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OPENSEQ.org
TmNrdDG
Genes: A B A+B
Length: 651 183 687
Sequences: 1199 1691 639
Seq/Len: 1.84 9.24 0.93
MirrorTree (Pazo et al. 2001) 0.78
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 0.00 0.00 0.64
2 0.00 0.01 0.70
5 0.00 0.01 0.75
10 0.00 0.01 0.76
20 0.00 0.01 0.77
100 0.01 0.02 0.79
∞ 0.02 0.08 0.90
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
175_G 81_L 1.49 0.74 0.01
572_N 71_A 1.42 0.69 0.01
473_V 74_V 1.31 0.60 0.01
311_K 159_T 1.27 0.56 0.01
568_E 13_P 1.26 0.56 0.01
381_L 160_F 1.26 0.55 0.01
603_E 143_R 1.23 0.53 0.01
218_Q 42_L 1.09 0.40 0.00
184_W 110_T 1.08 0.39 0.00
492_F 136_R 1.03 0.35 0.00
63_V 110_T 1.02 0.34 0.00
446_S 39_T 1.02 0.34 0.00
104_E 87_E 1.00 0.33 0.00
157_Q 81_L 1.00 0.32 0.00
225_S 19_S 1.00 0.32 0.00
480_E 75_F 0.98 0.31 0.00
544_G 9_F 0.98 0.31 0.00
167_S 154_H 0.98 0.31 0.00
394_L 143_R 0.98 0.31 0.00
379_I 159_T 0.98 0.31 0.00
167_S 74_V 0.97 0.30 0.00
492_F 53_V 0.97 0.30 0.00
406_A 139_H 0.97 0.30 0.00
573_M 110_T 0.94 0.28 0.00
619_I 11_D 0.93 0.27 0.00
382_E 53_V 0.93 0.27 0.00
486_H 98_E 0.93 0.27 0.00
466_G 142_R 0.91 0.25 0.00
538_N 59_E 0.90 0.25 0.00
479_E 41_H 0.90 0.25 0.00
263_L 125_Y 0.89 0.24 0.00
489_G 79_E 0.89 0.24 0.00
183_M 107_V 0.88 0.24 0.00
406_A 141_Y 0.88 0.23 0.00
280_F 109_F 0.87 0.23 0.00
469_F 133_V 0.86 0.23 0.00
62_R 112_R 0.85 0.22 0.00
394_L 33_M 0.85 0.22 0.00
480_E 106_V 0.85 0.22 0.00
108_N 160_F 0.85 0.22 0.00
383_S 19_S 0.85 0.22 0.00
446_S 71_A 0.85 0.22 0.00
389_K 106_V 0.85 0.21 0.00
380_A 92_L 0.84 0.21 0.00
599_A 112_R 0.84 0.21 0.00
435_Y 112_R 0.84 0.21 0.00
474_L 92_L 0.84 0.21 0.00
541_R 141_Y 0.84 0.21 0.00
544_G 63_S 0.84 0.21 0.00
201_L 136_R 0.83 0.21 0.00
63_V 160_F 0.83 0.20 0.00
201_L 52_V 0.82 0.20 0.00
400_L 92_L 0.82 0.20 0.00
482_E 118_V 0.82 0.20 0.00
483_K 94_K 0.81 0.20 0.00
465_E 155_I 0.81 0.20 0.00
165_F 64_L 0.81 0.19 0.00
431_L 21_Y 0.81 0.19 0.00
411_I 23_Q 0.81 0.19 0.00
586_A 53_V 0.80 0.19 0.00
374_V 144_D 0.79 0.18 0.00
232_Y 126_V 0.79 0.18 0.00
514_F 16_Y 0.79 0.18 0.00
380_A 18_V 0.79 0.18 0.00
379_I 94_K 0.78 0.18 0.00
407_A 89_M 0.78 0.18 0.00
517_K 110_T 0.77 0.17 0.00
54_T 30_K 0.77 0.17 0.00
582_V 96_F 0.76 0.17 0.00
263_L 39_T 0.76 0.17 0.00
483_K 47_K 0.76 0.17 0.00
482_E 141_Y 0.76 0.17 0.00
262_A 29_P 0.76 0.17 0.00
567_E 118_V 0.76 0.17 0.00
136_K 59_E 0.75 0.16 0.00
363_D 136_R 0.75 0.16 0.00
166_A 74_V 0.75 0.16 0.00
450_M 76_L 0.75 0.16 0.00
508_Q 26_D 0.75 0.16 0.00
199_D 138_L 0.74 0.16 0.00
488_Y 157_R 0.74 0.16 0.00
196_I 141_Y 0.74 0.16 0.00
400_L 79_E 0.74 0.16 0.00
183_M 49_P 0.74 0.15 0.00
479_E 57_I 0.73 0.15 0.00
583_M 11_D 0.73 0.15 0.00
537_L 107_V 0.73 0.15 0.00
483_K 145_G 0.73 0.15 0.00
101_E 143_R 0.73 0.15 0.00
381_L 41_H 0.72 0.15 0.00
432_N 114_P 0.72 0.15 0.00
191_L 82_A 0.72 0.15 0.00
169_Q 23_Q 0.72 0.15 0.00
120_A 19_S 0.72 0.15 0.00
387_R 106_V 0.72 0.15 0.00
640_R 137_Y 0.72 0.15 0.00
308_I 39_T 0.71 0.14 0.00
475_D 150_K 0.71 0.14 0.00
187_V 9_F 0.71 0.14 0.00
466_G 92_L 0.71 0.14 0.00
325_A 116_D 0.71 0.14 0.00
386_D 95_M 0.71 0.14 0.00
476_T 94_K 0.71 0.14 0.00
582_V 142_R 0.71 0.14 0.00
529_P 37_P 0.70 0.14 0.00
263_L 49_P 0.70 0.14 0.00
468_V 155_I 0.70 0.14 0.00
508_Q 154_H 0.69 0.14 0.00
385_G 125_Y 0.69 0.13 0.00
108_N 13_P 0.69 0.13 0.00
509_K 154_H 0.69 0.13 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)
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