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OPENSEQ.org
138
Genes: A B A+B
Length: 286 522 729
Sequences: 10046 1288 549
Seq/Len: 35.13 2.47 0.75
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 0.03 0.13 0.20
2 0.03 0.33 0.43
5 0.03 0.41 0.55
10 0.05 0.43 0.65
20 0.06 0.44 0.68
100 0.10 0.47 0.75
∞ 0.19 0.50 0.83
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
32_K 83_K 1.68 0.80 0.04
73_E 322_D 1.38 0.59 0.02
33_V 368_L 1.19 0.43 0.01
80_Y 306_G 1.15 0.40 0.01
182_L 239_I 1.13 0.38 0.01
33_V 438_P 1.11 0.37 0.01
194_E 150_T 1.09 0.35 0.01
5_C 134_L 1.08 0.34 0.01
197_I 339_I 1.07 0.34 0.01
57_I 102_F 1.07 0.33 0.01
33_V 413_P 1.05 0.32 0.01
50_H 167_N 1.04 0.31 0.01
195_L 372_P 1.04 0.31 0.01
78_A 248_V 1.04 0.31 0.01
78_A 328_L 1.03 0.30 0.01
273_I 243_L 1.02 0.30 0.01
82_G 244_S 1.01 0.29 0.01
197_I 365_R 1.01 0.29 0.01
103_I 158_G 1.01 0.29 0.01
199_L 421_Y 1.00 0.28 0.01
81_G 242_M 0.99 0.27 0.01
194_E 500_I 0.96 0.26 0.01
228_I 489_A 0.96 0.25 0.01
171_Y 491_Q 0.95 0.25 0.01
194_E 123_V 0.94 0.24 0.01
166_K 365_R 0.93 0.24 0.00
231_D 444_N 0.93 0.24 0.00
194_E 442_I 0.93 0.24 0.00
33_V 344_T 0.93 0.23 0.00
202_K 453_D 0.92 0.23 0.00
82_G 74_A 0.92 0.23 0.00
117_D 326_E 0.91 0.22 0.00
199_L 258_E 0.91 0.22 0.00
166_K 89_H 0.90 0.22 0.00
245_R 244_S 0.90 0.21 0.00
171_Y 311_E 0.88 0.21 0.00
202_K 392_I 0.88 0.21 0.00
262_D 403_K 0.88 0.20 0.00
262_D 468_I 0.88 0.20 0.00
174_S 468_I 0.87 0.20 0.00
81_G 203_I 0.87 0.20 0.00
245_R 407_A 0.87 0.20 0.00
73_E 271_Y 0.87 0.20 0.00
81_G 305_E 0.86 0.20 0.00
25_A 500_I 0.86 0.20 0.00
50_H 247_G 0.85 0.19 0.00
197_I 305_E 0.85 0.19 0.00
84_K 226_V 0.85 0.19 0.00
80_Y 451_Q 0.85 0.19 0.00
209_H 134_L 0.85 0.19 0.00
251_K 280_M 0.85 0.19 0.00
105_A 115_D 0.84 0.18 0.00
75_V 177_E 0.84 0.18 0.00
257_N 365_R 0.83 0.18 0.00
229_E 413_P 0.83 0.18 0.00
204_G 368_L 0.83 0.18 0.00
249_D 290_V 0.82 0.18 0.00
169_V 376_M 0.82 0.17 0.00
117_D 406_D 0.82 0.17 0.00
118_D 226_V 0.82 0.17 0.00
229_E 286_A 0.82 0.17 0.00
115_Y 389_P 0.81 0.17 0.00
116_E 262_T 0.81 0.17 0.00
78_A 403_K 0.81 0.17 0.00
5_C 433_V 0.81 0.17 0.00
56_T 500_I 0.81 0.17 0.00
257_N 487_E 0.81 0.17 0.00
147_I 158_G 0.81 0.17 0.00
274_M 403_K 0.81 0.17 0.00
254_V 440_F 0.81 0.17 0.00
249_D 406_D 0.80 0.17 0.00
74_D 342_S 0.80 0.17 0.00
31_K 378_L 0.80 0.17 0.00
257_N 442_I 0.80 0.16 0.00
122_V 305_E 0.80 0.16 0.00
205_T 166_N 0.80 0.16 0.00
82_G 343_L 0.80 0.16 0.00
255_I 308_W 0.79 0.16 0.00
205_T 236_F 0.79 0.16 0.00
205_T 380_K 0.79 0.16 0.00
180_G 500_I 0.79 0.16 0.00
65_G 90_G 0.79 0.16 0.00
171_Y 357_S 0.79 0.16 0.00
66_T 366_F 0.79 0.16 0.00
4_Q 448_K 0.78 0.15 0.00
145_Q 444_N 0.78 0.15 0.00
259_I 239_I 0.78 0.15 0.00
84_K 267_Q 0.78 0.15 0.00
162_N 320_G 0.77 0.15 0.00
73_E 342_S 0.77 0.15 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 B, there is a high ratio (0.44 > 0.4) of paralogs.
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