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OPENSEQ.org
SIR_FDIII
Genes: A B A+B
Length: 585 97 646
Sequences: 1860 5687 893
Seq/Len: 3.18 58.63 1.38
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 0.04 0.02 0.00
2 0.04 0.03 0.00
5 0.04 0.03 0.01
10 0.04 0.04 0.02
20 0.04 0.05 0.04
100 0.04 0.09 0.28
∞ 0.08 0.19 1.31
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
301_I 85_D 1.09 0.51 0.00
514_I 54_S 0.97 0.39 0.00
485_V 53_E 0.96 0.38 0.00
112_L 24_Y 0.84 0.27 0.00
75_T 36_L 0.84 0.27 0.00
398_V 21_D 0.83 0.27 0.00
374_V 5_V 0.82 0.26 0.00
251_V 22_D 0.81 0.25 0.00
569_D 34_V 0.80 0.25 0.00
546_F 5_V 0.77 0.22 0.00
483_V 83_K 0.77 0.22 0.00
549_W 52_I 0.77 0.22 0.00
82_V 22_D 0.76 0.21 0.00
390_I 16_E 0.75 0.21 0.00
563_T 51_K 0.75 0.21 0.00
82_V 39_S 0.75 0.21 0.00
411_I 26_L 0.75 0.20 0.00
549_W 34_V 0.74 0.20 0.00
401_T 33_G 0.74 0.20 0.00
132_G 89_H 0.74 0.20 0.00
329_D 63_S 0.74 0.20 0.00
229_V 72_E 0.73 0.19 0.00
301_I 87_V 0.73 0.19 0.00
428_L 5_V 0.72 0.19 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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