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OPENSEQ.org
UreH vs UreC Hpylori
Genes: A B A+B
Length: 265 567 759
Sequences: 1384 889 832
Seq/Len: 5.22 1.57 1.1
MirrorTree (Pazo et al. 2001) 0.64
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 0.08 0.09 0.01
2 0.08 0.09 0.11
5 0.08 0.09 0.92
10 0.08 0.09 0.99
20 0.08 0.09 1.00
100 0.08 0.09 1.01
∞ 0.10 0.12 1.05
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
87_N 537_N 1.72 0.90 0.30
146_R 539_E 1.38 0.71 0.13
236_L 404_L 1.22 0.56 0.08
105_A 130_G 1.21 0.56 0.08
147_V 539_E 1.21 0.56 0.08
37_A 324_K 1.21 0.56 0.07
147_V 304_F 1.06 0.42 0.04
149_R 539_E 1.05 0.41 0.04
39_F 327_K 1.01 0.37 0.04
35_L 566_I 1.01 0.37 0.04
133_S 421_V 1.00 0.36 0.04
198_L 205_L 0.99 0.36 0.03
164_I 389_K 0.99 0.35 0.03
142_I 424_V 0.98 0.34 0.03
174_D 183_A 0.98 0.34 0.03
4_Y 304_F 0.95 0.32 0.03
150_N 539_E 0.93 0.30 0.03
32_P 80_Y 0.91 0.29 0.03
189_C 245_I 0.91 0.29 0.03
151_E 539_E 0.91 0.28 0.02
104_N 447_I 0.89 0.27 0.02
239_L 294_L 0.89 0.27 0.02
131_R 186_E 0.89 0.27 0.02
247_L 517_C 0.89 0.27 0.02
134_S 447_I 0.88 0.26 0.02
258_T 525_M 0.87 0.26 0.02
32_P 215_G 0.87 0.26 0.02
138_Y 477_F 0.86 0.25 0.02
195_T 270_T 0.86 0.25 0.02
196_H 334_D 0.86 0.25 0.02
130_L 434_L 0.85 0.24 0.02
119_N 309_E 0.85 0.24 0.02
115_I 443_K 0.85 0.24 0.02
174_D 145_T 0.84 0.23 0.02
159_H 327_K 0.83 0.23 0.02
93_A 509_R 0.83 0.23 0.02
81_S 478_A 0.83 0.23 0.02
46_A 525_M 0.82 0.22 0.02
105_A 506_G 0.82 0.22 0.02
126_T 289_G 0.82 0.22 0.02
69_I 367_V 0.81 0.22 0.02
204_N 245_I 0.81 0.21 0.02
109_F 353_I 0.80 0.21 0.02
174_D 496_A 0.80 0.21 0.02
93_A 334_D 0.80 0.21 0.01
86_H 339_P 0.79 0.21 0.01
240_A 68_I 0.79 0.20 0.01
58_M 166_N 0.77 0.19 0.01
198_L 73_I 0.77 0.19 0.01
118_E 209_I 0.77 0.19 0.01
118_E 461_A 0.77 0.19 0.01
86_H 122_E 0.76 0.19 0.01
81_S 334_D 0.76 0.19 0.01
198_L 213_A 0.76 0.18 0.01
72_N 209_I 0.75 0.18 0.01
189_C 103_Q 0.75 0.18 0.01
80_Q 77_T 0.75 0.18 0.01
189_C 527_F 0.75 0.18 0.01
28_F 401_K 0.75 0.18 0.01
87_N 330_V 0.74 0.18 0.01
77_I 309_E 0.74 0.17 0.01
136_L 304_F 0.74 0.17 0.01
49_M 271_F 0.74 0.17 0.01
118_E 539_E 0.74 0.17 0.01
252_K 289_G 0.74 0.17 0.01
105_A 371_I 0.74 0.17 0.01
178_L 143_I 0.74 0.17 0.01
245_P 286_K 0.73 0.17 0.01
61_D 340_Q 0.73 0.17 0.01
140_E 330_V 0.73 0.17 0.01
114_L 103_Q 0.72 0.17 0.01
115_I 546_D 0.72 0.16 0.01
128_I 291_H 0.72 0.16 0.01
67_L 489_I 0.71 0.16 0.01
109_F 185_E 0.71 0.16 0.01
164_I 563_L 0.71 0.16 0.01
34_K 76_Y 0.71 0.16 0.01
245_P 288_A 0.71 0.16 0.01
56_G 380_K 0.71 0.16 0.01
129_S 151_V 0.70 0.15 0.01
140_E 123_G 0.70 0.15 0.01
151_E 226_P 0.70 0.15 0.01
156_N 77_T 0.70 0.15 0.01
243_S 189_M 0.70 0.15 0.01
28_F 512_L 0.70 0.15 0.01
144_A 103_Q 0.70 0.15 0.01
117_F 525_M 0.70 0.15 0.01
225_A 461_A 0.69 0.15 0.01
163_S 436_S 0.69 0.15 0.01
59_K 339_P 0.69 0.15 0.01
42_K 545_V 0.69 0.15 0.01
67_L 500_G 0.69 0.15 0.01
8_S 287_V 0.69 0.15 0.01
253_I 521_T 0.69 0.15 0.01
116_P 517_C 0.69 0.15 0.01
236_L 487_A 0.69 0.15 0.01
10_L 87_K 0.68 0.14 0.01
205_C 293_I 0.68 0.14 0.01
111_P 361_S 0.68 0.14 0.01
195_T 334_D 0.68 0.14 0.01
66_Q 529_D 0.68 0.14 0.01
88_T 424_V 0.68 0.14 0.01
145_G 368_G 0.68 0.14 0.01
79_S 253_A 0.68 0.14 0.01
174_D 86_I 0.68 0.14 0.01
22_C 80_Y 0.67 0.14 0.01
19_D 404_L 0.67 0.14 0.01
84_K 340_Q 0.67 0.14 0.01
50_L 227_S 0.67 0.14 0.01
233_H 455_L 0.67 0.14 0.01
254_A 357_T 0.67 0.14 0.01
182_T 351_M 0.67 0.14 0.01
145_G 158_G 0.67 0.14 0.01
105_A 104_D 0.67 0.14 0.01
21_R 182_R 0.66 0.14 0.01
51_L 415_H 0.66 0.14 0.01
34_K 476_M 0.66 0.14 0.01
146_R 226_P 0.66 0.14 0.01
86_H 110_L 0.66 0.14 0.01
250_R 525_M 0.66 0.14 0.01
32_P 77_T 0.66 0.13 0.01
196_H 353_I 0.66 0.13 0.01
22_C 285_I 0.66 0.13 0.01
44_D 71_A 0.66 0.13 0.01
174_D 310_A 0.66 0.13 0.01
233_H 104_D 0.66 0.13 0.01
127_T 87_K 0.66 0.13 0.01
70_G 177_L 0.66 0.13 0.01
128_I 529_D 0.66 0.13 0.01
19_D 182_R 0.66 0.13 0.01
44_D 560_L 0.66 0.13 0.01
99_I 372_T 0.66 0.13 0.01
180_P 353_I 0.65 0.13 0.01
4_Y 339_P 0.65 0.13 0.01
73_C 258_D 0.65 0.13 0.01
108_D 238_K 0.65 0.13 0.01
233_H 447_I 0.65 0.13 0.01
59_K 560_L 0.65 0.13 0.01
52_A 163_D 0.65 0.13 0.01
169_K 291_H 0.65 0.13 0.01
236_L 447_I 0.65 0.13 0.01
51_L 482_K 0.65 0.13 0.01
237_K 216_F 0.65 0.13 0.01
78_T 108_N 0.65 0.13 0.01
57_L 187_Y 0.65 0.13 0.01
191_F 215_G 0.65 0.13 0.01
108_D 324_K 0.65 0.13 0.01
137_L 526_Q 0.64 0.13 0.01
50_L 506_G 0.64 0.13 0.01
206_P 73_I 0.64 0.13 0.01
86_H 549_E 0.64 0.13 0.01
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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