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OPENSEQ.org
ybgI and ybgL
Genes: A B A+B
Length: 310 244 516
Sequences: 2297 1683 1507
Seq/Len: 7.41 6.9 2.92
MirrorTree (Pazo et al. 2001) 0.70
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 0.05 1.18
2 0.00 0.05 2.29
5 0.00 0.05 2.68
10 0.01 0.06 2.68
20 0.02 0.06 2.70
100 0.03 0.06 2.72
∞ 0.10 0.10 2.83
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
226_S 174_R 0.84 0.44 0.00
49_N 99_V 0.82 0.42 0.00
240_G 174_R 0.81 0.41 0.00
169_L 91_A 0.79 0.38 0.00
250_Q 219_G 0.77 0.36 0.00
182_Y 214_T 0.76 0.34 0.00
70_F 233_S 0.72 0.30 0.00
96_A 167_A 0.71 0.30 0.00
60_L 102_H 0.69 0.28 0.00
226_S 163_R 0.68 0.27 0.00
126_G 51_S 0.66 0.25 0.00
225_L 160_F 0.66 0.24 0.00
229_L 180_L 0.66 0.24 0.00
240_G 171_L 0.65 0.24 0.00
244_V 3_I 0.64 0.23 0.00
256_P 174_R 0.64 0.23 0.00
277_P 226_A 0.64 0.23 0.00
55_I 79_Y 0.64 0.23 0.00
51_P 142_S 0.63 0.22 0.00
226_S 179_A 0.63 0.22 0.00
205_N 113_A 0.63 0.22 0.00
99_R 50_N 0.62 0.22 0.00
226_S 111_N 0.62 0.21 0.00
49_N 51_S 0.62 0.21 0.00
238_H 215_V 0.61 0.20 0.00
207_M 58_P 0.61 0.20 0.00
240_G 160_F 0.61 0.20 0.00
229_L 144_L 0.61 0.20 0.00
256_P 111_N 0.61 0.20 0.00
23_Q 76_E 0.61 0.20 0.00
200_L 42_A 0.61 0.20 0.00
228_G 129_A 0.59 0.19 0.00
9_M 187_A 0.59 0.19 0.00
92_L 173_S 0.58 0.18 0.00
234_V 194_M 0.58 0.18 0.00
110_R 110_Y 0.58 0.18 0.00
250_Q 58_P 0.58 0.18 0.00
226_S 164_G 0.58 0.18 0.00
129_S 50_N 0.58 0.18 0.00
4_I 155_T 0.58 0.18 0.00
250_Q 111_N 0.57 0.17 0.00
251_T 39_T 0.57 0.17 0.00
240_G 179_A 0.57 0.17 0.00
240_G 163_R 0.57 0.17 0.00
256_P 180_L 0.57 0.17 0.00
252_T 113_A 0.56 0.17 0.00
26_I 141_G 0.56 0.17 0.00
255_Y 174_R 0.56 0.17 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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