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OPENSEQ.org
PilT-3C
Genes: A B A+B
Length: 356 405 731
Sequences: 5681 3552 2805
Seq/Len: 15.96 8.77 3.84
MirrorTree (Pazo et al. 2001) 0.67
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.16 0.00 3.34
2 0.17 0.00 3.38
5 0.19 0.00 3.57
10 0.20 0.00 3.66
20 0.21 0.01 3.69
100 0.23 0.05 3.76
∞ 0.28 0.15 3.89
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
155_H 183_V 1.11 0.82 0.07
257_L 120_A 1.02 0.74 0.05
163_L 178_A 1.01 0.73 0.05
189_A 393_Y 0.99 0.70 0.04
317_L 223_Y 0.97 0.69 0.04
243_D 397_F 0.93 0.64 0.04
227_G 176_I 0.90 0.60 0.03
94_A 195_F 0.87 0.56 0.03
177_R 195_F 0.84 0.52 0.03
243_D 393_Y 0.80 0.47 0.02
226_F 213_V 0.80 0.47 0.02
263_G 366_V 0.75 0.40 0.02
203_V 320_M 0.74 0.39 0.02
15_G 373_M 0.74 0.39 0.02
221_T 345_G 0.73 0.38 0.02
317_L 67_L 0.73 0.37 0.02
155_H 94_Q 0.72 0.36 0.02
155_H 395_P 0.72 0.36 0.02
138_S 394_L 0.72 0.36 0.02
155_H 73_Q 0.71 0.36 0.02
237_T 380_F 0.71 0.35 0.02
19_L 258_A 0.71 0.35 0.02
155_H 195_F 0.70 0.34 0.02
258_S 191_V 0.69 0.33 0.02
236_K 176_I 0.69 0.33 0.02
57_T 376_M 0.69 0.33 0.02
226_F 105_I 0.69 0.33 0.02
332_T 216_L 0.68 0.31 0.01
21_L 10_S 0.67 0.31 0.01
332_T 175_T 0.67 0.31 0.01
108_D 258_A 0.66 0.30 0.01
97_F 389_V 0.66 0.29 0.01
107_A 135_L 0.66 0.29 0.01
174_L 399_L 0.66 0.29 0.01
180_G 395_P 0.66 0.29 0.01
264_V 141_V 0.66 0.29 0.01
221_T 342_E 0.65 0.29 0.01
155_H 391_A 0.65 0.28 0.01
21_L 119_D 0.65 0.28 0.01
159_L 87_C 0.65 0.28 0.01
8_F 135_L 0.64 0.28 0.01
27_P 64_T 0.64 0.28 0.01
82_F 371_A 0.64 0.28 0.01
238_I 299_G 0.64 0.28 0.01
107_A 389_V 0.64 0.28 0.01
106_S 373_M 0.64 0.28 0.01
138_S 100_F 0.64 0.27 0.01
7_L 273_F 0.64 0.27 0.01
219_A 386_G 0.63 0.27 0.01
99_I 324_L 0.63 0.27 0.01
97_F 106_R 0.63 0.27 0.01
217_S 156_I 0.63 0.27 0.01
233_S 353_K 0.63 0.26 0.01
94_A 393_Y 0.62 0.26 0.01
260_S 345_G 0.62 0.26 0.01
155_H 397_F 0.62 0.26 0.01
261_L 298_A 0.62 0.26 0.01
246_P 83_P 0.62 0.25 0.01
21_L 118_A 0.61 0.25 0.01
15_G 323_P 0.61 0.25 0.01
261_L 254_F 0.61 0.24 0.01
138_S 278_G 0.61 0.24 0.01
27_P 384_T 0.61 0.24 0.01
121_Q 230_L 0.61 0.24 0.01
94_A 183_V 0.60 0.24 0.01
264_V 229_G 0.60 0.24 0.01
120_T 162_L 0.60 0.23 0.01
159_L 121_L 0.60 0.23 0.01
216_M 101_K 0.60 0.23 0.01
32_H 101_K 0.60 0.23 0.01
189_A 195_F 0.60 0.23 0.01
258_S 262_G 0.60 0.23 0.01
264_V 275_R 0.60 0.23 0.01
243_D 396_I 0.60 0.23 0.01
246_P 202_F 0.60 0.23 0.01
116_V 311_R 0.59 0.23 0.01
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)
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