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OPENSEQ.org
Interaction of E Coli K-12 W3110 nrdD and its Activase
Genes: A B A+B
Length: 712 154 849
Sequences: 1316 2469 1140
Seq/Len: 1.85 16.03 1.34
MirrorTree (Pazo et al. 2001) 0.83
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 1.04
2 0.00 0.00 1.23
5 0.00 0.01 1.29
10 0.00 0.01 1.30
20 0.01 0.01 1.32
100 0.01 0.02 1.33
∞ 0.02 0.08 1.40
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
626_D 67_Q 1.35 0.74 0.01
619_K 15_P 1.28 0.68 0.01
224_T 77_L 1.14 0.55 0.01
617_N 16_G 1.11 0.52 0.01
623_D 67_Q 1.08 0.49 0.01
592_D 65_K 0.95 0.37 0.01
258_Y 135_L 0.94 0.35 0.01
512_Q 151_H 0.92 0.34 0.01
202_S 150_V 0.91 0.32 0.00
561_F 127_V 0.90 0.32 0.00
151_V 99_K 0.90 0.32 0.00
417_A 19_C 0.85 0.27 0.00
102_I 120_V 0.82 0.25 0.00
567_V 101_I 0.81 0.25 0.00
306_I 48_T 0.81 0.24 0.00
308_E 57_N 0.80 0.24 0.00
561_F 50_A 0.80 0.24 0.00
203_T 71_L 0.80 0.24 0.00
157_G 124_N 0.80 0.24 0.00
411_L 90_Q 0.79 0.23 0.00
425_A 90_Q 0.79 0.23 0.00
358_S 21_L 0.78 0.23 0.00
478_E 150_V 0.78 0.22 0.00
78_A 22_F 0.77 0.22 0.00
561_F 45_Q 0.77 0.21 0.00
589_D 3_Y 0.76 0.21 0.00
121_D 107_Y 0.76 0.21 0.00
9_D 144_G 0.76 0.21 0.00
319_G 32_G 0.76 0.21 0.00
325_A 104_W 0.76 0.21 0.00
660_F 137_D 0.76 0.21 0.00
288_T 20_T 0.76 0.21 0.00
539_F 55_I 0.75 0.20 0.00
564_V 105_T 0.75 0.20 0.00
530_Q 141_I 0.75 0.20 0.00
216_A 70_S 0.74 0.20 0.00
245_K 130_K 0.74 0.20 0.00
246_T 59_L 0.74 0.20 0.00
72_G 154_R 0.74 0.20 0.00
558_T 135_L 0.74 0.20 0.00
632_V 69_I 0.74 0.19 0.00
253_P 114_A 0.73 0.19 0.00
266_E 8_P 0.73 0.19 0.00
209_A 5_Q 0.73 0.19 0.00
168_P 20_T 0.72 0.19 0.00
449_L 11_I 0.72 0.19 0.00
416_I 90_Q 0.72 0.18 0.00
234_P 141_I 0.72 0.18 0.00
619_K 67_Q 0.72 0.18 0.00
436_V 31_P 0.72 0.18 0.00
664_K 123_I 0.72 0.18 0.00
588_Y 15_P 0.71 0.18 0.00
352_L 88_L 0.71 0.18 0.00
257_G 141_I 0.71 0.18 0.00
216_A 150_V 0.71 0.18 0.00
558_T 57_N 0.71 0.18 0.00
400_H 130_K 0.71 0.18 0.00
54_N 90_Q 0.71 0.18 0.00
565_P 118_Q 0.71 0.18 0.00
538_G 10_D 0.70 0.17 0.00
207_V 13_N 0.70 0.17 0.00
586_N 114_A 0.70 0.17 0.00
497_T 127_V 0.70 0.17 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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