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OPENSEQ.org
PilT-4C
Genes: A B A+B
Length: 365 405 735
Sequences: 5394 3552 2792
Seq/Len: 14.78 8.77 3.8
MirrorTree (Pazo et al. 2001) 0.66
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 0.17 0.00 3.28
2 0.18 0.00 3.33
5 0.20 0.00 3.50
10 0.21 0.00 3.61
20 0.22 0.01 3.63
100 0.24 0.05 3.70
∞ 0.29 0.15 3.83
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
318_T 223_Y 1.04 0.76 0.02
155_H 183_V 1.02 0.74 0.02
257_L 120_A 0.97 0.68 0.02
163_I 178_A 0.92 0.62 0.02
189_A 393_Y 0.92 0.62 0.02
243_D 397_F 0.89 0.59 0.02
177_R 195_F 0.85 0.53 0.01
15_G 373_M 0.82 0.49 0.01
226_L 213_V 0.78 0.44 0.01
94_A 195_F 0.77 0.43 0.01
21_I 119_D 0.77 0.42 0.01
138_S 394_L 0.76 0.42 0.01
227_A 176_I 0.76 0.41 0.01
301_H 7_E 0.75 0.40 0.01
108_E 258_A 0.75 0.40 0.01
318_T 67_L 0.75 0.40 0.01
138_S 278_G 0.74 0.40 0.01
243_D 393_Y 0.74 0.40 0.01
203_V 320_M 0.74 0.39 0.01
155_H 73_Q 0.74 0.39 0.01
333_S 175_T 0.73 0.38 0.01
237_T 380_F 0.71 0.36 0.01
57_T 258_A 0.71 0.36 0.01
106_T 373_M 0.70 0.34 0.01
333_S 216_L 0.70 0.34 0.01
264_V 229_G 0.70 0.34 0.01
120_A 162_L 0.69 0.33 0.01
261_L 254_F 0.69 0.32 0.01
221_T 345_G 0.68 0.32 0.01
258_S 262_G 0.68 0.32 0.01
27_P 64_T 0.67 0.31 0.01
258_S 191_V 0.67 0.30 0.01
97_F 106_R 0.67 0.30 0.01
264_V 141_V 0.67 0.30 0.01
116_V 311_R 0.66 0.30 0.01
82_F 371_A 0.66 0.30 0.01
263_G 366_V 0.66 0.29 0.01
107_F 135_L 0.66 0.29 0.01
155_H 94_Q 0.66 0.29 0.01
333_S 313_A 0.65 0.28 0.01
21_I 10_S 0.64 0.27 0.01
99_V 324_L 0.64 0.27 0.01
97_F 389_V 0.64 0.27 0.01
216_L 101_K 0.64 0.27 0.01
138_S 388_L 0.64 0.27 0.01
155_H 395_P 0.63 0.27 0.01
180_G 118_A 0.63 0.26 0.01
261_L 298_A 0.63 0.26 0.01
261_L 302_V 0.63 0.26 0.01
212_I 382_G 0.63 0.26 0.01
236_Q 366_V 0.63 0.26 0.01
156_I 80_S 0.62 0.26 0.01
163_I 112_E 0.62 0.26 0.01
272_N 301_K 0.62 0.26 0.01
264_V 275_R 0.62 0.25 0.01
202_L 392_M 0.61 0.25 0.01
107_F 389_V 0.61 0.25 0.01
226_L 105_I 0.61 0.24 0.01
155_H 195_F 0.61 0.24 0.01
238_I 92_S 0.61 0.24 0.01
114_V 255_A 0.61 0.24 0.01
233_S 353_K 0.61 0.24 0.01
238_I 299_G 0.61 0.24 0.01
27_P 384_T 0.61 0.24 0.01
155_H 210_T 0.61 0.24 0.01
7_L 273_F 0.61 0.24 0.01
193_I 283_S 0.60 0.24 0.01
174_V 399_L 0.60 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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