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OPENSEQ.org
PafA-PanB
Genes: A B A+B
Length: 452 281 711
Sequences: 488 2518 124
Seq/Len: 1.08 8.96 0.17
MirrorTree (Pazo et al. 2001) 0.41
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 0.11 0.08 0.00
2 0.28 0.08 0.00
5 0.64 0.08 0.00
10 0.80 0.08 0.00
20 0.85 0.08 0.00
100 0.85 0.08 0.01
∞ 0.86 0.10 0.17
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
323_T 77_I 1.47 0.27 0.00
80_R 251_Y 1.46 0.27 0.00
326_D 118_A 1.37 0.23 0.00
337_Y 72_D 1.36 0.23 0.00
27_D 215_I 1.36 0.23 0.00
234_I 251_Y 1.33 0.21 0.00
349_K 154_A 1.33 0.21 0.00
385_I 144_C 1.27 0.19 0.00
373_K 132_L 1.21 0.17 0.00
12_F 20_K 1.18 0.16 0.00
255_V 109_A 1.17 0.16 0.00
152_C 65_A 1.17 0.16 0.00
281_E 215_I 1.13 0.15 0.00
113_T 255_G 1.12 0.14 0.00
332_K 122_L 1.11 0.14 0.00
278_I 87_R 1.10 0.14 0.00
371_Q 204_E 1.09 0.14 0.00
269_G 248_V 1.08 0.13 0.00
385_I 182_I 1.07 0.13 0.00
122_C 154_A 1.07 0.13 0.00
342_D 83_I 1.07 0.13 0.00
280_R 226_C 1.07 0.13 0.00
385_I 214_T 1.07 0.13 0.00
174_H 255_G 1.07 0.13 0.00
146_V 182_I 1.06 0.13 0.00
84_W 218_V 1.06 0.13 0.00
174_H 188_V 1.05 0.13 0.00
452_M 218_V 1.05 0.13 0.00
88_D 123_K 1.05 0.12 0.00
344_E 263_M 1.05 0.12 0.00
385_I 210_T 1.04 0.12 0.00
151_I 65_A 1.03 0.12 0.00
201_E 143_A 1.01 0.11 0.00
351_A 52_E 1.00 0.11 0.00
281_E 197_V 1.00 0.11 0.00
71_S 65_A 0.99 0.11 0.00
363_G 97_L 0.99 0.11 0.00
403_E 179_E 0.98 0.11 0.00
233_M 90_V 0.98 0.11 0.00
8_I 205_L 0.97 0.11 0.00
337_Y 102_L 0.97 0.11 0.00
170_Q 103_P 0.97 0.11 0.00
157_V 79_I 0.97 0.11 0.00
277_D 29_W 0.97 0.11 0.00
283_Y 264_Q 0.97 0.11 0.00
303_V 254_V 0.97 0.11 0.00
337_Y 119_T 0.96 0.10 0.00
280_R 44_Y 0.96 0.10 0.00
303_V 251_Y 0.96 0.10 0.00
201_E 224_P 0.96 0.10 0.00
262_R 204_E 0.96 0.10 0.00
347_H 179_E 0.95 0.10 0.00
151_I 85_L 0.95 0.10 0.00
262_R 195_A 0.95 0.10 0.00
286_A 188_V 0.94 0.10 0.00
259_V 132_L 0.94 0.10 0.00
356_A 279_H 0.94 0.10 0.00
152_C 69_Y 0.94 0.10 0.00
349_K 146_T 0.94 0.10 0.00
344_E 143_A 0.94 0.10 0.00
389_V 83_I 0.94 0.10 0.00
228_A 73_T 0.94 0.10 0.00
266_R 83_I 0.93 0.10 0.00
266_R 125_G 0.93 0.10 0.00
250_R 49_I 0.93 0.10 0.00
109_F 248_V 0.93 0.10 0.00
434_C 106_S 0.93 0.10 0.00
178_G 68_V 0.92 0.10 0.00
402_G 135_G 0.92 0.10 0.00
216_S 251_Y 0.92 0.10 0.00
150_L 156_I 0.92 0.10 0.00
291_Q 142_I 0.92 0.10 0.00
384_E 154_A 0.92 0.10 0.00
285_R 188_V 0.92 0.10 0.00
50_N 110_G 0.92 0.10 0.00
309_Q 248_V 0.91 0.09 0.00
142_L 156_I 0.91 0.09 0.00
73_V 65_A 0.91 0.09 0.00
387_E 145_L 0.91 0.09 0.00
317_D 78_S 0.91 0.09 0.00
410_E 69_Y 0.91 0.09 0.00
46_V 120_R 0.90 0.09 0.00
218_T 80_D 0.90 0.09 0.00
347_H 218_V 0.90 0.09 0.00
147_T 218_V 0.90 0.09 0.00
91_V 218_V 0.89 0.09 0.00
281_E 138_V 0.89 0.09 0.00
150_L 81_E 0.89 0.09 0.00
275_A 29_W 0.89 0.09 0.00
281_E 227_D 0.89 0.09 0.00
378_R 186_I 0.89 0.09 0.00
226_T 268_E 0.89 0.09 0.00
257_H 142_I 0.89 0.09 0.00
447_R 260_R 0.89 0.09 0.00
105_D 179_E 0.88 0.09 0.00
352_Q 68_V 0.88 0.09 0.00
257_H 123_K 0.88 0.09 0.00
265_V 141_Q 0.88 0.09 0.00
219_T 147_A 0.88 0.09 0.00
384_E 92_G 0.88 0.09 0.00
439_R 266_A 0.88 0.09 0.00
347_H 90_V 0.88 0.09 0.00
88_D 150_I 0.88 0.09 0.00
166_Y 145_L 0.87 0.09 0.00
352_Q 154_A 0.87 0.09 0.00
304_D 83_I 0.87 0.09 0.00
156_K 249_K 0.87 0.09 0.00
273_A 127_A 0.87 0.09 0.00
51_G 129_A 0.87 0.09 0.00
286_A 79_I 0.86 0.09 0.00
352_Q 85_L 0.86 0.09 0.00
236_S 108_E 0.86 0.09 0.00
110_K 247_F 0.86 0.09 0.00
80_R 266_A 0.86 0.09 0.00
278_I 33_G 0.86 0.08 0.00
106_I 265_Y 0.86 0.08 0.00
276_L 35_K 0.86 0.08 0.00
432_V 25_H 0.86 0.08 0.00
190_I 96_A 0.86 0.08 0.00
380_T 100_A 0.85 0.08 0.00
224_V 227_D 0.85 0.08 0.00
203_Y 175_G 0.85 0.08 0.00
260_T 98_V 0.85 0.08 0.00
227_A 97_L 0.85 0.08 0.00
85_V 69_Y 0.85 0.08 0.00
152_C 81_E 0.85 0.08 0.00
311_D 204_E 0.85 0.08 0.00
166_Y 118_A 0.84 0.08 0.00
337_Y 248_V 0.84 0.08 0.00
122_C 215_I 0.84 0.08 0.00
80_R 194_F 0.84 0.08 0.00
285_R 142_I 0.84 0.08 0.00
323_T 23_T 0.83 0.08 0.00
276_L 179_E 0.83 0.08 0.00
363_G 228_G 0.83 0.08 0.00
302_V 121_F 0.83 0.08 0.00
365_G 230_V 0.83 0.08 0.00
288_E 71_Y 0.83 0.08 0.00
185_R 227_D 0.83 0.08 0.00
410_E 73_T 0.83 0.08 0.00
94_E 271_G 0.83 0.08 0.00
262_R 73_T 0.83 0.08 0.00
215_M 277_D 0.82 0.08 0.00
269_G 126_G 0.82 0.08 0.00
338_Q 50_F 0.82 0.08 0.00
278_I 175_G 0.82 0.08 0.00
200_A 120_R 0.82 0.08 0.00
408_A 96_A 0.82 0.08 0.00
146_V 147_A 0.82 0.08 0.00
293_R 92_G 0.81 0.08 0.00
255_V 110_G 0.81 0.08 0.00
122_C 227_D 0.81 0.08 0.00
85_V 190_E 0.81 0.08 0.00
120_Y 154_A 0.81 0.08 0.00
436_D 260_R 0.81 0.08 0.00
227_A 203_A 0.81 0.08 0.00
198_A 26_L 0.81 0.07 0.00
12_F 195_A 0.81 0.07 0.00
224_V 210_T 0.81 0.07 0.00
46_V 123_K 0.80 0.07 0.00
150_L 189_A 0.80 0.07 0.00
289_H 239_F 0.80 0.07 0.00
80_R 79_I 0.80 0.07 0.00
359_D 201_V 0.80 0.07 0.00
234_I 162_S 0.80 0.07 0.00
364_R 68_V 0.80 0.07 0.00
365_G 38_M 0.80 0.07 0.00
200_A 170_R 0.80 0.07 0.00
46_V 245_A 0.80 0.07 0.00
263_R 34_H 0.80 0.07 0.00
80_R 248_V 0.79 0.07 0.00
294_E 106_S 0.79 0.07 0.00
358_H 122_L 0.79 0.07 0.00
410_E 127_A 0.79 0.07 0.00
353_L 258_L 0.79 0.07 0.00
304_D 215_I 0.79 0.07 0.00
151_I 142_I 0.79 0.07 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.86 > 0.4) of paralogs.
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