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OPENSEQ.org
UvrD_MutL
Genes: A B A+B
Length: 720 615 1229
Sequences: 3643 884 340
Seq/Len: 5.06 1.44 0.28
MirrorTree (Pazo et al. 2001) 0.46
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 0.11 0.05 0.00
2 0.11 0.05 0.00
5 0.11 0.05 0.00
10 0.11 0.05 0.00
20 0.11 0.05 0.01
100 0.12 0.05 0.04
∞ 0.17 0.05 0.25
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
71_R 264_R 1.72 0.54 0.00
562_A 185_V 1.26 0.26 0.00
363_L 46_I 1.26 0.26 0.00
388_I 175_I 1.24 0.25 0.00
39_L 217_G 1.21 0.23 0.00
554_V 322_I 1.21 0.23 0.00
367_L 163_T 1.20 0.23 0.00
602_G 310_V 1.20 0.23 0.00
410_V 292_L 1.14 0.20 0.00
158_H 42_I 1.14 0.20 0.00
27_V 523_I 1.12 0.20 0.00
158_H 91_S 1.11 0.19 0.00
393_S 91_S 1.11 0.19 0.00
552_D 145_L 1.03 0.16 0.00
210_Y 34_S 1.03 0.16 0.00
159_I 105_V 1.01 0.15 0.00
388_I 228_E 1.01 0.15 0.00
170_W 491_K 0.99 0.15 0.00
320_L 185_V 0.99 0.15 0.00
367_L 442_V 0.99 0.15 0.00
572_I 108_L 0.99 0.15 0.00
491_R 106_S 0.99 0.15 0.00
575_M 263_M 0.99 0.15 0.00
330_A 107_R 0.99 0.15 0.00
352_I 20_V 0.99 0.15 0.00
484_V 59_N 0.98 0.14 0.00
328_D 322_I 0.98 0.14 0.00
233_I 104_S 0.97 0.14 0.00
217_I 322_I 0.97 0.14 0.00
388_I 287_A 0.97 0.14 0.00
310_T 110_L 0.97 0.14 0.00
72_H 329_V 0.96 0.14 0.00
610_L 110_L 0.96 0.14 0.00
427_R 543_I 0.95 0.14 0.00
602_G 145_L 0.95 0.13 0.00
106_N 562_A 0.95 0.13 0.00
206_I 215_I 0.94 0.13 0.00
126_L 322_I 0.94 0.13 0.00
94_A 567_S 0.93 0.13 0.00
562_A 228_E 0.93 0.13 0.00
39_L 105_V 0.92 0.13 0.00
122_L 328_S 0.91 0.12 0.00
111_F 276_C 0.91 0.12 0.00
335_N 290_L 0.91 0.12 0.00
215_T 34_S 0.91 0.12 0.00
101_H 472_L 0.91 0.12 0.00
179_E 325_G 0.90 0.12 0.00
97_L 162_R 0.90 0.12 0.00
509_L 104_S 0.90 0.12 0.00
184_A 185_V 0.90 0.12 0.00
406_A 541_E 0.90 0.12 0.00
592_L 106_S 0.90 0.12 0.00
134_E 171_I 0.90 0.12 0.00
243_V 322_I 0.90 0.12 0.00
569_Q 289_V 0.89 0.12 0.00
552_D 325_G 0.89 0.12 0.00
186_L 543_I 0.88 0.12 0.00
97_L 116_E 0.88 0.12 0.00
92_G 189_L 0.88 0.11 0.00
330_A 472_L 0.88 0.11 0.00
219_V 145_L 0.87 0.11 0.00
391_A 225_L 0.87 0.11 0.00
612_L 266_R 0.87 0.11 0.00
371_S 444_S 0.87 0.11 0.00
292_A 110_L 0.87 0.11 0.00
418_I 567_S 0.87 0.11 0.00
231_A 59_N 0.87 0.11 0.00
418_I 486_I 0.87 0.11 0.00
329_E 279_K 0.86 0.11 0.00
320_L 67_E 0.86 0.11 0.00
346_A 34_S 0.86 0.11 0.00
279_L 311_R 0.86 0.11 0.00
318_I 125_A 0.86 0.11 0.00
388_I 196_V 0.85 0.11 0.00
233_I 185_V 0.85 0.11 0.00
391_A 322_I 0.85 0.11 0.00
56_S 145_L 0.85 0.11 0.00
27_V 194_K 0.85 0.11 0.00
586_L 481_A 0.85 0.11 0.00
558_T 559_Q 0.85 0.10 0.00
458_L 454_N 0.85 0.10 0.00
74_I 192_N 0.85 0.10 0.00
183_R 240_V 0.85 0.10 0.00
217_I 2_P 0.84 0.10 0.00
391_A 106_S 0.84 0.10 0.00
426_V 290_L 0.84 0.10 0.00
74_I 514_F 0.84 0.10 0.00
310_T 44_I 0.84 0.10 0.00
183_R 557_I 0.84 0.10 0.00
213_R 181_A 0.84 0.10 0.00
428_Q 322_I 0.84 0.10 0.00
226_N 110_L 0.84 0.10 0.00
484_V 326_V 0.84 0.10 0.00
636_L 293_E 0.83 0.10 0.00
562_A 263_M 0.83 0.10 0.00
110_D 154_T 0.83 0.10 0.00
367_L 216_C 0.83 0.10 0.00
296_L 225_L 0.83 0.10 0.00
352_I 66_D 0.83 0.10 0.00
294_N 608_A 0.83 0.10 0.00
608_Q 227_I 0.83 0.10 0.00
570_V 272_I 0.83 0.10 0.00
599_A 524_R 0.83 0.10 0.00
47_M 109_T 0.82 0.10 0.00
266_R 89_I 0.82 0.10 0.00
607_M 539_I 0.82 0.10 0.00
166_V 194_K 0.82 0.10 0.00
426_V 264_R 0.82 0.10 0.00
354_Y 89_I 0.82 0.10 0.00
392_L 546_L 0.82 0.10 0.00
391_A 568_E 0.82 0.10 0.00
469_A 524_R 0.82 0.10 0.00
155_R 215_I 0.81 0.10 0.00
622_G 171_I 0.81 0.10 0.00
262_E 523_I 0.81 0.10 0.00
388_I 263_M 0.81 0.10 0.00
266_R 243_P 0.81 0.10 0.00
169_T 326_V 0.81 0.10 0.00
575_M 7_P 0.81 0.10 0.00
512_L 294_I 0.81 0.10 0.00
333_V 7_P 0.81 0.10 0.00
59_A 55_R 0.81 0.10 0.00
62_F 473_T 0.81 0.10 0.00
231_A 100_A 0.80 0.10 0.00
140_R 496_E 0.80 0.10 0.00
62_F 294_I 0.80 0.10 0.00
92_G 113_R 0.80 0.09 0.00
173_V 91_S 0.80 0.09 0.00
125_R 185_V 0.80 0.09 0.00
259_A 245_H 0.80 0.09 0.00
552_D 129_D 0.80 0.09 0.00
558_T 442_V 0.80 0.09 0.00
333_V 264_R 0.80 0.09 0.00
315_G 505_S 0.80 0.09 0.00
231_A 108_L 0.79 0.09 0.00
410_V 152_Y 0.79 0.09 0.00
545_G 120_A 0.79 0.09 0.00
426_V 272_I 0.79 0.09 0.00
30_G 577_A 0.79 0.09 0.00
348_A 34_S 0.79 0.09 0.00
558_T 246_T 0.79 0.09 0.00
503_Q 188_N 0.79 0.09 0.00
363_L 488_L 0.79 0.09 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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