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OPENSEQ.org
ftszftsi Ecoli
Genes: A B A+B
Length: 383 588 867
Sequences: 2098 5960 1605
Seq/Len: 5.48 10.14 1.85
MirrorTree (Pazo et al. 2001) 0.65
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 0.06 0.00
2 0.02 0.06 0.01
5 0.02 0.06 0.15
10 0.02 0.07 0.98
20 0.02 0.07 1.65
100 0.03 0.10 1.78
∞ 0.05 0.23 2.13
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
60_I 38_L 1.06 0.57 0.00
121_K 189_I 0.97 0.47 0.00
286_A 45_L 0.97 0.47 0.00
119_V 385_L 0.97 0.47 0.00
183_G 480_G 0.97 0.47 0.00
128_V 32_L 0.96 0.46 0.00
230_A 427_Q 0.94 0.44 0.00
302_M 269_T 0.93 0.43 0.00
115_V 308_T 0.88 0.37 0.00
116_V 215_G 0.87 0.36 0.00
226_G 479_G 0.86 0.35 0.00
162_T 369_L 0.86 0.35 0.00
80_A 365_S 0.85 0.34 0.00
233_E 234_L 0.85 0.34 0.00
228_G 54_V 0.84 0.34 0.00
115_V 75_T 0.84 0.33 0.00
281_T 218_I 0.83 0.33 0.00
35_E 232_L 0.83 0.32 0.00
38_E 409_D 0.82 0.32 0.00
228_G 417_F 0.82 0.31 0.00
60_I 239_R 0.81 0.30 0.00
180_D 318_L 0.80 0.29 0.00
151_T 471_M 0.80 0.29 0.00
123_L 526_F 0.79 0.28 0.00
150_I 172_G 0.78 0.28 0.00
180_D 189_I 0.78 0.28 0.00
95_A 417_F 0.78 0.27 0.00
80_A 367_L 0.77 0.27 0.00
148_Q 74_I 0.77 0.27 0.00
318_D 232_L 0.77 0.27 0.00
121_K 468_V 0.77 0.27 0.00
16_I 468_V 0.77 0.26 0.00
116_V 93_A 0.76 0.26 0.00
183_G 475_A 0.76 0.26 0.00
147_E 37_F 0.76 0.26 0.00
183_G 269_T 0.75 0.25 0.00
57_T 62_L 0.75 0.25 0.00
176_I 354_G 0.75 0.25 0.00
177_S 467_V 0.75 0.25 0.00
233_E 417_F 0.75 0.25 0.00
60_I 198_K 0.74 0.25 0.00
286_A 282_N 0.74 0.24 0.00
305_E 235_S 0.74 0.24 0.00
181_A 205_G 0.73 0.24 0.00
92_L 409_D 0.73 0.24 0.00
206_M 61_S 0.73 0.24 0.00
76_V 287_S 0.73 0.24 0.00
205_L 486_I 0.73 0.23 0.00
308_V 113_L 0.73 0.23 0.00
300_P 525_R 0.73 0.23 0.00
282_I 34_A 0.73 0.23 0.00
219_E 284_N 0.73 0.23 0.00
264_I 271_E 0.72 0.23 0.00
79_N 42_V 0.72 0.23 0.00
302_M 528_L 0.72 0.23 0.00
167_K 395_G 0.72 0.23 0.00
40_F 470_M 0.72 0.23 0.00
152_E 139_L 0.72 0.22 0.00
18_V 434_T 0.72 0.22 0.00
58_I 552_A 0.71 0.22 0.00
208_V 559_R 0.71 0.22 0.00
244_I 236_I 0.71 0.22 0.00
214_R 431_V 0.71 0.22 0.00
283_R 156_L 0.71 0.22 0.00
55_G 518_V 0.71 0.22 0.00
180_D 276_A 0.71 0.22 0.00
52_T 69_T 0.71 0.22 0.00
97_M 416_S 0.70 0.22 0.00
191_G 419_Y 0.70 0.21 0.00
163_I 393_L 0.70 0.21 0.00
21_G 357_Q 0.70 0.21 0.00
230_A 370_A 0.70 0.21 0.00
218_S 327_S 0.70 0.21 0.00
315_I 205_G 0.69 0.21 0.00
300_P 354_G 0.69 0.21 0.00
179_L 293_A 0.69 0.21 0.00
48_A 41_R 0.69 0.21 0.00
88_L 513_A 0.69 0.21 0.00
264_I 177_H 0.69 0.21 0.00
282_I 531_V 0.69 0.21 0.00
98_V 122_D 0.69 0.20 0.00
269_D 352_L 0.69 0.20 0.00
92_L 91_I 0.69 0.20 0.00
91_A 285_N 0.69 0.20 0.00
245_S 383_F 0.69 0.20 0.00
315_I 371_M 0.69 0.20 0.00
136_N 91_I 0.68 0.20 0.00
34_I 355_V 0.68 0.20 0.00
162_T 32_L 0.68 0.20 0.00
150_I 159_I 0.68 0.20 0.00
33_R 82_L 0.68 0.20 0.00
72_A 343_D 0.68 0.20 0.00
118_E 272_V 0.68 0.20 0.00
16_I 143_V 0.68 0.20 0.00
171_V 471_M 0.68 0.20 0.00
234_D 298_T 0.68 0.20 0.00
252_I 303_F 0.68 0.20 0.00
272_L 499_K 0.68 0.20 0.00
244_I 278_S 0.68 0.19 0.00
296_T 319_Q 0.68 0.19 0.00
187_D 86_V 0.67 0.19 0.00
115_V 33_L 0.67 0.19 0.00
76_V 328_V 0.67 0.19 0.00
125_I 93_A 0.67 0.19 0.00
234_D 375_A 0.67 0.19 0.00
87_A 36_A 0.67 0.19 0.00
94_G 195_S 0.67 0.19 0.00
269_D 218_I 0.67 0.19 0.00
192_A 278_S 0.67 0.19 0.00
259_G 234_L 0.67 0.19 0.00
259_G 248_L 0.67 0.19 0.00
121_K 277_N 0.67 0.19 0.00
73_N 46_Q 0.67 0.19 0.00
290_A 46_Q 0.67 0.19 0.00
159_S 311_P 0.66 0.19 0.00
163_I 255_N 0.66 0.19 0.00
26_V 122_D 0.66 0.19 0.00
252_I 514_Y 0.66 0.19 0.00
304_D 365_S 0.66 0.19 0.00
141_K 201_T 0.66 0.18 0.00
206_M 539_K 0.66 0.18 0.00
242_M 459_F 0.66 0.18 0.00
313_T 284_N 0.66 0.18 0.00
308_V 63_R 0.66 0.18 0.00
82_D 226_S 0.66 0.18 0.00
311_V 24_F 0.66 0.18 0.00
75_E 459_F 0.66 0.18 0.00
180_D 415_F 0.66 0.18 0.00
231_S 530_V 0.66 0.18 0.00
265_T 93_A 0.65 0.18 0.00
101_A 229_A 0.65 0.18 0.00
115_V 184_V 0.65 0.18 0.00
251_D 364_V 0.65 0.18 0.00
145_F 471_M 0.65 0.18 0.00
282_I 556_G 0.65 0.18 0.00
147_E 176_A 0.65 0.18 0.00
57_T 235_S 0.65 0.18 0.00
272_L 507_Y 0.65 0.18 0.00
85_R 259_S 0.65 0.18 0.00
198_E 308_T 0.65 0.18 0.00
96_D 399_G 0.65 0.18 0.00
18_V 452_P 0.64 0.17 0.00
274_E 416_S 0.64 0.17 0.00
233_E 42_V 0.64 0.17 0.00
151_T 51_D 0.64 0.17 0.00
216_V 385_L 0.64 0.17 0.00
306_L 502_G 0.64 0.17 0.00
58_I 246_R 0.64 0.17 0.00
213_V 313_V 0.64 0.17 0.00
282_I 481_G 0.64 0.17 0.00
307_R 276_A 0.64 0.17 0.00
154_S 500_K 0.64 0.17 0.00
154_S 532_I 0.64 0.17 0.00
161_I 420_G 0.64 0.17 0.00
266_A 514_Y 0.64 0.17 0.00
186_N 514_Y 0.64 0.17 0.00
76_V 269_T 0.64 0.17 0.00
153_L 534_D 0.64 0.17 0.00
279_G 414_T 0.63 0.17 0.00
75_E 525_R 0.63 0.17 0.00
183_G 91_I 0.63 0.17 0.00
157_V 417_F 0.63 0.17 0.00
282_I 513_A 0.63 0.17 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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