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OPENSEQ.org
GRK1-Rho
Genes: A B A+B
Length: 563 348 844
Sequences: 236 17504 75
Seq/Len: 0.42 50.3 0.09
MirrorTree (Pazo et al. 2001) 0.23
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 0.03 0.13 0.00
2 0.03 0.15 0.01
5 0.03 0.18 0.01
10 0.04 0.20 0.02
20 0.04 0.23 0.04
100 0.04 0.27 0.08
∞ 0.04 0.28 0.08
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
269_I 210_V 1.18 0.11 0.00
301_I 52_F 1.17 0.11 0.00
458_L 224_G 1.09 0.10 0.00
53_S 218_I 1.03 0.09 0.00
157_L 55_N 1.03 0.09 0.00
313_I 215_P 1.01 0.08 0.00
494_K 76_L 0.99 0.08 0.00
56_L 46_L 0.97 0.08 0.00
376_F 214_I 0.94 0.07 0.00
331_V 206_Y 0.93 0.07 0.00
458_L 290_I 0.93 0.07 0.00
292_P 290_I 0.93 0.07 0.00
74_Q 318_L 0.91 0.07 0.00
537_D 321_I 0.89 0.07 0.00
259_T 167_C 0.88 0.07 0.00
101_D 133_I 0.88 0.07 0.00
297_Y 83_D 0.88 0.07 0.00
258_E 214_I 0.87 0.07 0.00
301_I 319_T 0.87 0.06 0.00
420_S 67_K 0.86 0.06 0.00
307_H 137_V 0.86 0.06 0.00
398_K 55_N 0.86 0.06 0.00
458_L 218_I 0.86 0.06 0.00
515_P 226_L 0.86 0.06 0.00
363_L 165_L 0.85 0.06 0.00
94_D 264_C 0.84 0.06 0.00
92_I 205_I 0.84 0.06 0.00
423_S 134_E 0.83 0.06 0.00
31_R 290_I 0.83 0.06 0.00
424_K 153_A 0.83 0.06 0.00
165_Y 96_Y 0.83 0.06 0.00
420_S 214_I 0.82 0.06 0.00
453_P 82_A 0.82 0.06 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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