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OPENSEQ.org
PcrA vs MutL (A, 10-650) (B, 90-627)
Genes: A B A+B
Length: 641 538 1159
Sequences: 6870 3171 1373
Seq/Len: 10.72 5.89 1.18
MirrorTree (Pazo et al. 2001) 0.15
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 0.06 0.06 0.00
2 0.06 0.06 0.00
5 0.06 0.06 0.00
10 0.07 0.06 0.02
20 0.07 0.06 0.04
100 0.14 0.06 0.19
∞ 0.24 0.06 1.16
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
362_L 16_S 1.14 0.51 0.00
209_Q 488_I 1.11 0.48 0.00
312_I 92_H 1.11 0.48 0.00
9_E 232_I 0.99 0.37 0.00
194_F 154_R 0.99 0.37 0.00
362_L 526_S 0.97 0.35 0.00
404_R 18_S 0.95 0.34 0.00
559_A 186_L 0.95 0.34 0.00
115_V 205_V 0.92 0.31 0.00
367_L 28_E 0.92 0.31 0.00
235_Q 440_V 0.90 0.29 0.00
604_E 55_I 0.90 0.29 0.00
609_L 199_T 0.88 0.28 0.00
211_I 426_V 0.88 0.27 0.00
331_I 440_V 0.87 0.27 0.00
367_L 526_S 0.86 0.26 0.00
512_N 443_H 0.84 0.25 0.00
5_P 132_L 0.84 0.25 0.00
122_E 162_S 0.83 0.24 0.00
371_I 232_I 0.83 0.24 0.00
387_L 423_L 0.83 0.24 0.00
556_L 153_T 0.82 0.24 0.00
347_I 526_S 0.81 0.23 0.00
211_I 90_L 0.79 0.21 0.00
169_A 170_K 0.78 0.21 0.00
85_S 347_V 0.77 0.20 0.00
164_V 143_V 0.76 0.19 0.00
626_E 447_F 0.76 0.19 0.00
198_P 198_I 0.75 0.19 0.00
53_I 88_I 0.75 0.19 0.00
402_F 169_I 0.74 0.18 0.00
513_F 94_E 0.74 0.18 0.00
20_L 74_V 0.74 0.18 0.00
552_T 169_I 0.74 0.18 0.00
378_Y 89_A 0.73 0.18 0.00
32_L 186_L 0.73 0.18 0.00
347_I 191_H 0.73 0.18 0.00
322_G 440_V 0.73 0.18 0.00
227_V 95_V 0.73 0.18 0.00
360_E 163_V 0.72 0.17 0.00
608_Y 197_E 0.72 0.17 0.00
367_L 71_M 0.71 0.17 0.00
515_Q 483_S 0.71 0.17 0.00
200_V 416_I 0.71 0.17 0.00
331_I 14_I 0.71 0.17 0.00
87_C 198_I 0.71 0.17 0.00
138_T 88_I 0.71 0.16 0.00
144_N 16_S 0.70 0.16 0.00
64_K 17_V 0.70 0.16 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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