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OPENSEQ.org
pgktdh
Genes: A B A+B
Length: 416 332 724
Sequences: 1858 3049 851
Seq/Len: 4.47 9.18 1.18
MirrorTree (Pazo et al. 2001) 0.51
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 0.00 0.00 1.01
2 0.01 0.01 1.08
5 0.01 0.01 1.11
10 0.01 0.01 1.13
20 0.01 0.01 1.14
100 0.01 0.02 1.22
∞ 0.01 0.11 1.65
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
150_H 3_R 0.90 0.29 0.00
259_A 129_F 0.89 0.28 0.00
25_F 320_T 0.88 0.28 0.00
397_S 138_Y 0.81 0.23 0.00
308_G 164_D 0.80 0.22 0.00
192_L 83_L 0.77 0.20 0.00
327_A 31_L 0.76 0.19 0.00
368_I 309_V 0.74 0.18 0.00
390_V 217_K 0.74 0.18 0.00
229_V 323_V 0.73 0.18 0.00
34_I 112_A 0.73 0.18 0.00
311_G 279_V 0.73 0.18 0.00
279_V 256_I 0.73 0.18 0.00
51_L 54_Y 0.72 0.17 0.00
376_T 123_S 0.72 0.17 0.00
67_P 132_G 0.72 0.17 0.00
399_E 182_T 0.72 0.17 0.00
366_T 3_R 0.71 0.17 0.00
56_R 267_K 0.70 0.16 0.00
148_F 140_S 0.70 0.16 0.00
195_F 31_L 0.69 0.16 0.00
62_S 245_V 0.69 0.16 0.00
192_L 255_E 0.69 0.15 0.00
320_K 262_A 0.69 0.15 0.00
240_F 279_V 0.68 0.15 0.00
186_F 208_S 0.68 0.15 0.00
397_S 318_Y 0.68 0.15 0.00
115_V 106_A 0.68 0.15 0.00
308_G 4_V 0.68 0.15 0.00
290_F 320_T 0.67 0.14 0.00
270_K 252_T 0.67 0.14 0.00
147_K 79_D 0.66 0.14 0.00
405_E 235_T 0.66 0.14 0.00
325_T 62_D 0.66 0.14 0.00
204_R 276_E 0.66 0.14 0.00
114_S 225_K 0.66 0.14 0.00
210_L 237_D 0.66 0.14 0.00
326_V 176_V 0.66 0.14 0.00
47_I 60_H 0.66 0.14 0.00
318_S 5_A 0.66 0.14 0.00
381_Y 205_I 0.65 0.14 0.00
215_V 144_I 0.65 0.14 0.00
240_F 277_D 0.65 0.14 0.00
278_V 20_A 0.65 0.13 0.00
125_I 271_V 0.65 0.13 0.00
240_F 324_D 0.64 0.13 0.00
56_R 178_S 0.64 0.13 0.00
14_L 247_L 0.63 0.13 0.00
344_E 63_K 0.63 0.13 0.00
149_R 204_I 0.63 0.13 0.00
9_V 273_G 0.63 0.13 0.00
188_L 297_A 0.63 0.12 0.00
9_V 50_T 0.63 0.12 0.00
347_A 307_K 0.62 0.12 0.00
271_A 42_A 0.62 0.12 0.00
67_P 317_G 0.62 0.12 0.00
291_S 86_G 0.62 0.12 0.00
174_M 144_I 0.62 0.12 0.00
44_L 230_A 0.62 0.12 0.00
233_I 84_P 0.62 0.12 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)
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