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OPENSEQ.org
RP tcs contact residue analysis
Genes: A B A+B
Length: 485 247 686
Sequences: 11590 28853 6530
Seq/Len: 23.9 116.81 9.52
MirrorTree (Pazo et al. 2001) 0.56
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 0.01 8.05
2 0.01 0.02 8.14
5 0.01 0.04 8.32
10 0.03 0.06 8.56
20 0.05 0.09 8.92
100 0.11 0.18 10.64
∞ 0.20 0.24 12.22
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
266_T 32_I 2.37 1.00 1.00
273_E 124_S 2.31 1.00 1.00
270_G 35_L 2.02 1.00 0.99
285_M 34_E 1.97 1.00 0.99
262_R 120_T 1.45 1.00 0.91
309_R 102_D 1.38 0.99 0.89
292_S 31_N 1.30 0.99 0.85
296_R 29_E 1.24 0.98 0.82
293_E 31_N 1.14 0.97 0.74
277_Q 126_E 1.07 0.95 0.68
274_L 39_S 1.02 0.93 0.62
289_R 31_N 0.99 0.91 0.59
289_R 34_E 0.99 0.91 0.58
267_T 32_I 0.98 0.91 0.57
271_F 35_L 0.92 0.87 0.50
295_S 124_S 0.89 0.84 0.47
267_T 31_N 0.89 0.84 0.46
267_T 29_E 0.84 0.79 0.40
273_E 104_L 0.80 0.74 0.35
273_E 126_E 0.79 0.73 0.34
263_T 32_I 0.79 0.73 0.34
273_E 125_L 0.72 0.63 0.26
274_L 38_V 0.71 0.60 0.24
278_G 42_F 0.69 0.58 0.23
282_D 41_K 0.68 0.56 0.21
286_L 38_V 0.67 0.54 0.20
271_F 175_S 0.64 0.49 0.18
277_Q 39_S 0.62 0.46 0.16
262_R 102_D 0.61 0.45 0.15
271_F 31_N 0.61 0.44 0.15
377_H 216_S 0.60 0.43 0.14
255_T 101_R 0.59 0.41 0.13
215_V 164_E 0.59 0.40 0.13
428_A 30_A 0.56 0.35 0.11
274_L 125_L 0.55 0.34 0.10
277_Q 43_Q 0.54 0.32 0.10
289_R 35_L 0.53 0.31 0.10
271_F 38_V 0.52 0.30 0.09
219_S 97_F 0.52 0.30 0.09
282_D 38_V 0.52 0.29 0.09
274_L 35_L 0.51 0.29 0.09
263_T 29_E 0.49 0.26 0.08
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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