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OPENSEQ.org
SprA Nter 1689 (A, 1-175)
Genes: A B A+B
Length: 175 110 277
Sequences: 6611 633 279
Seq/Len: 37.78 5.75 1.01
MirrorTree (Pazo et al. 2001) 0.47
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 0.05 0.00 0.00
2 0.05 0.00 0.00
5 0.05 0.00 0.00
10 0.05 0.00 0.01
20 0.05 0.00 0.04
100 0.05 0.00 0.48
∞ 0.06 0.00 0.98
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
129_V 54_L 1.47 0.75 0.01
138_E 76_M 1.27 0.59 0.01
8_I 65_K 1.22 0.54 0.01
142_Y 18_L 1.19 0.51 0.01
145_I 19_E 1.11 0.44 0.01
38_N 57_K 1.10 0.43 0.01
137_A 101_S 1.09 0.43 0.01
97_E 55_T 1.09 0.42 0.01
94_K 59_Y 1.07 0.40 0.01
87_E 45_G 1.05 0.38 0.00
83_K 101_S 1.03 0.37 0.00
137_A 54_L 1.02 0.36 0.00
80_L 55_T 1.00 0.34 0.00
27_I 72_F 0.99 0.33 0.00
119_A 15_K 0.98 0.33 0.00
83_K 53_V 0.97 0.32 0.00
167_V 12_S 0.96 0.31 0.00
52_K 65_K 0.94 0.29 0.00
170_I 18_L 0.94 0.29 0.00
10_L 72_F 0.92 0.28 0.00
49_L 28_Y 0.92 0.28 0.00
137_A 45_G 0.92 0.28 0.00
84_E 102_S 0.91 0.27 0.00
98_N 72_F 0.90 0.26 0.00
157_S 34_T 0.90 0.26 0.00
24_T 39_Y 0.89 0.26 0.00
35_I 66_E 0.89 0.26 0.00
139_A 58_E 0.88 0.25 0.00
140_K 54_L 0.88 0.25 0.00
65_L 34_T 0.88 0.25 0.00
87_E 57_K 0.87 0.24 0.00
59_E 18_L 0.86 0.24 0.00
11_A 68_R 0.86 0.23 0.00
13_I 19_E 0.86 0.23 0.00
139_A 107_I 0.85 0.23 0.00
85_L 97_Y 0.85 0.23 0.00
15_A 49_D 0.85 0.23 0.00
88_E 5_D 0.85 0.23 0.00
145_I 36_R 0.84 0.22 0.00
4_Q 38_I 0.83 0.21 0.00
57_K 72_F 0.83 0.21 0.00
163_I 100_N 0.83 0.21 0.00
48_Q 69_R 0.82 0.21 0.00
162_D 103_L 0.82 0.21 0.00
55_K 59_Y 0.81 0.21 0.00
24_T 55_T 0.80 0.20 0.00
63_K 43_V 0.80 0.20 0.00
12_L 65_K 0.80 0.20 0.00
134_Q 24_I 0.79 0.20 0.00
78_K 58_E 0.79 0.19 0.00
18_S 69_R 0.79 0.19 0.00
160_R 99_I 0.79 0.19 0.00
76_T 16_M 0.78 0.19 0.00
19_Q 67_S 0.78 0.19 0.00
138_E 57_K 0.78 0.19 0.00
29_Y 39_Y 0.78 0.18 0.00
54_Q 73_R 0.78 0.18 0.00
75_K 61_D 0.78 0.18 0.00
104_Q 25_L 0.77 0.18 0.00
47_S 34_T 0.77 0.18 0.00
123_K 38_I 0.77 0.18 0.00
4_Q 72_F 0.77 0.18 0.00
63_K 20_N 0.77 0.18 0.00
73_G 53_V 0.77 0.18 0.00
97_E 73_R 0.77 0.18 0.00
90_E 70_D 0.77 0.18 0.00
165_D 57_K 0.77 0.18 0.00
62_A 80_D 0.77 0.18 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
10736 1.01 SprA Nter 1689 (A, 1-175) Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10735 0.04 SprA Nter 1689 (A, 1-175) Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) Killed - Shared
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