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OPENSEQ.org
1XQSAC
Genes: A B A+B
Length: 280 191 450
Sequences: 5821 5886 149
Seq/Len: 20.79 30.82 0.33
MirrorTree (Pazo et al. 2001) 0.16
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 0.03 0.02
2 0.06 0.04 0.04
5 0.08 0.05 0.08
10 0.08 0.06 0.17
20 0.09 0.07 0.32
100 0.13 0.09 1.06
∞ 0.18 0.16 2.19
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
172_A 144_A 1.30 0.31 0.00
187_G 72_D 1.18 0.25 0.00
75_L 100_A 1.16 0.24 0.00
221_V 151_I 1.12 0.22 0.00
41_R 73_I 1.10 0.21 0.00
102_E 67_R 1.01 0.17 0.00
168_K 79_A 1.00 0.17 0.00
87_A 145_K 0.99 0.16 0.00
257_E 168_K 0.98 0.16 0.00
110_L 131_R 0.96 0.15 0.00
91_G 173_F 0.94 0.14 0.00
198_L 59_N 0.94 0.14 0.00
225_P 104_I 0.93 0.14 0.00
48_L 76_N 0.93 0.14 0.00
90_I 98_T 0.92 0.14 0.00
66_G 166_V 0.91 0.13 0.00
226_Q 62_V 0.89 0.13 0.00
238_L 144_A 0.88 0.13 0.00
148_L 15_V 0.86 0.12 0.00
156_L 150_Q 0.84 0.11 0.00
40_E 100_A 0.84 0.11 0.00
82_L 76_N 0.84 0.11 0.00
57_N 170_L 0.83 0.11 0.00
136_L 82_R 0.83 0.11 0.00
202_V 122_F 0.82 0.11 0.00
89_L 118_T 0.82 0.11 0.00
90_I 108_F 0.82 0.11 0.00
161_Q 166_V 0.82 0.11 0.00
90_I 36_I 0.81 0.11 0.00
125_V 151_I 0.81 0.11 0.00
244_H 151_I 0.81 0.10 0.00
172_A 29_I 0.81 0.10 0.00
122_C 154_L 0.81 0.10 0.00
126_R 29_I 0.80 0.10 0.00
188_T 152_H 0.80 0.10 0.00
76_E 117_I 0.80 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
7402 0.03 1XQS_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
3541 0.33 1XQSAC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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