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OPENSEQ.org
ISCA2_IBA57
Genes: A B A+B
Length: 327 111 394
Sequences: 4327 3210 132
Seq/Len: 13.23 28.92 0.34
MirrorTree (Pazo et al. 2001) 0.91
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 0.03 0.04 0.01
2 0.05 0.04 0.01
5 0.07 0.04 0.05
10 0.07 0.04 0.20
20 0.09 0.04 0.30
100 0.10 0.06 0.79
∞ 0.17 0.16 2.80
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
98_E 54_R 1.72 0.60 0.00
155_I 37_S 1.62 0.53 0.00
44_L 29_L 1.60 0.52 0.00
127_E 63_V 1.54 0.48 0.00
142_G 57_E 1.53 0.47 0.00
133_V 7_I 1.52 0.47 0.00
264_I 63_V 1.52 0.46 0.00
21_C 22_E 1.44 0.41 0.00
205_D 77_Q 1.40 0.38 0.00
281_F 73_V 1.39 0.38 0.00
162_T 65_V 1.39 0.37 0.00
78_L 22_E 1.36 0.36 0.00
263_G 37_S 1.35 0.35 0.00
111_L 61_A 1.31 0.33 0.00
156_L 67_S 1.29 0.32 0.00
179_V 47_T 1.27 0.30 0.00
281_F 17_L 1.27 0.30 0.00
205_D 108_S 1.22 0.27 0.00
232_I 57_E 1.22 0.27 0.00
291_A 20_I 1.22 0.27 0.00
127_E 29_L 1.18 0.25 0.00
204_R 47_T 1.16 0.24 0.00
129_R 98_Q 1.16 0.24 0.00
182_G 57_E 1.16 0.24 0.00
41_L 29_L 1.15 0.24 0.00
279_G 35_G 1.15 0.23 0.00
279_G 36_C 1.15 0.23 0.00
279_G 38_G 1.15 0.23 0.00
279_G 103_C 1.15 0.23 0.00
86_L 37_S 1.14 0.23 0.00
243_M 22_E 1.13 0.23 0.00
127_E 17_L 1.13 0.23 0.00
34_G 79_D 1.12 0.22 0.00
291_A 102_S 1.11 0.22 0.00
176_P 39_F 1.11 0.21 0.00
271_L 73_V 1.10 0.21 0.00
86_L 73_V 1.09 0.20 0.00
235_E 66_D 1.08 0.20 0.00
64_R 63_V 1.08 0.20 0.00
183_R 37_S 1.08 0.20 0.00
107_L 43_F 1.07 0.20 0.00
70_F 29_L 1.07 0.20 0.00
145_S 7_I 1.04 0.19 0.00
263_G 17_L 1.03 0.18 0.00
106_A 73_V 1.03 0.18 0.00
204_R 39_F 1.03 0.18 0.00
179_V 77_Q 1.03 0.18 0.00
178_L 62_R 1.03 0.18 0.00
51_L 80_F 1.01 0.17 0.00
127_E 37_S 1.01 0.17 0.00
95_F 57_E 1.01 0.17 0.00
148_E 17_L 1.01 0.17 0.00
155_I 17_L 1.01 0.17 0.00
38_A 18_L 1.00 0.17 0.00
84_Y 24_S 1.00 0.17 0.00
227_T 15_Q 1.00 0.17 0.00
170_L 86_R 0.99 0.17 0.00
70_F 18_L 0.99 0.17 0.00
167_W 62_R 0.99 0.17 0.00
43_G 15_Q 0.99 0.17 0.00
86_L 17_L 0.98 0.16 0.00
148_E 37_S 0.98 0.16 0.00
279_G 101_C 0.97 0.16 0.00
276_Q 63_V 0.96 0.15 0.00
34_G 35_G 0.96 0.15 0.00
34_G 36_C 0.96 0.15 0.00
34_G 38_G 0.96 0.15 0.00
34_G 103_C 0.96 0.15 0.00
83_L 31_V 0.96 0.15 0.00
227_T 37_S 0.95 0.15 0.00
281_F 37_S 0.95 0.15 0.00
291_A 69_S 0.95 0.15 0.00
215_E 56_F 0.95 0.15 0.00
204_R 81_S 0.94 0.15 0.00
99_C 78_V 0.93 0.14 0.00
268_A 37_S 0.93 0.14 0.00
279_G 95_P 0.93 0.14 0.00
279_G 89_F 0.93 0.14 0.00
279_G 94_N 0.93 0.14 0.00
279_G 106_S 0.93 0.14 0.00
133_V 80_F 0.93 0.14 0.00
215_E 12_S 0.93 0.14 0.00
229_G 91_V 0.93 0.14 0.00
279_G 28_R 0.93 0.14 0.00
270_V 78_V 0.92 0.14 0.00
21_C 81_S 0.92 0.14 0.00
107_L 102_S 0.92 0.14 0.00
65_A 76_A 0.92 0.14 0.00
75_G 35_G 0.92 0.14 0.00
75_G 36_C 0.92 0.14 0.00
75_G 38_G 0.92 0.14 0.00
75_G 103_C 0.92 0.14 0.00
278_V 55_V 0.91 0.14 0.00
273_A 11_D 0.91 0.14 0.00
138_P 55_V 0.91 0.14 0.00
263_G 73_V 0.90 0.13 0.00
246_I 23_G 0.90 0.13 0.00
41_L 7_I 0.90 0.13 0.00
151_G 37_S 0.90 0.13 0.00
182_G 47_T 0.90 0.13 0.00
233_G 35_G 0.90 0.13 0.00
233_G 36_C 0.90 0.13 0.00
233_G 38_G 0.90 0.13 0.00
233_G 103_C 0.90 0.13 0.00
278_V 8_R 0.90 0.13 0.00
93_S 56_F 0.90 0.13 0.00
274_S 80_F 0.90 0.13 0.00
174_E 67_S 0.90 0.13 0.00
88_E 70_L 0.90 0.13 0.00
41_L 67_S 0.90 0.13 0.00
224_V 52_D 0.89 0.13 0.00
33_R 57_E 0.89 0.13 0.00
140_A 7_I 0.89 0.13 0.00
290_L 102_S 0.89 0.13 0.00
206_L 86_R 0.89 0.13 0.00
33_R 18_L 0.88 0.13 0.00
190_Y 45_L 0.88 0.13 0.00
123_E 98_Q 0.87 0.12 0.00
38_A 7_I 0.87 0.12 0.00
142_G 10_T 0.87 0.12 0.00
192_Q 45_L 0.87 0.12 0.00
83_L 63_V 0.86 0.12 0.00
88_E 63_V 0.86 0.12 0.00
110_H 22_E 0.86 0.12 0.00
290_L 16_R 0.86 0.12 0.00
171_T 73_V 0.86 0.12 0.00
105_G 18_L 0.86 0.12 0.00
45_L 82_Q 0.86 0.12 0.00
93_S 15_Q 0.86 0.12 0.00
182_G 108_S 0.85 0.12 0.00
225_S 80_F 0.85 0.12 0.00
31_R 65_V 0.85 0.12 0.00
184_L 22_E 0.85 0.12 0.00
186_D 53_D 0.85 0.12 0.00
151_G 29_L 0.85 0.12 0.00
190_Y 72_F 0.85 0.12 0.00
86_L 19_E 0.84 0.12 0.00
31_R 22_E 0.84 0.12 0.00
34_G 31_V 0.84 0.12 0.00
288_V 19_E 0.84 0.12 0.00
42_L 80_F 0.84 0.11 0.00
279_G 13_C 0.83 0.11 0.00
67_Y 80_F 0.83 0.11 0.00
289_G 85_I 0.83 0.11 0.00
72_N 8_R 0.83 0.11 0.00
240_T 56_F 0.83 0.11 0.00
155_I 98_Q 0.83 0.11 0.00
34_G 69_S 0.83 0.11 0.00
113_L 80_F 0.82 0.11 0.00
54_P 70_L 0.82 0.11 0.00
263_G 64_V 0.82 0.11 0.00
291_A 45_L 0.82 0.11 0.00
114_Y 57_E 0.82 0.11 0.00
36_D 84_L 0.82 0.11 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
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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