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OPENSEQ.org
2NUU-2
Genes: A B A+B
Length: 112 572 678
Sequences: 2544 2534 51
Seq/Len: 22.71 4.43 0.08
MirrorTree (Pazo et al. 2001) 0.59
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 0.04 0.01 0.00
2 0.06 0.01 0.01
5 0.06 0.01 0.02
10 0.06 0.01 0.05
20 0.06 0.01 0.07
100 0.07 0.05 0.31
∞ 0.19 0.12 1.26
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
65_I 42_F 1.72 0.24 0.00
61_I 536_I 1.71 0.24 0.00
4_V 370_R 1.62 0.21 0.00
17_R 300_F 1.61 0.21 0.00
70_L 476_M 1.48 0.17 0.00
10_P 79_L 1.44 0.16 0.00
59_V 491_S 1.40 0.15 0.00
73_V 376_I 1.38 0.15 0.00
100_I 42_F 1.37 0.14 0.00
28_L 365_R 1.34 0.14 0.00
96_L 433_A 1.31 0.13 0.00
110_A 551_A 1.31 0.13 0.00
4_V 476_M 1.25 0.12 0.00
96_L 126_A 1.25 0.12 0.00
74_I 413_R 1.21 0.11 0.00
9_K 533_K 1.20 0.11 0.00
97_Q 493_A 1.20 0.11 0.00
33_V 302_D 1.20 0.11 0.00
60_K 5_L 1.18 0.10 0.00
60_K 517_M 1.18 0.10 0.00
14_E 389_F 1.18 0.10 0.00
7_I 124_E 1.17 0.10 0.00
30_V 137_L 1.17 0.10 0.00
112_L 433_A 1.17 0.10 0.00
64_A 353_F 1.14 0.10 0.00
7_I 277_V 1.12 0.10 0.00
4_V 244_Q 1.11 0.09 0.00
61_I 433_A 1.11 0.09 0.00
49_A 408_Y 1.11 0.09 0.00
109_E 94_D 1.10 0.09 0.00
67_D 419_F 1.10 0.09 0.00
23_I 77_M 1.10 0.09 0.00
28_L 149_S 1.08 0.09 0.00
74_I 424_E 1.08 0.09 0.00
100_I 410_Q 1.08 0.09 0.00
4_V 389_F 1.08 0.09 0.00
73_V 182_A 1.07 0.09 0.00
9_K 427_V 1.07 0.09 0.00
110_A 291_V 1.06 0.09 0.00
109_E 229_N 1.06 0.09 0.00
15_D 157_L 1.06 0.09 0.00
17_R 533_K 1.06 0.09 0.00
67_D 261_I 1.05 0.09 0.00
110_A 198_L 1.05 0.08 0.00
76_I 137_L 1.05 0.08 0.00
31_T 540_N 1.04 0.08 0.00
36_F 15_A 1.03 0.08 0.00
107_A 277_V 1.03 0.08 0.00
74_I 253_A 1.03 0.08 0.00
15_D 456_T 1.03 0.08 0.00
100_I 389_F 1.03 0.08 0.00
108_D 166_E 1.03 0.08 0.00
5_T 277_V 1.02 0.08 0.00
22_S 418_A 1.02 0.08 0.00
7_I 305_A 1.02 0.08 0.00
71_D 54_E 1.02 0.08 0.00
110_A 411_E 1.02 0.08 0.00
106_E 102_A 1.02 0.08 0.00
70_L 250_A 1.01 0.08 0.00
95_E 493_A 1.01 0.08 0.00
31_T 371_D 1.00 0.08 0.00
55_F 341_L 1.00 0.08 0.00
6_V 363_M 1.00 0.08 0.00
61_I 34_Q 0.99 0.08 0.00
61_I 192_M 0.99 0.08 0.00
61_I 392_I 0.99 0.08 0.00
86_I 427_V 0.99 0.08 0.00
25_I 494_E 0.99 0.07 0.00
4_V 280_V 0.98 0.07 0.00
6_V 354_L 0.98 0.07 0.00
95_E 517_M 0.98 0.07 0.00
60_K 392_I 0.98 0.07 0.00
26_Q 260_A 0.98 0.07 0.00
41_G 332_T 0.98 0.07 0.00
68_D 507_D 0.98 0.07 0.00
25_I 436_T 0.97 0.07 0.00
17_R 407_I 0.97 0.07 0.00
36_F 388_M 0.97 0.07 0.00
4_V 380_S 0.97 0.07 0.00
110_A 205_G 0.97 0.07 0.00
79_K 419_F 0.96 0.07 0.00
54_N 348_K 0.96 0.07 0.00
49_A 511_T 0.96 0.07 0.00
102_I 477_S 0.96 0.07 0.00
34_K 300_F 0.96 0.07 0.00
101_R 391_M 0.96 0.07 0.00
74_I 373_L 0.96 0.07 0.00
55_F 524_M 0.95 0.07 0.00
71_D 235_I 0.95 0.07 0.00
97_Q 284_E 0.95 0.07 0.00
53_V 511_T 0.95 0.07 0.00
11_F 427_V 0.95 0.07 0.00
64_A 389_F 0.95 0.07 0.00
1_M 529_I 0.95 0.07 0.00
96_L 404_E 0.95 0.07 0.00
31_T 242_Q 0.95 0.07 0.00
99_V 305_A 0.94 0.07 0.00
76_I 325_S 0.94 0.07 0.00
17_R 439_R 0.94 0.07 0.00
56_L 74_G 0.94 0.07 0.00
82_Y 320_A 0.94 0.07 0.00
28_L 52_Q 0.93 0.07 0.00
5_T 111_A 0.93 0.07 0.00
73_V 442_A 0.93 0.07 0.00
94_A 443_K 0.93 0.07 0.00
45_L 280_V 0.93 0.07 0.00
61_I 402_R 0.92 0.07 0.00
59_V 326_Q 0.92 0.07 0.00
21_S 405_I 0.92 0.07 0.00
74_I 393_I 0.92 0.07 0.00
69_Q 154_E 0.92 0.07 0.00
91_I 158_V 0.92 0.07 0.00
1_M 391_M 0.92 0.07 0.00
110_A 185_R 0.91 0.07 0.00
59_V 254_K 0.91 0.07 0.00
76_I 476_M 0.91 0.07 0.00
61_I 196_L 0.91 0.07 0.00
97_Q 186_T 0.91 0.07 0.00
52_S 49_A 0.91 0.07 0.00
17_R 524_M 0.91 0.07 0.00
9_K 300_F 0.91 0.07 0.00
71_D 268_V 0.90 0.07 0.00
60_K 231_T 0.90 0.07 0.00
3_L 162_L 0.90 0.06 0.00
111_A 194_R 0.90 0.06 0.00
33_V 376_I 0.89 0.06 0.00
45_L 203_G 0.89 0.06 0.00
94_A 380_S 0.89 0.06 0.00
1_M 524_M 0.89 0.06 0.00
45_L 506_G 0.89 0.06 0.00
74_I 76_I 0.89 0.06 0.00
95_E 85_E 0.89 0.06 0.00
112_L 157_L 0.88 0.06 0.00
76_I 1_I 0.88 0.06 0.00
99_V 219_L 0.88 0.06 0.00
72_E 543_D 0.88 0.06 0.00
65_I 261_I 0.88 0.06 0.00
71_D 115_E 0.88 0.06 0.00
8_I 33_D 0.88 0.06 0.00
102_I 506_G 0.88 0.06 0.00
81_A 9_G 0.88 0.06 0.00
13_L 137_L 0.88 0.06 0.00
74_I 11_A 0.88 0.06 0.00
55_F 276_T 0.88 0.06 0.00
101_R 262_T 0.88 0.06 0.00
70_L 55_T 0.88 0.06 0.00
75_D 499_G 0.88 0.06 0.00
44_E 265_G 0.88 0.06 0.00
107_A 71_I 0.87 0.06 0.00
92_F 119_D 0.87 0.06 0.00
53_V 537_R 0.87 0.06 0.00
102_I 15_A 0.87 0.06 0.00
56_L 300_F 0.87 0.06 0.00
9_K 74_G 0.86 0.06 0.00
76_I 78_L 0.86 0.06 0.00
64_A 296_T 0.86 0.06 0.00
61_I 540_N 0.86 0.06 0.00
112_L 127_A 0.86 0.06 0.00
12_K 503_E 0.86 0.06 0.00
62_D 270_V 0.86 0.06 0.00
95_E 260_A 0.86 0.06 0.00
28_L 201_I 0.86 0.06 0.00
100_I 530_P 0.86 0.06 0.00
3_L 72_F 0.85 0.06 0.00
108_D 270_V 0.85 0.06 0.00
31_T 532_I 0.85 0.06 0.00
56_L 41_R 0.85 0.06 0.00
85_K 470_S 0.85 0.06 0.00
78_S 208_T 0.85 0.06 0.00
61_I 36_D 0.85 0.06 0.00
8_I 537_R 0.85 0.06 0.00
22_S 387_I 0.85 0.06 0.00
74_I 185_R 0.85 0.06 0.00
23_I 322_A 0.85 0.06 0.00
45_L 78_L 0.85 0.06 0.00
65_I 249_K 0.85 0.06 0.00
106_E 503_E 0.85 0.06 0.00
75_D 196_L 0.85 0.06 0.00
8_I 345_N 0.85 0.06 0.00
21_S 401_L 0.84 0.06 0.00
112_L 358_A 0.84 0.06 0.00
59_V 87_E 0.84 0.06 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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