 0.66 0.41
29_L 36_A 1.22 0.65 0.39
18_I 47_M 1.20 0.63 0.38
94_E 27_A 1.15 0.58 0.32
90_T 164_Y 1.13 0.56 0.30
90_T 192_I 1.12 0.55 0.30
20_L 63_V 1.10 0.53 0.28
36_F 27_A 1.09 0.52 0.27
40_R 37_G 1.06 0.50 0.25
16_F 47_M 1.06 0.49 0.24
33_G 136_V 1.06 0.49 0.24
68_F 183_V 1.05 0.48 0.24
20_L 15_D 1.04 0.47 0.23
24_I 28_T 1.00 0.43 0.20
115_V 40_A 1.00 0.43 0.19
33_G 72_L 0.99 0.42 0.19
117_L 161_G 0.98 0.41 0.18
40_R 24_L 0.98 0.41 0.18
112_A 74_V 0.97 0.40 0.17
80_V 184_A 0.97 0.40 0.17
47_N 60_Q 0.96 0.39 0.17
92_I 15_D 0.95 0.38 0.16
90_T 18_A 0.94 0.37 0.16
37_L 180_H 0.94 0.37 0.16
23_A 23_F 0.93 0.36 0.15
115_V 110_S 0.92 0.35 0.14
38_G 173_G 0.92 0.35 0.14
99_G 183_V 0.91 0.34 0.14
25_G 52_D 0.91 0.34 0.14
29_L 123_T 0.91 0.34 0.14
21_I 19_T 0.91 0.34 0.14
29_L 67_E 0.91 0.34 0.14
97_W 66_V 0.89 0.33 0.13
67_K 162_S 0.89 0.32 0.12
119_R 45_N 0.88 0.32 0.12
112_A 91_I 0.86 0.30 0.11
119_R 180_H 0.86 0.30 0.11
18_I 149_A 0.86 0.30 0.11
100_F 161_G 0.86 0.30 0.11
124_D 40_A 0.86 0.30 0.11
20_L 120_E 0.86 0.30 0.11
18_I 70_T 0.86 0.29 0.11
95_S 36_A 0.86 0.29 0.11
108_F 102_L 0.85 0.29 0.11
67_K 175_A 0.84 0.28 0.10
34_G 52_D 0.84 0.28 0.10
105_I 93_A 0.83 0.28 0.10
33_G 41_W 0.83 0.27 0.10
23_A 130_W 0.82 0.27 0.09
93_R 73_T 0.82 0.26 0.09
115_V 88_E 0.81 0.26 0.09
93_R 59_I 0.81 0.26 0.09
44_R 27_A 0.81 0.26 0.09
40_R 188_D 0.81 0.25 0.09
82_A 27_A 0.80 0.25 0.08
23_A 48_N 0.80 0.25 0.08
28_C 14_G 0.80 0.25 0.08
47_N 177_Q 0.79 0.24 0.08
63_R 29_A 0.79 0.24 0.08
56_S 181_I 0.79 0.24 0.08
100_F 18_A 0.78 0.23 0.07
12_H 44_V 0.78 0.23 0.07
29_L 179_L 0.78 0.23 0.07
109_V 30_G 0.77 0.23 0.07
92_I 172_R 0.77 0.23 0.07
27_C 27_A 0.77 0.23 0.07
49_P 78_G 0.77 0.23 0.07
122_A 175_A 0.77 0.23 0.07
24_I 183_V 0.77 0.22 0.07
112_A 125_D 0.77 0.22 0.07
36_F 67_E 0.77 0.22 0.07
32_V 106_S 0.76 0.22 0.07
23_A 70_T 0.76 0.22 0.07
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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