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OPENSEQ.org
PCC Me (A, 1-450)
Genes: A B A+B
Length: 450 510 940
Sequences: 11784 3878 1701
Seq/Len: 26.19 7.6 1.81
MirrorTree (Pazo et al. 2001) 0.44
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 0.02 0.01 0.82
2 0.02 0.01 1.27
5 0.03 0.01 1.56
10 0.05 0.01 1.71
20 0.07 0.02 1.77
100 0.12 0.04 1.99
∞ 0.22 0.13 2.57
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
100_I 358_F 0.95 0.44 0.00
445_F 214_A 0.95 0.43 0.00
287_L 193_T 0.94 0.42 0.00
351_S 397_I 0.92 0.41 0.00
277_V 218_T 0.90 0.38 0.00
108_G 396_I 0.90 0.38 0.00
68_D 290_V 0.88 0.36 0.00
103_I 446_D 0.86 0.35 0.00
195_D 37_E 0.84 0.33 0.00
375_T 286_L 0.83 0.32 0.00
395_V 356_V 0.82 0.31 0.00
406_E 75_V 0.81 0.30 0.00
426_F 231_D 0.81 0.30 0.00
339_V 480_H 0.81 0.30 0.00
146_T 123_I 0.81 0.30 0.00
78_V 321_F 0.81 0.29 0.00
7_I 322_V 0.80 0.29 0.00
131_V 37_E 0.79 0.28 0.00
374_D 269_L 0.76 0.26 0.00
335_V 45_H 0.76 0.25 0.00
433_H 138_A 0.75 0.25 0.00
414_A 230_N 0.75 0.25 0.00
120_K 401_A 0.75 0.24 0.00
57_A 117_K 0.74 0.24 0.00
103_I 22_K 0.74 0.24 0.00
5_I 43_L 0.74 0.24 0.00
419_G 206_V 0.73 0.23 0.00
221_V 242_L 0.73 0.23 0.00
304_T 397_I 0.73 0.23 0.00
384_A 119_R 0.73 0.23 0.00
5_I 356_V 0.73 0.23 0.00
121_K 123_I 0.73 0.23 0.00
78_V 22_K 0.72 0.23 0.00
82_Y 158_P 0.72 0.23 0.00
394_L 162_V 0.72 0.22 0.00
266_V 338_S 0.71 0.22 0.00
284_F 193_T 0.71 0.22 0.00
179_E 352_S 0.71 0.22 0.00
327_Q 319_V 0.69 0.20 0.00
327_Q 123_I 0.69 0.20 0.00
385_I 377_K 0.69 0.20 0.00
130_T 332_V 0.69 0.20 0.00
384_A 51_F 0.69 0.20 0.00
7_I 286_L 0.69 0.20 0.00
126_A 76_T 0.69 0.20 0.00
107_P 352_S 0.69 0.20 0.00
209_I 272_L 0.68 0.20 0.00
313_I 228_F 0.68 0.20 0.00
239_I 250_I 0.68 0.20 0.00
422_H 210_E 0.68 0.20 0.00
355_L 40_E 0.68 0.19 0.00
17_I 236_L 0.68 0.19 0.00
189_S 40_E 0.68 0.19 0.00
391_I 207_T 0.67 0.19 0.00
349_L 364_F 0.67 0.19 0.00
250_E 230_N 0.67 0.19 0.00
5_I 489_A 0.67 0.19 0.00
204_T 160_I 0.67 0.19 0.00
110_I 123_I 0.67 0.19 0.00
394_L 236_L 0.67 0.19 0.00
7_I 161_S 0.67 0.19 0.00
400_T 303_Y 0.67 0.19 0.00
109_A 308_I 0.67 0.19 0.00
239_I 397_I 0.67 0.18 0.00
299_V 75_V 0.66 0.18 0.00
371_V 17_L 0.66 0.18 0.00
49_V 123_I 0.66 0.18 0.00
376_G 314_V 0.66 0.18 0.00
228_E 203_N 0.65 0.18 0.00
4_K 218_T 0.65 0.17 0.00
278_A 86_V 0.65 0.17 0.00
287_L 476_V 0.65 0.17 0.00
347_N 123_I 0.65 0.17 0.00
198_F 279_K 0.65 0.17 0.00
86_S 129_G 0.65 0.17 0.00
403_E 273_I 0.65 0.17 0.00
211_I 75_V 0.64 0.17 0.00
391_I 218_T 0.64 0.17 0.00
78_V 302_A 0.64 0.17 0.00
244_S 53_M 0.64 0.17 0.00
421_R 75_V 0.64 0.17 0.00
280_Q 476_V 0.64 0.17 0.00
421_R 394_V 0.64 0.17 0.00
156_M 198_V 0.64 0.17 0.00
95_L 123_I 0.64 0.17 0.00
254_K 215_K 0.63 0.17 0.00
86_S 342_A 0.63 0.16 0.00
432_A 123_I 0.63 0.16 0.00
395_V 88_L 0.63 0.16 0.00
35_A 181_I 0.63 0.16 0.00
97_E 290_V 0.63 0.16 0.00
402_L 356_V 0.63 0.16 0.00
213_V 97_G 0.63 0.16 0.00
209_I 83_G 0.63 0.16 0.00
203_I 342_A 0.62 0.16 0.00
425_P 123_I 0.62 0.16 0.00
398_A 476_V 0.62 0.16 0.00
231_I 183_M 0.62 0.16 0.00
239_I 293_E 0.62 0.16 0.00
420_I 88_L 0.62 0.16 0.00
126_A 402_F 0.62 0.16 0.00
255_M 88_L 0.62 0.16 0.00
67_I 341_A 0.62 0.16 0.00
66_I 272_L 0.62 0.16 0.00
102_F 275_D 0.62 0.16 0.00
285_Y 394_V 0.62 0.16 0.00
239_I 40_E 0.62 0.16 0.00
434_P 247_A 0.62 0.16 0.00
242_A 182_F 0.62 0.16 0.00
267_N 241_L 0.61 0.15 0.00
54_A 230_N 0.61 0.15 0.00
24_M 33_L 0.61 0.15 0.00
120_K 271_T 0.61 0.15 0.00
395_V 240_R 0.61 0.15 0.00
443_T 474_D 0.61 0.15 0.00
389_P 145_E 0.61 0.15 0.00
371_V 473_I 0.61 0.15 0.00
44_M 322_V 0.61 0.15 0.00
198_F 433_K 0.61 0.15 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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