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OPENSEQ.org
TPR-kinase
Genes: A B A+B
Length: 141 286 400
Sequences: 2799 2859 58
Seq/Len: 19.85 10 0.14
MirrorTree (Pazo et al. 2001) 0.23
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.06 0.01
2 0.05 0.06 0.01
5 0.08 0.08 0.04
10 0.08 0.08 0.07
20 0.08 0.09 0.14
100 0.10 0.12 0.50
∞ 0.13 0.17 1.18
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
98_V 117_M 1.38 0.21 0.00
92_E 148_L 1.31 0.18 0.00
49_A 26_F 1.22 0.15 0.00
112_G 141_I 1.19 0.15 0.00
105_L 153_I 1.14 0.13 0.00
67_A 205_S 1.11 0.13 0.00
128_L 275_P 1.09 0.12 0.00
105_L 235_D 1.09 0.12 0.00
88_F 71_I 1.08 0.12 0.00
94_S 26_F 1.07 0.12 0.00
68_R 148_L 1.06 0.12 0.00
84_V 213_M 1.06 0.11 0.00
73_M 259_K 1.01 0.10 0.00
33_A 254_L 0.98 0.10 0.00
105_L 270_E 0.97 0.10 0.00
91_F 28_V 0.97 0.10 0.00
71_F 205_S 0.97 0.10 0.00
32_Q 200_K 0.97 0.10 0.00
84_V 267_S 0.96 0.09 0.00
125_N 26_F 0.95 0.09 0.00
76_A 270_E 0.95 0.09 0.00
63_E 129_I 0.94 0.09 0.00
42_Y 46_A 0.94 0.09 0.00
96_G 155_N 0.93 0.09 0.00
24_N 86_M 0.93 0.09 0.00
67_A 28_V 0.93 0.09 0.00
67_A 146_L 0.92 0.09 0.00
98_V 235_D 0.91 0.09 0.00
85_H 26_F 0.91 0.09 0.00
40_D 130_V 0.91 0.08 0.00
55_F 205_S 0.90 0.08 0.00
86_I 213_M 0.90 0.08 0.00
32_Q 113_Y 0.89 0.08 0.00
119_L 246_P 0.89 0.08 0.00
69_D 211_Y 0.88 0.08 0.00
67_A 200_K 0.88 0.08 0.00
49_A 154_A 0.88 0.08 0.00
105_L 44_E 0.88 0.08 0.00
74_A 143_D 0.87 0.08 0.00
28_G 36_Y 0.87 0.08 0.00
35_E 129_I 0.86 0.08 0.00
132_Q 230_L 0.86 0.08 0.00
109_V 168_S 0.84 0.07 0.00
89_A 230_L 0.84 0.07 0.00
113_A 132_S 0.84 0.07 0.00
79_K 264_Q 0.84 0.07 0.00
99_K 276_Y 0.84 0.07 0.00
127_N 210_L 0.83 0.07 0.00
4_W 204_W 0.83 0.07 0.00
106_Q 213_M 0.83 0.07 0.00
33_A 20_G 0.82 0.07 0.00
34_I 136_P 0.82 0.07 0.00
102_K 113_Y 0.82 0.07 0.00
84_V 254_L 0.81 0.07 0.00
122_A 154_A 0.81 0.07 0.00
97_N 128_G 0.81 0.07 0.00
74_A 17_I 0.81 0.07 0.00
69_D 36_Y 0.81 0.07 0.00
24_N 211_Y 0.80 0.07 0.00
24_N 31_E 0.79 0.07 0.00
75_R 243_P 0.79 0.07 0.00
108_A 160_D 0.79 0.07 0.00
82_A 252_D 0.79 0.07 0.00
101_S 205_S 0.79 0.07 0.00
72_Q 70_K 0.79 0.07 0.00
34_I 80_T 0.79 0.07 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)
ID Seq/Len Name Options I_Prob Status
3293 1.25 TPR-kinase Δgene:(1, ∞) A:(1E-04, 4) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3201 0.14 TPR-kinase Δgene:(1, 20) A:(1E-04, 4) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3200 0 TPR-kinase Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 2) msa: Jackhmmer (2015_06) Killed - Shared
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