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OPENSEQ.org
cI_C_cIII_cytb
Genes: A B A+B
Length: 509 450 883
Sequences: 3158 3165 1458
Seq/Len: 6.2 7.03 1.65
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.00 0.04
2 0.00 0.00 0.14
5 0.00 0.00 0.92
10 0.01 0.00 0.98
20 0.01 0.00 1.02
100 0.01 0.00 1.08
∞ 0.02 0.01 1.52
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
141_F 398_A 1.38 0.81 0.07
272_L 59_I 1.29 0.75 0.06
390_F 334_I 1.20 0.67 0.04
434_V 25_I 1.19 0.66 0.04
413_G 137_L 1.12 0.60 0.03
428_G 200_L 1.11 0.59 0.03
103_L 138_M 1.11 0.58 0.03
263_L 151_W 1.07 0.55 0.03
368_T 63_I 1.07 0.55 0.03
337_A 64_V 1.07 0.54 0.03
476_V 258_V 1.02 0.49 0.03
342_V 71_P 1.01 0.48 0.02
480_F 395_A 1.01 0.48 0.02
143_W 156_F 0.98 0.45 0.02
301_G 354_V 0.97 0.43 0.02
113_Q 176_I 0.95 0.42 0.02
46_L 284_N 0.95 0.41 0.02
306_F 269_F 0.94 0.41 0.02
90_M 405_L 0.94 0.41 0.02
345_M 291_H 0.94 0.41 0.02
401_T 383_M 0.94 0.41 0.02
416_Q 248_F 0.94 0.40 0.02
222_L 180_L 0.94 0.40 0.02
475_L 207_A 0.93 0.40 0.02
31_I 258_V 0.93 0.39 0.02
401_T 93_L 0.93 0.39 0.02
179_Q 394_L 0.93 0.39 0.02
360_G 124_P 0.92 0.39 0.02
263_L 296_W 0.92 0.39 0.02
428_G 272_N 0.92 0.38 0.02
431_F 93_L 0.92 0.38 0.02
415_F 345_L 0.92 0.38 0.02
32_A 136_Y 0.92 0.38 0.02
166_T 156_F 0.91 0.38 0.02
240_L 110_I 0.91 0.37 0.02
40_L 93_L 0.90 0.37 0.02
83_I 395_A 0.90 0.37 0.02
380_K 175_A 0.90 0.37 0.02
321_S 139_M 0.90 0.36 0.02
157_W 151_W 0.90 0.36 0.02
345_M 151_W 0.89 0.36 0.02
303_W 61_T 0.89 0.36 0.02
174_F 225_T 0.89 0.35 0.02
432_A 51_L 0.89 0.35 0.02
226_G 92_M 0.89 0.35 0.02
249_S 156_F 0.88 0.35 0.01
102_V 137_L 0.88 0.35 0.01
364_E 158_G 0.88 0.34 0.01
102_V 405_L 0.88 0.34 0.01
190_L 117_Y 0.88 0.34 0.01
139_F 297_Y 0.88 0.34 0.01
143_W 361_P 0.87 0.34 0.01
165_K 370_L 0.87 0.34 0.01
473_V 213_I 0.87 0.33 0.01
414_S 211_V 0.86 0.33 0.01
368_T 180_L 0.86 0.33 0.01
488_T 211_V 0.86 0.33 0.01
130_V 248_F 0.86 0.33 0.01
477_L 218_T 0.86 0.33 0.01
360_G 35_I 0.86 0.33 0.01
350_L 269_F 0.86 0.33 0.01
141_F 60_A 0.86 0.32 0.01
329_A 172_V 0.85 0.32 0.01
262_I 250_I 0.85 0.32 0.01
328_I 356_S 0.85 0.32 0.01
258_D 260_L 0.84 0.31 0.01
100_L 93_L 0.84 0.31 0.01
315_I 222_N 0.84 0.30 0.01
142_F 301_F 0.83 0.30 0.01
386_A 72_H 0.83 0.30 0.01
100_L 96_L 0.83 0.30 0.01
39_T 330_F 0.83 0.30 0.01
389_L 343_M 0.83 0.30 0.01
408_F 204_V 0.83 0.29 0.01
230_A 369_L 0.82 0.29 0.01
82_A 246_P 0.82 0.29 0.01
271_L 113_F 0.82 0.29 0.01
368_T 227_V 0.82 0.29 0.01
229_I 139_M 0.82 0.29 0.01
447_K 256_L 0.82 0.29 0.01
324_G 280_Y 0.82 0.29 0.01
174_F 414_I 0.82 0.29 0.01
235_M 51_L 0.82 0.29 0.01
189_I 257_A 0.81 0.29 0.01
97_L 176_I 0.81 0.28 0.01
262_I 39_K 0.81 0.28 0.01
444_Y 394_L 0.81 0.28 0.01
99_V 284_N 0.81 0.28 0.01
321_S 195_F 0.81 0.28 0.01
327_L 108_V 0.81 0.28 0.01
448_A 344_A 0.81 0.28 0.01
215_M 266_I 0.81 0.28 0.01
228_F 108_V 0.80 0.28 0.01
346_I 263_F 0.80 0.27 0.01
94_T 382_A 0.80 0.27 0.01
314_L 72_H 0.80 0.27 0.01
476_V 78_A 0.80 0.27 0.01
341_A 216_F 0.80 0.27 0.01
458_P 172_V 0.79 0.27 0.01
224_M 209_V 0.79 0.27 0.01
439_M 357_G 0.79 0.27 0.01
132_L 371_A 0.79 0.27 0.01
293_L 206_A 0.79 0.27 0.01
160_K 350_D 0.79 0.26 0.01
261_G 222_N 0.79 0.26 0.01
304_M 94_R 0.79 0.26 0.01
263_L 291_H 0.78 0.26 0.01
341_A 333_V 0.78 0.26 0.01
277_P 136_Y 0.78 0.26 0.01
115_F 412_G 0.78 0.26 0.01
270_G 361_P 0.78 0.26 0.01
341_A 379_W 0.78 0.25 0.01
473_V 380_V 0.78 0.25 0.01
321_S 108_V 0.78 0.25 0.01
401_T 131_V 0.77 0.25 0.01
173_K 126_E 0.77 0.25 0.01
97_L 88_N 0.77 0.25 0.01
95_G 280_Y 0.77 0.25 0.01
396_L 165_L 0.77 0.25 0.01
91_V 209_V 0.77 0.25 0.01
116_F 374_F 0.77 0.25 0.01
344_Q 39_K 0.77 0.25 0.01
226_G 61_T 0.77 0.25 0.01
473_V 407_I 0.77 0.25 0.01
412_F 29_V 0.77 0.25 0.01
286_F 103_L 0.77 0.25 0.01
230_A 156_F 0.77 0.24 0.01
126_G 73_V 0.77 0.24 0.01
233_V 158_G 0.77 0.24 0.01
133_A 248_F 0.76 0.24 0.01
275_S 256_L 0.76 0.24 0.01
361_Q 227_V 0.76 0.24 0.01
225_L 258_V 0.76 0.24 0.01
427_F 174_E 0.76 0.24 0.01
102_V 348_W 0.76 0.24 0.01
396_L 33_L 0.76 0.24 0.01
262_I 131_V 0.76 0.24 0.01
311_I 353_R 0.76 0.24 0.01
215_M 375_V 0.76 0.24 0.01
284_A 375_V 0.76 0.24 0.01
360_G 300_P 0.76 0.24 0.01
445_F 213_I 0.75 0.23 0.01
493_I 361_P 0.75 0.23 0.01
66_E 334_I 0.75 0.23 0.01
343_I 205_I 0.75 0.23 0.01
134_I 93_L 0.75 0.23 0.01
9_I 284_N 0.75 0.23 0.01
167_R 260_L 0.75 0.23 0.01
294_G 116_L 0.75 0.23 0.01
286_F 404_F 0.75 0.23 0.01
183_L 178_T 0.75 0.23 0.01
141_F 334_I 0.75 0.23 0.01
298_I 138_M 0.75 0.23 0.01
429_L 257_A 0.74 0.23 0.01
377_L 110_I 0.74 0.23 0.01
450_S 258_V 0.74 0.23 0.01
428_G 138_M 0.74 0.23 0.01
400_G 356_S 0.74 0.23 0.01
249_S 291_H 0.74 0.23 0.01
272_L 406_I 0.74 0.23 0.01
232_A 197_L 0.74 0.23 0.01
338_Y 156_F 0.74 0.23 0.01
396_L 242_L 0.74 0.23 0.01
475_L 53_F 0.74 0.22 0.01
91_V 116_L 0.74 0.22 0.01
86_L 392_I 0.74 0.22 0.01
330_I 89_G 0.74 0.22 0.01
187_I 139_M 0.73 0.22 0.01
329_A 239_K 0.73 0.22 0.01
401_T 376_V 0.73 0.22 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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