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OPENSEQ.org
SurA
Genes: A B A+B
Length: 346 404 735
Sequences: 27450 1711 131
Seq/Len: 79.34 4.24 0.18
MirrorTree (Pazo et al. 2001) 0.19
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.10 0.00 0.00
2 0.12 0.00 0.01
5 0.14 0.01 0.02
10 0.16 0.01 0.06
20 0.19 0.01 0.17
100 0.24 0.02 0.84
∞ 0.27 0.04 1.66
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
213_G 128_I 1.50 0.30 0.00
245_T 126_I 1.40 0.25 0.00
335_D 166_D 1.28 0.20 0.00
215_G 339_G 1.26 0.20 0.00
209_A 126_I 1.22 0.18 0.00
303_T 128_I 1.20 0.17 0.00
273_P 133_V 1.20 0.17 0.00
155_N 65_V 1.19 0.17 0.00
58_Y 126_I 1.17 0.16 0.00
186_Y 235_I 1.17 0.16 0.00
198_S 340_Q 1.16 0.16 0.00
239_T 30_A 1.10 0.14 0.00
259_F 339_G 1.10 0.14 0.00
40_F 126_I 1.10 0.14 0.00
230_N 150_L 1.09 0.14 0.00
204_D 249_L 1.08 0.14 0.00
312_T 338_K 1.08 0.14 0.00
307_N 65_V 1.07 0.14 0.00
324_N 129_L 1.06 0.13 0.00
298_V 304_F 1.06 0.13 0.00
321_L 236_R 1.06 0.13 0.00
231_N 90_M 1.05 0.13 0.00
15_G 13_V 1.05 0.13 0.00
202_R 400_K 1.04 0.12 0.00
316_Y 67_I 1.03 0.12 0.00
273_P 8_V 1.01 0.12 0.00
204_D 55_I 1.01 0.12 0.00
259_F 359_T 1.01 0.12 0.00
178_D 13_V 1.00 0.12 0.00
263_A 187_D 0.99 0.12 0.00
79_G 171_A 0.99 0.12 0.00
40_F 4_V 0.99 0.11 0.00
259_F 74_Q 0.99 0.11 0.00
180_V 9_N 0.99 0.11 0.00
260_E 246_V 0.98 0.11 0.00
224_G 178_I 0.98 0.11 0.00
238_Y 341_M 0.98 0.11 0.00
267_F 328_A 0.97 0.11 0.00
346_F 13_V 0.97 0.11 0.00
272_R 126_I 0.96 0.11 0.00
255_K 86_T 0.96 0.11 0.00
320_L 126_I 0.96 0.11 0.00
236_A 96_Y 0.96 0.11 0.00
322_D 341_M 0.96 0.11 0.00
211_Y 206_Q 0.95 0.11 0.00
47_T 279_A 0.95 0.10 0.00
147_V 293_G 0.94 0.10 0.00
54_G 250_R 0.94 0.10 0.00
302_A 166_D 0.94 0.10 0.00
238_Y 90_M 0.94 0.10 0.00
30_D 225_T 0.94 0.10 0.00
345_Q 341_M 0.94 0.10 0.00
312_T 290_I 0.94 0.10 0.00
88_F 321_T 0.93 0.10 0.00
94_Y 243_I 0.93 0.10 0.00
278_L 203_N 0.93 0.10 0.00
239_T 112_M 0.92 0.10 0.00
312_T 132_E 0.92 0.10 0.00
230_N 170_E 0.92 0.10 0.00
321_L 234_P 0.91 0.10 0.00
282_G 43_R 0.91 0.10 0.00
148_Q 172_E 0.91 0.10 0.00
312_T 7_V 0.91 0.10 0.00
312_T 291_K 0.91 0.10 0.00
299_D 222_A 0.90 0.09 0.00
241_T 268_L 0.90 0.09 0.00
342_L 399_V 0.90 0.09 0.00
308_K 100_N 0.90 0.09 0.00
224_G 229_G 0.90 0.09 0.00
297_Y 232_V 0.90 0.09 0.00
98_Y 13_V 0.89 0.09 0.00
336_N 208_G 0.89 0.09 0.00
236_A 56_I 0.89 0.09 0.00
173_L 178_I 0.89 0.09 0.00
312_T 292_S 0.88 0.09 0.00
273_P 341_M 0.88 0.09 0.00
300_V 128_I 0.88 0.09 0.00
237_Q 387_A 0.88 0.09 0.00
73_T 345_V 0.88 0.09 0.00
90_Y 292_S 0.88 0.09 0.00
145_F 113_I 0.88 0.09 0.00
340_L 71_Q 0.87 0.09 0.00
210_A 166_D 0.87 0.09 0.00
321_L 158_P 0.87 0.09 0.00
280_S 229_G 0.87 0.09 0.00
252_W 310_S 0.87 0.09 0.00
318_I 72_L 0.87 0.09 0.00
340_L 401_I 0.87 0.09 0.00
103_W 13_V 0.87 0.09 0.00
340_L 86_T 0.86 0.09 0.00
141_D 168_V 0.86 0.09 0.00
279_Q 324_I 0.86 0.09 0.00
58_Y 1_V 0.86 0.09 0.00
299_D 340_Q 0.86 0.09 0.00
148_Q 13_V 0.86 0.09 0.00
24_S 76_I 0.86 0.09 0.00
224_G 50_L 0.86 0.09 0.00
235_A 399_V 0.85 0.09 0.00
224_G 318_G 0.85 0.09 0.00
235_A 179_V 0.85 0.09 0.00
84_D 339_G 0.85 0.09 0.00
312_T 247_N 0.85 0.09 0.00
78_A 130_P 0.85 0.09 0.00
300_V 85_M 0.85 0.09 0.00
183_S 113_I 0.85 0.08 0.00
182_G 132_E 0.85 0.08 0.00
234_L 107_Q 0.85 0.08 0.00
278_L 128_I 0.85 0.08 0.00
320_L 348_S 0.84 0.08 0.00
194_G 128_I 0.84 0.08 0.00
63_N 341_M 0.84 0.08 0.00
321_L 178_I 0.84 0.08 0.00
149_Y 187_D 0.84 0.08 0.00
146_A 126_I 0.84 0.08 0.00
195_G 243_I 0.84 0.08 0.00
86_G 111_E 0.84 0.08 0.00
184_I 291_K 0.83 0.08 0.00
311_S 138_Q 0.83 0.08 0.00
183_S 47_M 0.83 0.08 0.00
169_G 13_V 0.83 0.08 0.00
61_Q 359_T 0.83 0.08 0.00
250_L 246_V 0.83 0.08 0.00
284_N 329_F 0.83 0.08 0.00
314_V 244_L 0.83 0.08 0.00
184_I 71_Q 0.83 0.08 0.00
277_Y 336_L 0.83 0.08 0.00
223_G 74_Q 0.83 0.08 0.00
297_Y 189_G 0.83 0.08 0.00
254_N 152_L 0.83 0.08 0.00
182_G 261_V 0.82 0.08 0.00
247_V 244_L 0.82 0.08 0.00
324_N 13_V 0.82 0.08 0.00
254_N 73_D 0.82 0.08 0.00
319_N 13_V 0.82 0.08 0.00
126_N 268_L 0.82 0.08 0.00
300_V 390_M 0.82 0.08 0.00
321_L 274_M 0.82 0.08 0.00
331_G 399_V 0.82 0.08 0.00
226_K 41_T 0.82 0.08 0.00
279_Q 109_R 0.82 0.08 0.00
244_A 173_S 0.82 0.08 0.00
193_I 115_S 0.82 0.08 0.00
26_N 128_I 0.82 0.08 0.00
344_Y 65_V 0.82 0.08 0.00
240_Q 340_Q 0.82 0.08 0.00
183_S 51_I 0.82 0.08 0.00
145_F 22_M 0.81 0.08 0.00
42_G 8_V 0.81 0.08 0.00
234_L 129_L 0.81 0.08 0.00
225_L 221_Q 0.81 0.08 0.00
259_F 215_L 0.81 0.08 0.00
68_E 226_A 0.81 0.08 0.00
233_Y 187_D 0.81 0.08 0.00
52_G 8_V 0.81 0.08 0.00
213_G 206_Q 0.81 0.08 0.00
184_I 40_A 0.81 0.08 0.00
321_L 384_E 0.81 0.08 0.00
243_N 304_F 0.81 0.08 0.00
152_K 103_T 0.81 0.08 0.00
343_V 383_S 0.81 0.08 0.00
239_T 248_D 0.81 0.08 0.00
253_A 265_X 0.81 0.08 0.00
273_P 361_N 0.81 0.08 0.00
239_T 215_L 0.81 0.08 0.00
205_A 249_L 0.81 0.08 0.00
189_E 88_D 0.81 0.08 0.00
310_M 74_Q 0.81 0.08 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)
ID Seq/Len Name Options I_Prob Status
3381 0.18 SurA Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3376 0 SurA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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