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OPENSEQ.org
cI_K_cIII_isp_Pdenitr
Genes: A B A+B
Length: 101 190 287
Sequences: 1319 1539 437
Seq/Len: 13.06 8.1 1.52
MirrorTree (Pazo et al. 2001) 0.65
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 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.09
∞ 0.03 0.04 1.50
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
47_F 41_Q 1.30 0.74 0.02
19_I 163_G 1.28 0.72 0.02
76_I 56_V 1.26 0.70 0.01
2_I 48_V 1.22 0.66 0.01
45_I 146_D 1.21 0.65 0.01
81_L 98_I 1.17 0.62 0.01
2_I 24_A 1.13 0.58 0.01
39_M 23_T 1.11 0.56 0.01
17_T 186_T 1.10 0.55 0.01
31_V 184_D 1.09 0.54 0.01
63_T 24_A 1.08 0.52 0.01
55_G 184_D 1.05 0.49 0.01
99_M 153_P 1.04 0.49 0.01
19_I 122_A 1.02 0.47 0.01
20_F 79_R 1.02 0.46 0.01
79_A 174_L 0.99 0.44 0.01
20_F 65_T 0.99 0.43 0.01
3_G 9_G 0.99 0.43 0.01
64_M 148_G 0.99 0.43 0.01
99_M 175_H 0.99 0.43 0.01
17_T 96_Q 0.96 0.41 0.01
31_V 88_A 0.96 0.41 0.01
2_I 103_Q 0.94 0.39 0.01
76_I 35_A 0.94 0.38 0.01
34_M 33_A 0.93 0.37 0.01
13_I 188_K 0.93 0.37 0.01
46_N 165_I 0.91 0.35 0.01
17_T 7_H 0.91 0.35 0.01
1_M 114_D 0.90 0.35 0.01
4_L 26_A 0.90 0.34 0.01
2_I 34_A 0.89 0.34 0.01
10_V 66_Q 0.89 0.33 0.01
47_F 38_L 0.89 0.33 0.01
48_V 32_G 0.89 0.33 0.01
17_T 105_S 0.89 0.33 0.01
11_G 115_E 0.88 0.33 0.01
31_V 187_I 0.88 0.33 0.01
89_G 168_G 0.88 0.32 0.01
6_H 87_Q 0.88 0.32 0.01
57_L 93_D 0.87 0.32 0.01
3_G 127_V 0.87 0.32 0.01
48_V 120_D 0.87 0.32 0.01
76_I 65_T 0.87 0.31 0.01
39_M 34_A 0.86 0.31 0.01
39_M 47_D 0.85 0.30 0.01
54_L 28_T 0.85 0.30 0.01
46_N 173_N 0.84 0.29 0.01
94_E 158_H 0.84 0.29 0.01
94_E 145_G 0.84 0.29 0.01
52_T 78_I 0.84 0.29 0.01
1_M 25_G 0.83 0.29 0.01
81_L 62_E 0.83 0.29 0.01
18_G 137_C 0.83 0.28 0.00
18_G 155_H 0.83 0.28 0.00
39_M 118_T 0.83 0.28 0.00
99_M 116_N 0.83 0.28 0.00
76_I 187_I 0.82 0.28 0.00
47_F 163_G 0.82 0.27 0.00
72_A 73_G 0.81 0.27 0.00
45_I 13_A 0.81 0.27 0.00
69_V 135_L 0.81 0.27 0.00
79_A 157_S 0.81 0.27 0.00
24_V 63_T 0.81 0.27 0.00
85_F 47_D 0.81 0.27 0.00
47_F 66_Q 0.81 0.26 0.00
94_E 83_E 0.80 0.26 0.00
17_T 114_D 0.80 0.26 0.00
29_V 159_Y 0.80 0.26 0.00
3_G 18_F 0.80 0.26 0.00
11_G 96_Q 0.80 0.26 0.00
55_G 183_D 0.80 0.25 0.00
30_I 23_T 0.79 0.25 0.00
18_G 134_H 0.79 0.25 0.00
39_M 20_Y 0.79 0.25 0.00
29_V 181_F 0.79 0.25 0.00
100_K 40_N 0.79 0.25 0.00
1_M 172_Q 0.79 0.25 0.00
8_L 31_A 0.79 0.25 0.00
49_A 125_W 0.79 0.25 0.00
35_S 43_N 0.79 0.25 0.00
43_V 25_G 0.79 0.25 0.00
30_I 141_G 0.78 0.24 0.00
31_V 35_A 0.78 0.24 0.00
62_F 52_A 0.78 0.24 0.00
52_T 189_L 0.78 0.24 0.00
61_V 19_L 0.77 0.24 0.00
18_G 132_C 0.77 0.24 0.00
63_T 138_V 0.77 0.23 0.00
43_V 65_T 0.77 0.23 0.00
13_I 111_P 0.76 0.23 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
2936 1.01 cI_K_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2935 2 cI_K_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2925 1.52 cI_K_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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