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OPENSEQ.org
ISCA2_IBA57
Genes: A B A+B
Length: 327 111 406
Sequences: 16461 6758 403
Seq/Len: 50.34 60.88 0.99
MirrorTree (Pazo et al. 2001) 0.82
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 0.01 0.00 0.06
2 0.01 0.00 0.06
5 0.02 0.00 0.19
10 0.15 0.00 0.65
20 0.18 0.00 0.92
100 0.19 0.01 2.29
∞ 0.24 0.07 7.61
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
205_D 17_L 1.84 0.92 0.48
264_I 37_S 1.81 0.91 0.46
239_R 11_D 1.63 0.84 0.32
257_D 11_D 1.48 0.75 0.22
265_T 63_V 1.36 0.66 0.16
205_D 63_V 1.27 0.58 0.12
309_G 23_G 1.20 0.52 0.09
290_L 76_A 1.19 0.51 0.09
205_D 47_T 1.19 0.51 0.09
281_F 37_S 1.16 0.48 0.08
70_F 29_L 1.14 0.46 0.07
291_A 7_I 1.10 0.43 0.07
126_P 29_L 1.09 0.41 0.06
264_I 73_V 1.09 0.41 0.06
314_L 108_S 1.08 0.41 0.06
167_W 63_V 1.08 0.40 0.06
155_I 37_S 1.06 0.39 0.06
122_V 99_Q 1.03 0.37 0.05
217_N 61_A 1.02 0.36 0.05
312_V 5_G 1.02 0.36 0.05
149_R 77_Q 1.01 0.34 0.05
95_F 10_T 1.00 0.34 0.04
178_L 49_I 0.98 0.32 0.04
314_L 40_Q 0.96 0.31 0.04
35_P 20_I 0.96 0.30 0.04
182_G 108_S 0.96 0.30 0.04
5_S 63_V 0.95 0.30 0.04
129_R 73_V 0.93 0.28 0.03
304_I 73_V 0.93 0.28 0.03
50_P 57_E 0.92 0.28 0.03
205_D 29_L 0.92 0.28 0.03
72_N 73_V 0.91 0.27 0.03
269_T 63_V 0.91 0.26 0.03
32_V 24_S 0.89 0.25 0.03
281_F 73_V 0.89 0.25 0.03
99_C 84_L 0.89 0.25 0.03
17_A 29_L 0.89 0.25 0.03
54_P 22_E 0.89 0.25 0.03
99_C 45_L 0.88 0.25 0.03
86_L 17_L 0.88 0.24 0.03
264_I 17_L 0.86 0.23 0.02
218_L 63_V 0.85 0.23 0.02
265_T 77_Q 0.84 0.22 0.02
133_V 11_D 0.84 0.22 0.02
296_E 55_V 0.84 0.22 0.02
73_V 29_L 0.83 0.22 0.02
138_P 77_Q 0.83 0.21 0.02
306_A 81_S 0.83 0.21 0.02
8_S 108_S 0.82 0.21 0.02
19_W 55_V 0.81 0.20 0.02
93_S 96_Q 0.81 0.20 0.02
257_D 98_Q 0.81 0.20 0.02
292_L 100_G 0.79 0.19 0.02
217_N 39_F 0.79 0.19 0.02
233_G 79_D 0.79 0.19 0.02
307_S 59_G 0.79 0.19 0.02
185_G 61_A 0.78 0.18 0.02
289_G 100_G 0.78 0.18 0.02
131_W 63_V 0.78 0.18 0.02
97_L 55_V 0.78 0.18 0.02
8_S 17_L 0.78 0.18 0.02
65_A 107_F 0.78 0.18 0.02
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
9764 0.99 ISCA2_IBA57 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.48 Done - Shared
9701 0.34 ISCA2_IBA57 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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