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OPENSEQ.org
T4NrdDG
Genes: A B A+B
Length: 605 156 752
Sequences: 1329 3192 1155
Seq/Len: 2.2 20.46 1.54
MirrorTree (Pazo et al. 2001) 0.80
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 1.19
2 0.00 0.00 1.42
5 0.00 0.01 1.49
10 0.00 0.01 1.50
20 0.01 0.01 1.52
100 0.01 0.03 1.54
∞ 0.02 0.12 1.65
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
518_K 15_P 1.41 0.82 0.07
128_T 75_L 1.27 0.71 0.05
522_A 65_Q 1.25 0.69 0.04
525_D 65_Q 1.15 0.60 0.03
322_I 88_S 1.10 0.56 0.03
106_G 145_L 1.01 0.46 0.02
324_L 151_G 0.95 0.40 0.02
464_K 114_E 0.95 0.40 0.02
162_Y 131_L 0.94 0.38 0.02
55_M 97_K 0.92 0.36 0.02
516_N 16_G 0.91 0.36 0.01
263_K 150_D 0.90 0.35 0.01
249_P 88_S 0.90 0.34 0.01
421_T 55_L 0.89 0.34 0.01
419_I 68_T 0.88 0.33 0.01
170_D 8_P 0.87 0.32 0.01
120_A 68_T 0.87 0.32 0.01
381_K 69_L 0.86 0.31 0.01
559_F 133_T 0.85 0.30 0.01
335_Q 88_S 0.85 0.30 0.01
460_Y 123_I 0.85 0.30 0.01
487_F 15_P 0.85 0.30 0.01
491_S 63_Y 0.85 0.30 0.01
460_Y 45_Q 0.83 0.29 0.01
429_Q 136_L 0.82 0.28 0.01
317_L 137_W 0.82 0.27 0.01
209_M 28_H 0.80 0.26 0.01
519_G 139_G 0.79 0.25 0.01
306_L 126_K 0.78 0.25 0.01
457_T 131_L 0.78 0.24 0.01
431_T 21_L 0.78 0.24 0.01
249_P 122_I 0.77 0.24 0.01
415_I 123_I 0.77 0.24 0.01
256_L 86_L 0.77 0.24 0.01
138_P 145_L 0.77 0.24 0.01
418_E 130_N 0.76 0.23 0.01
223_G 32_G 0.76 0.23 0.01
359_L 11_F 0.76 0.23 0.01
454_K 56_A 0.76 0.23 0.01
435_G 73_D 0.75 0.22 0.01
161_N 141_D 0.75 0.22 0.01
197_I 129_K 0.75 0.22 0.01
323_A 19_V 0.74 0.22 0.01
466_V 99_I 0.74 0.22 0.01
149_E 150_D 0.74 0.22 0.01
423_M 128_E 0.73 0.21 0.01
192_T 20_V 0.73 0.21 0.01
113_A 5_R 0.73 0.21 0.01
178_Y 76_Y 0.73 0.21 0.01
425_A 40_N 0.73 0.21 0.01
149_E 126_K 0.72 0.20 0.01
422_K 88_S 0.72 0.20 0.01
209_M 60_S 0.72 0.20 0.01
353_M 131_L 0.72 0.20 0.01
260_C 1_M 0.72 0.20 0.01
407_L 123_I 0.71 0.20 0.01
26_D 105_Y 0.71 0.20 0.01
242_V 87_V 0.71 0.19 0.01
136_L 6_I 0.71 0.19 0.01
455_L 67_L 0.70 0.19 0.01
317_L 88_S 0.70 0.19 0.01
209_M 90_V 0.70 0.19 0.01
61_G 66_G 0.70 0.19 0.01
145_A 145_L 0.70 0.19 0.01
107_V 69_L 0.69 0.18 0.01
460_Y 117_K 0.69 0.18 0.01
160_L 54_E 0.69 0.18 0.01
267_P 74_P 0.69 0.18 0.01
489_K 68_T 0.69 0.18 0.01
478_V 17_C 0.69 0.18 0.01
50_V 39_W 0.69 0.18 0.01
179_E 41_A 0.69 0.18 0.01
463_V 103_T 0.69 0.18 0.01
414_D 21_L 0.69 0.18 0.01
177_A 34_Y 0.68 0.18 0.01
149_E 50_N 0.68 0.18 0.01
290_C 35_N 0.68 0.18 0.01
113_A 37_S 0.68 0.18 0.01
430_W 119_V 0.68 0.18 0.01
249_P 115_M 0.68 0.18 0.01
464_K 108_E 0.68 0.18 0.01
184_T 66_G 0.68 0.18 0.01
240_E 145_L 0.68 0.17 0.01
262_S 117_K 0.68 0.17 0.01
518_K 65_Q 0.67 0.17 0.01
229_P 102_W 0.67 0.17 0.01
196_T 103_T 0.67 0.17 0.01
389_L 103_T 0.67 0.17 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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