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OPENSEQ.org
Complexe NarL-NarX
Genes: A B A+B
Length: 216 598 799
Sequences: 37243 712 344
Seq/Len: 172.42 1.19 0.43
MirrorTree (Pazo et al. 2001) 0.77
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 0.01 0.00 0.35
2 0.02 0.00 0.36
5 0.04 0.00 0.36
10 0.07 0.00 0.38
20 0.11 0.00 0.42
100 0.21 0.01 0.60
∞ 0.26 0.08 0.80
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
11_L 246_Q 1.70 0.66 0.00
32_I 462_R 1.47 0.49 0.00
114_E 360_Q 1.40 0.44 0.00
39_S 464_A 1.35 0.41 0.00
83_I 108_N 1.31 0.38 0.00
68_L 456_L 1.28 0.36 0.00
11_L 161_V 1.24 0.33 0.00
84_V 343_I 1.21 0.31 0.00
60_L 258_L 1.21 0.31 0.00
185_S 384_Q 1.21 0.31 0.00
102_G 538_G 1.20 0.30 0.00
74_L 123_V 1.18 0.29 0.00
157_T 451_T 1.17 0.28 0.00
11_L 385_L 1.16 0.28 0.00
177_A 223_L 1.16 0.28 0.00
191_V 156_H 1.14 0.27 0.00
120_L 408_C 1.11 0.26 0.00
33_T 534_V 1.11 0.25 0.00
9_I 429_E 1.11 0.25 0.00
141_S 495_Q 1.11 0.25 0.00
109_K 540_G 1.10 0.25 0.00
109_K 552_G 1.10 0.25 0.00
36_G 112_P 1.09 0.24 0.00
11_L 459_P 1.08 0.24 0.00
109_K 536_D 1.08 0.24 0.00
109_K 509_N 1.08 0.23 0.00
114_E 198_T 1.07 0.23 0.00
161_R 220_S 1.07 0.23 0.00
167_I 557_R 1.07 0.23 0.00
71_L 241_L 1.06 0.23 0.00
10_L 514_S 1.06 0.23 0.00
9_I 539_C 1.06 0.22 0.00
193_H 405_S 1.06 0.22 0.00
185_S 461_L 1.06 0.22 0.00
132_E 431_L 1.05 0.22 0.00
34_V 429_E 1.05 0.22 0.00
184_E 230_L 1.05 0.22 0.00
9_I 276_Q 1.05 0.22 0.00
210_V 14_Q 1.05 0.22 0.00
95_V 254_A 1.05 0.22 0.00
113_P 445_L 1.05 0.22 0.00
74_L 143_R 1.05 0.22 0.00
132_E 195_R 1.04 0.22 0.00
172_P 577_T 1.03 0.21 0.00
27_S 578_E 1.03 0.21 0.00
83_I 299_E 1.01 0.20 0.00
11_L 450_T 1.01 0.20 0.00
157_T 495_Q 1.01 0.20 0.00
67_G 540_G 1.00 0.20 0.00
67_G 552_G 1.00 0.20 0.00
45_I 333_R 1.00 0.20 0.00
159_R 502_I 1.00 0.20 0.00
22_V 567_C 1.00 0.20 0.00
83_I 171_I 0.99 0.19 0.00
112_E 438_L 0.99 0.19 0.00
198_M 491_V 0.99 0.19 0.00
22_V 199_Q 0.99 0.19 0.00
60_L 272_L 0.99 0.19 0.00
59_D 540_G 0.98 0.19 0.00
59_D 552_G 0.98 0.19 0.00
67_G 536_D 0.98 0.19 0.00
67_G 509_N 0.98 0.19 0.00
85_V 286_L 0.98 0.19 0.00
100_K 217_N 0.97 0.18 0.00
22_V 15_V 0.97 0.18 0.00
9_I 275_L 0.97 0.18 0.00
69_E 331_K 0.97 0.18 0.00
102_G 512_K 0.96 0.18 0.00
59_D 536_D 0.96 0.18 0.00
59_D 509_N 0.96 0.18 0.00
33_T 515_Q 0.96 0.18 0.00
113_P 503_A 0.96 0.18 0.00
83_I 107_R 0.96 0.18 0.00
8_T 573_E 0.96 0.18 0.00
76_E 534_V 0.95 0.18 0.00
123_A 177_R 0.95 0.18 0.00
162_D 152_V 0.95 0.17 0.00
181_D 472_Y 0.94 0.17 0.00
185_S 36_L 0.94 0.17 0.00
85_V 161_V 0.94 0.17 0.00
182_I 443_A 0.94 0.17 0.00
31_D 90_A 0.94 0.17 0.00
213_E 151_T 0.94 0.17 0.00
45_I 217_N 0.93 0.17 0.00
199_K 246_Q 0.93 0.17 0.00
44_G 259_H 0.93 0.17 0.00
205_E 346_A 0.93 0.17 0.00
72_D 116_R 0.93 0.17 0.00
35_V 70_D 0.93 0.17 0.00
192_K 414_S 0.92 0.16 0.00
192_K 445_L 0.92 0.16 0.00
79_L 242_E 0.92 0.16 0.00
44_G 507_L 0.92 0.16 0.00
163_I 152_V 0.92 0.16 0.00
167_I 534_V 0.92 0.16 0.00
93_E 334_L 0.91 0.16 0.00
85_V 420_G 0.91 0.16 0.00
9_I 210_A 0.91 0.16 0.00
130_L 63_A 0.91 0.16 0.00
34_V 93_D 0.91 0.16 0.00
87_S 366_V 0.91 0.16 0.00
142_L 250_F 0.91 0.16 0.00
194_M 195_R 0.91 0.16 0.00
85_V 271_V 0.91 0.15 0.00
185_S 95_Q 0.91 0.15 0.00
40_N 573_E 0.90 0.15 0.00
62_M 338_H 0.90 0.15 0.00
12_I 142_D 0.90 0.15 0.00
135_T 450_T 0.90 0.15 0.00
179_R 10_T 0.90 0.15 0.00
120_L 235_Q 0.90 0.15 0.00
75_R 373_L 0.90 0.15 0.00
198_M 273_N 0.90 0.15 0.00
9_I 411_M 0.90 0.15 0.00
91_H 431_L 0.89 0.15 0.00
55_L 569_V 0.89 0.15 0.00
35_V 27_L 0.89 0.15 0.00
161_R 480_V 0.89 0.15 0.00
22_V 563_L 0.89 0.15 0.00
136_P 165_L 0.89 0.15 0.00
157_T 397_E 0.89 0.15 0.00
11_L 502_I 0.88 0.15 0.00
98_A 414_S 0.88 0.15 0.00
154_N 413_V 0.88 0.15 0.00
7_A 541_V 0.88 0.15 0.00
68_L 462_R 0.88 0.14 0.00
69_E 114_L 0.88 0.14 0.00
191_V 26_G 0.88 0.14 0.00
26_I 341_Y 0.87 0.14 0.00
86_F 472_Y 0.87 0.14 0.00
98_A 187_A 0.87 0.14 0.00
157_T 501_Q 0.87 0.14 0.00
65_M 583_F 0.87 0.14 0.00
194_M 271_V 0.87 0.14 0.00
98_A 471_E 0.87 0.14 0.00
94_D 58_Y 0.87 0.14 0.00
103_A 512_K 0.86 0.14 0.00
36_G 370_T 0.86 0.14 0.00
35_V 236_E 0.86 0.14 0.00
75_R 397_E 0.86 0.14 0.00
41_G 502_I 0.86 0.14 0.00
87_S 420_G 0.86 0.14 0.00
16_P 583_F 0.86 0.14 0.00
102_G 540_G 0.86 0.14 0.00
102_G 552_G 0.86 0.14 0.00
206_A 388_M 0.86 0.14 0.00
209_W 503_A 0.86 0.14 0.00
55_L 194_H 0.86 0.14 0.00
84_V 64_V 0.85 0.14 0.00
74_L 129_Q 0.85 0.14 0.00
99_L 47_I 0.85 0.14 0.00
8_T 534_V 0.85 0.14 0.00
24_Q 445_L 0.85 0.14 0.00
99_L 534_V 0.85 0.14 0.00
32_I 62_A 0.85 0.13 0.00
14_D 540_G 0.85 0.13 0.00
14_D 552_G 0.85 0.13 0.00
11_L 378_H 0.85 0.13 0.00
163_I 554_I 0.85 0.13 0.00
9_I 11_L 0.85 0.13 0.00
44_G 435_R 0.84 0.13 0.00
213_E 310_D 0.84 0.13 0.00
72_D 255_N 0.84 0.13 0.00
95_V 365_L 0.84 0.13 0.00
103_A 272_L 0.84 0.13 0.00
10_L 563_L 0.84 0.13 0.00
84_V 165_L 0.84 0.13 0.00
99_L 537_N 0.84 0.13 0.00
114_E 63_A 0.84 0.13 0.00
156_L 567_C 0.84 0.13 0.00
131_S 407_S 0.84 0.13 0.00
194_M 522_T 0.83 0.13 0.00
102_G 536_D 0.83 0.13 0.00
25_L 453_R 0.83 0.13 0.00
39_S 178_L 0.83 0.13 0.00
165_K 561_Q 0.83 0.13 0.00
102_G 509_N 0.83 0.13 0.00
22_V 218_N 0.83 0.13 0.00
83_I 580_V 0.83 0.13 0.00
27_S 503_A 0.83 0.13 0.00
213_E 209_M 0.83 0.13 0.00
45_I 429_E 0.83 0.13 0.00
34_V 193_S 0.83 0.13 0.00
205_E 149_I 0.83 0.13 0.00
16_P 504_R 0.83 0.13 0.00
85_V 18_I 0.83 0.13 0.00
157_T 411_M 0.83 0.13 0.00
13_D 512_K 0.83 0.13 0.00
185_S 217_N 0.82 0.13 0.00
109_K 538_G 0.82 0.13 0.00
162_D 420_G 0.82 0.13 0.00
192_K 410_K 0.82 0.13 0.00
110_D 445_L 0.82 0.13 0.00
8_T 207_N 0.82 0.13 0.00
22_V 96_L 0.82 0.13 0.00
14_D 536_D 0.82 0.13 0.00
193_H 365_L 0.82 0.13 0.00
110_D 444_Q 0.82 0.13 0.00
14_D 509_N 0.82 0.13 0.00
84_V 431_L 0.82 0.12 0.00
178_R 272_L 0.82 0.12 0.00
84_V 486_L 0.82 0.12 0.00
43_Q 275_L 0.81 0.12 0.00
101_R 162_F 0.81 0.12 0.00
175_M 572_R 0.81 0.12 0.00
199_K 200_R 0.81 0.12 0.00
128_M 476_F 0.81 0.12 0.00
117_L 147_M 0.81 0.12 0.00
33_T 338_H 0.81 0.12 0.00
33_T 584_I 0.81 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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