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OPENSEQ.org
1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS
Genes: A B A+B
Length: 143 108 237
Sequences: 10213 1288 653
Seq/Len: 71.42 11.93 2.76
MirrorTree (Pazo et al. 2001) 0.69
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 0.01 0.00 2.54
2 0.01 0.00 2.57
5 0.02 0.00 2.55
10 0.03 0.00 2.56
20 0.04 0.00 2.60
100 0.06 0.00 2.80
∞ 0.17 0.02 3.98
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
8_L 82_E 1.53 0.96 0.73
100_R 73_C 1.50 0.95 0.71
48_S 71_A 1.34 0.90 0.58
87_V 31_I 1.09 0.72 0.34
106_A 20_D 1.09 0.71 0.33
134_V 27_M 1.07 0.69 0.31
49_V 79_E 1.06 0.69 0.31
101_N 73_C 1.05 0.68 0.29
13_A 101_C 1.04 0.67 0.29
112_I 80_V 1.04 0.66 0.28
140_H 24_P 1.04 0.66 0.28
39_S 78_A 1.03 0.65 0.28
141_G 79_E 1.02 0.65 0.27
28_E 39_P 1.02 0.65 0.27
75_E 75_V 1.00 0.62 0.25
106_A 100_L 0.99 0.61 0.24
55_R 97_H 0.99 0.61 0.24
87_V 21_A 0.98 0.60 0.24
39_S 28_Y 0.98 0.60 0.23
135_V 82_E 0.97 0.59 0.23
127_H 68_Q 0.97 0.59 0.23
71_A 41_E 0.96 0.57 0.22
114_S 102_T 0.95 0.56 0.21
86_R 29_K 0.94 0.56 0.21
29_H 50_F 0.94 0.55 0.21
27_V 39_P 0.94 0.55 0.20
29_H 97_H 0.93 0.54 0.20
123_L 79_E 0.93 0.53 0.19
59_E 102_T 0.92 0.53 0.19
14_F 45_D 0.91 0.51 0.18
112_I 77_T 0.91 0.51 0.18
36_S 24_P 0.89 0.49 0.17
52_V 103_L 0.89 0.49 0.17
29_H 39_P 0.88 0.48 0.17
92_V 89_N 0.88 0.48 0.16
7_E 73_C 0.88 0.48 0.16
127_H 64_A 0.88 0.48 0.16
71_A 94_E 0.87 0.47 0.16
123_L 73_C 0.86 0.45 0.15
126_K 70_K 0.85 0.44 0.14
18_R 97_H 0.85 0.44 0.14
50_D 27_M 0.85 0.44 0.14
67_P 21_A 0.83 0.42 0.14
141_G 17_K 0.83 0.42 0.13
67_P 77_T 0.83 0.42 0.13
135_V 88_V 0.83 0.42 0.13
15_A 100_L 0.83 0.42 0.13
112_I 32_L 0.83 0.42 0.13
59_E 37_Y 0.83 0.41 0.13
106_A 90_K 0.83 0.41 0.13
122_Y 50_F 0.82 0.41 0.13
10_L 102_T 0.82 0.41 0.13
106_A 33_V 0.82 0.40 0.13
135_V 87_M 0.82 0.40 0.13
87_V 64_A 0.82 0.40 0.13
27_V 50_F 0.82 0.40 0.13
27_V 97_H 0.81 0.40 0.12
76_R 41_E 0.81 0.40 0.12
83_S 18_V 0.81 0.40 0.12
48_S 53_Y 0.81 0.40 0.12
37_N 82_E 0.81 0.39 0.12
34_L 77_T 0.81 0.39 0.12
13_A 39_P 0.80 0.38 0.12
50_D 103_L 0.80 0.38 0.12
32_L 80_V 0.80 0.38 0.12
7_E 101_C 0.80 0.38 0.12
92_V 65_V 0.80 0.38 0.12
28_E 33_V 0.80 0.38 0.12
141_G 16_E 0.80 0.38 0.12
126_K 12_Q 0.79 0.37 0.11
69_L 46_V 0.78 0.36 0.11
123_L 78_A 0.78 0.36 0.11
64_Q 41_E 0.78 0.36 0.11
58_L 61_L 0.78 0.36 0.11
12_M 101_C 0.78 0.35 0.10
93_F 75_V 0.77 0.35 0.10
46_A 17_K 0.77 0.35 0.10
8_L 63_L 0.77 0.34 0.10
70_P 72_I 0.76 0.34 0.10
7_E 69_G 0.76 0.34 0.10
21_R 65_V 0.76 0.33 0.10
89_Q 45_D 0.75 0.33 0.10
110_V 85_V 0.75 0.33 0.10
94_H 52_S 0.75 0.32 0.09
39_S 95_N 0.74 0.32 0.09
86_R 70_K 0.74 0.31 0.09
124_L 63_L 0.73 0.31 0.09
79_Q 75_V 0.73 0.30 0.09
23_E 67_Y 0.73 0.30 0.09
20_H 19_R 0.72 0.29 0.08
11_N 88_V 0.72 0.29 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
4117 2.42 1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4082 2.76 1R6C_X Clp protease subunit ClpA 2W9R_A Clp protease adaptor protein ClpS Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared
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