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OPENSEQ.org
EcfG_PhyR_Coev
Genes: A B A+B
Length: 218 266 437
Sequences: 16812 3488 201
Seq/Len: 77.12 13.11 0.46
MirrorTree (Pazo et al. 2001) 0.43
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 0.06 0.02 0.04
2 0.07 0.03 0.08
5 0.09 0.03 0.17
10 0.11 0.04 0.26
20 0.12 0.05 0.42
100 0.17 0.08 1.47
∞ 0.22 0.15 3.38
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
154_A 217_I 1.35 0.42 0.00
130_M 69_A 1.13 0.28 0.00
158_A 215_P 1.10 0.26 0.00
135_L 189_V 1.08 0.25 0.00
157_E 214_V 1.07 0.24 0.00
145_L 239_T 1.05 0.23 0.00
63_E 166_D 1.03 0.22 0.00
112_D 147_E 1.02 0.21 0.00
184_L 231_R 0.98 0.19 0.00
90_R 99_A 0.95 0.18 0.00
131_Q 145_I 0.95 0.18 0.00
73_Q 143_V 0.95 0.18 0.00
128_G 220_T 0.94 0.18 0.00
108_D 102_L 0.94 0.18 0.00
130_M 177_A 0.92 0.17 0.00
176_G 214_V 0.91 0.16 0.00
140_P 105_L 0.91 0.16 0.00
89_L 200_S 0.90 0.16 0.00
99_R 147_E 0.90 0.16 0.00
137_L 178_L 0.89 0.15 0.00
152_G 66_S 0.86 0.14 0.00
33_K 147_E 0.85 0.14 0.00
127_L 154_A 0.85 0.14 0.00
163_Q 71_L 0.85 0.14 0.00
164_V 220_T 0.84 0.14 0.00
157_E 200_S 0.84 0.14 0.00
46_F 220_T 0.83 0.14 0.00
137_L 144_L 0.83 0.13 0.00
68_A 189_V 0.81 0.13 0.00
72_R 128_I 0.81 0.13 0.00
139_Q 85_A 0.81 0.13 0.00
63_E 250_A 0.79 0.12 0.00
111_A 70_Q 0.79 0.12 0.00
47_G 146_I 0.79 0.12 0.00
158_A 149_E 0.78 0.12 0.00
139_Q 139_L 0.77 0.12 0.00
28_S 175_G 0.77 0.11 0.00
75_F 121_F 0.77 0.11 0.00
20_E 69_A 0.77 0.11 0.00
172_R 177_A 0.77 0.11 0.00
180_L 147_E 0.76 0.11 0.00
165_A 208_I 0.76 0.11 0.00
176_G 96_S 0.75 0.11 0.00
64_T 119_C 0.74 0.11 0.00
27_L 109_T 0.74 0.11 0.00
158_A 184_R 0.74 0.11 0.00
22_V 243_Q 0.74 0.11 0.00
59_D 19_R 0.74 0.10 0.00
22_V 150_P 0.74 0.10 0.00
85_T 251_I 0.74 0.10 0.00
60_L 142_E 0.74 0.10 0.00
98_R 149_E 0.74 0.10 0.00
113_R 252_G 0.73 0.10 0.00
56_L 167_V 0.73 0.10 0.00
147_L 217_I 0.73 0.10 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
4409 0.9 EcfG_PhyR_Coev Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4406 5.51 EcfG_PhyR_Coev Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4401 0.46 EcfG_PhyR_Coev Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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