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OPENSEQ.org
CheY-FliM3
Genes: A B A+B
Length: 129 334 440
Sequences: 24493 3269 151
Seq/Len: 189.87 9.79 0.34
MirrorTree (Pazo et al. 2001) 0.14
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 0.86 0.13 0.00
2 0.86 0.13 0.01
5 0.86 0.14 0.02
10 0.86 0.14 0.03
20 0.86 0.14 0.05
100 0.86 0.15 0.33
∞ 0.86 0.16 1.89
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
60_M 304_S 1.51 0.46 0.00
84_L 35_I 1.48 0.43 0.00
116_L 199_V 1.32 0.33 0.00
56_S 271_R 1.28 0.31 0.00
8_F 290_D 1.23 0.28 0.00
104_S 35_I 1.22 0.27 0.00
71_T 280_P 1.22 0.27 0.00
19_R 317_V 1.21 0.27 0.00
87_T 127_V 1.20 0.26 0.00
60_M 276_L 1.18 0.25 0.00
55_I 219_L 1.17 0.25 0.00
106_Y 317_V 1.16 0.24 0.00
110_P 302_L 1.15 0.24 0.00
60_M 278_L 1.14 0.23 0.00
58_W 23_D 1.13 0.23 0.00
60_M 35_I 1.09 0.21 0.00
110_P 199_V 1.08 0.20 0.00
12_D 224_I 1.06 0.19 0.00
60_M 102_L 1.05 0.19 0.00
116_L 132_G 1.05 0.19 0.00
54_I 157_M 1.04 0.18 0.00
62_N 317_V 1.01 0.17 0.00
25_L 79_I 0.99 0.17 0.00
83_V 179_Y 0.97 0.16 0.00
102_G 39_D 0.97 0.16 0.00
12_D 276_L 0.97 0.16 0.00
63_M 203_P 0.97 0.16 0.00
31_N 274_Q 0.95 0.15 0.00
54_I 253_Q 0.95 0.15 0.00
42_A 35_I 0.95 0.15 0.00
24_L 298_G 0.95 0.15 0.00
38_D 269_P 0.93 0.14 0.00
86_V 57_I 0.91 0.14 0.00
74_A 118_F 0.91 0.14 0.00
55_I 95_N 0.90 0.13 0.00
108_V 227_L 0.90 0.13 0.00
8_F 99_P 0.90 0.13 0.00
8_F 201_N 0.89 0.13 0.00
124_F 219_L 0.89 0.13 0.00
77_A 206_V 0.88 0.13 0.00
55_I 280_P 0.88 0.13 0.00
41_D 283_V 0.88 0.13 0.00
39_G 292_I 0.88 0.13 0.00
56_S 131_F 0.88 0.13 0.00
30_F 28_G 0.87 0.12 0.00
86_V 263_A 0.87 0.12 0.00
54_I 288_K 0.87 0.12 0.00
10_V 107_L 0.87 0.12 0.00
102_G 79_I 0.86 0.12 0.00
38_D 318_E 0.86 0.12 0.00
36_A 9_A 0.86 0.12 0.00
21_V 155_N 0.86 0.12 0.00
84_L 301_V 0.86 0.12 0.00
11_V 127_V 0.86 0.12 0.00
104_S 196_N 0.86 0.12 0.00
87_T 279_K 0.86 0.12 0.00
30_F 224_I 0.85 0.12 0.00
53_F 261_L 0.85 0.12 0.00
16_T 266_A 0.85 0.12 0.00
8_F 158_L 0.85 0.12 0.00
39_G 306_Y 0.85 0.12 0.00
11_V 277_K 0.85 0.12 0.00
53_F 114_G 0.85 0.12 0.00
21_V 215_F 0.85 0.12 0.00
39_G 118_F 0.84 0.12 0.00
97_A 298_G 0.84 0.12 0.00
69_L 274_Q 0.84 0.12 0.00
93_E 95_N 0.84 0.12 0.00
55_I 304_S 0.83 0.11 0.00
12_D 292_I 0.83 0.11 0.00
124_F 196_N 0.83 0.11 0.00
87_T 273_S 0.82 0.11 0.00
111_F 257_S 0.82 0.11 0.00
38_D 79_I 0.82 0.11 0.00
40_V 116_V 0.81 0.11 0.00
60_M 64_Q 0.81 0.11 0.00
29_G 314_A 0.81 0.11 0.00
10_V 254_V 0.81 0.11 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.86 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
9391 0.34 CheY-FliM3 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9389 0.75 CheY-FliM2 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9375 1.54 CheYFliM Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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