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OPENSEQ.org
cI_A_cIII_isp_Pnitri
Genes: A B A+B
Length: 121 190 303
Sequences: 4481 1692 481
Seq/Len: 37.03 8.91 1.59
MirrorTree (Pazo et al. 2001) 0.59
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 0.02
10 0.00 0.01 0.02
20 0.00 0.01 0.03
100 0.01 0.01 0.13
∞ 0.02 0.05 1.55
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
11_I 131_V 2.08 0.99 0.95
85_V 159_Y 1.41 0.82 0.63
28_A 67_L 1.39 0.81 0.61
103_A 32_G 1.27 0.72 0.49
28_A 36_W 1.21 0.67 0.44
28_A 176_I 1.21 0.67 0.43
89_S 22_A 1.20 0.66 0.42
31_V 22_A 1.11 0.57 0.33
36_N 174_L 1.11 0.57 0.33
32_I 24_A 1.10 0.56 0.32
11_I 42_M 1.08 0.54 0.30
39_P 9_G 1.04 0.49 0.26
13_V 42_M 1.03 0.49 0.26
51_A 176_I 1.02 0.48 0.24
85_V 23_T 1.00 0.46 0.23
13_V 144_A 0.97 0.43 0.20
12_L 94_L 0.96 0.41 0.20
35_R 32_G 0.94 0.40 0.18
24_V 184_D 0.94 0.39 0.18
19_S 23_T 0.94 0.39 0.18
17_M 84_D 0.93 0.39 0.18
114_K 175_H 0.93 0.39 0.18
100_V 12_G 0.92 0.38 0.17
15_L 10_D 0.92 0.38 0.17
21_L 48_V 0.92 0.38 0.17
27_L 31_A 0.91 0.37 0.16
35_R 19_L 0.91 0.37 0.16
80_L 32_G 0.91 0.36 0.16
32_I 112_A 0.91 0.36 0.16
117_A 170_A 0.91 0.36 0.16
29_A 133_T 0.90 0.35 0.15
26_I 47_D 0.89 0.35 0.15
18_A 18_F 0.89 0.34 0.14
24_V 31_A 0.88 0.34 0.14
62_R 162_S 0.88 0.34 0.14
17_M 98_I 0.88 0.33 0.14
15_L 117_R 0.86 0.32 0.13
72_I 126_L 0.86 0.32 0.13
18_A 43_N 0.86 0.32 0.13
33_A 31_A 0.86 0.32 0.13
103_A 39_V 0.85 0.31 0.12
28_A 13_A 0.85 0.31 0.12
95_F 173_N 0.85 0.31 0.12
87_F 24_A 0.84 0.30 0.12
50_N 66_Q 0.84 0.30 0.12
87_F 10_D 0.84 0.30 0.12
102_L 37_T 0.84 0.30 0.12
13_V 129_I 0.84 0.30 0.12
61_V 31_A 0.83 0.30 0.12
26_I 34_A 0.83 0.29 0.11
115_K 188_K 0.82 0.28 0.11
34_V 98_I 0.82 0.28 0.11
24_V 159_Y 0.82 0.28 0.11
31_V 33_A 0.82 0.28 0.11
42_V 78_I 0.82 0.28 0.11
27_L 101_S 0.82 0.28 0.11
62_R 157_S 0.81 0.28 0.10
75_L 179_A 0.81 0.28 0.10
5_L 33_A 0.81 0.27 0.10
33_A 28_T 0.81 0.27 0.10
114_K 140_I 0.81 0.27 0.10
19_S 58_V 0.80 0.27 0.10
44_A 150_W 0.80 0.27 0.10
62_R 170_A 0.80 0.27 0.10
94_A 56_V 0.80 0.27 0.10
95_F 158_H 0.80 0.27 0.10
86_S 109_D 0.80 0.26 0.10
93_V 186_T 0.79 0.26 0.10
44_A 190_G 0.79 0.26 0.10
50_N 20_Y 0.79 0.26 0.09
24_V 115_E 0.79 0.26 0.09
85_V 13_A 0.79 0.26 0.09
6_Q 66_Q 0.79 0.26 0.09
87_F 98_I 0.78 0.25 0.09
77_V 95_G 0.78 0.25 0.09
30_A 38_L 0.78 0.25 0.09
18_A 23_T 0.78 0.25 0.09
103_A 12_G 0.77 0.24 0.09
19_S 178_V 0.77 0.24 0.09
35_R 70_K 0.77 0.24 0.08
51_A 185_T 0.77 0.24 0.08
83_W 159_Y 0.77 0.24 0.08
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
3485 1.57 cI_A_10_cIII_isp_10_pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
2518 1.59 cI_A_cIII_isp_Pnitri Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
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