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OPENSEQ.org
Oxa23-OmpW
Genes: A B A+B
Length: 273 193 456
Sequences: 11667 9504 354
Seq/Len: 42.74 49.24 0.78
MirrorTree (Pazo et al. 2001) 0.25
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 0.03 0.04 0.02
2 0.03 0.05 0.06
5 0.04 0.06 0.14
10 0.05 0.06 0.38
20 0.06 0.07 0.76
100 0.15 0.18 2.82
∞ 0.23 0.25 5.56
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
262_L 8_I 1.34 0.57 0.00
12_S 54_P 1.31 0.54 0.00
52_V 102_F 1.24 0.48 0.00
228_G 136_G 1.21 0.46 0.00
16_S 131_V 1.17 0.42 0.00
52_V 60_F 1.14 0.40 0.00
25_I 29_S 1.02 0.30 0.00
46_E 168_V 1.01 0.29 0.00
52_V 149_D 1.00 0.29 0.00
152_F 155_V 1.00 0.29 0.00
265_K 60_F 0.99 0.28 0.00
152_F 67_A 0.99 0.28 0.00
60_K 21_N 0.98 0.28 0.00
231_T 165_S 0.93 0.24 0.00
49_T 60_F 0.92 0.24 0.00
165_W 14_S 0.92 0.23 0.00
138_I 187_L 0.91 0.23 0.00
52_V 134_D 0.90 0.22 0.00
141_D 60_F 0.89 0.21 0.00
12_S 156_F 0.88 0.21 0.00
83_M 151_K 0.88 0.21 0.00
14_F 112_I 0.88 0.21 0.00
262_L 27_G 0.88 0.21 0.00
99_E 78_D 0.88 0.21 0.00
145_K 5_A 0.86 0.20 0.00
173_T 113_G 0.86 0.20 0.00
104_K 143_F 0.86 0.20 0.00
16_S 151_K 0.85 0.19 0.00
196_Q 114_I 0.84 0.19 0.00
36_H 102_F 0.84 0.19 0.00
258_I 16_F 0.84 0.19 0.00
145_K 155_V 0.84 0.19 0.00
107_K 102_F 0.83 0.18 0.00
233_W 114_I 0.83 0.18 0.00
214_F 141_V 0.83 0.18 0.00
240_K 79_V 0.82 0.18 0.00
85_N 157_V 0.82 0.18 0.00
201_N 193_F 0.82 0.18 0.00
107_K 57_E 0.82 0.18 0.00
177_E 111_Y 0.81 0.17 0.00
122_A 21_N 0.80 0.17 0.00
140_L 148_A 0.80 0.17 0.00
177_E 129_D 0.80 0.17 0.00
207_E 102_F 0.80 0.17 0.00
9_V 69_L 0.79 0.17 0.00
26_N 69_L 0.79 0.17 0.00
16_S 15_S 0.79 0.17 0.00
193_E 15_S 0.79 0.16 0.00
134_L 112_I 0.78 0.16 0.00
45_D 21_N 0.77 0.15 0.00
12_S 185_Y 0.77 0.15 0.00
90_L 10_L 0.77 0.15 0.00
139_G 61_G 0.77 0.15 0.00
266_S 157_V 0.77 0.15 0.00
228_G 84_Q 0.77 0.15 0.00
91_E 154_G 0.76 0.15 0.00
49_T 89_I 0.76 0.15 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
0703 0.78 Oxa23-OmpW Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0701 5.68 Oxa23-OmpW Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0699 0.13 Oxa23-OmpW Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
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