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OPENSEQ.org
CAPRI T104
Genes: A B A+B
Length: 135 90 216
Sequences: 144 191 104
Seq/Len: 1.07 2.12 0.48
MirrorTree (Pazo et al. 2001) 0.38
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 0.00 0.40 0.46
2 0.01 0.43 0.46
5 0.01 0.44 0.46
10 0.01 0.44 0.46
20 0.01 0.44 0.46
100 0.01 0.44 0.46
∞ 0.01 0.45 0.46
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
73_F 35_E 1.98 0.84 0.14
84_P 46_E 1.78 0.74 0.09
84_P 56_G 1.72 0.70 0.07
123_S 67_T 1.71 0.70 0.07
94_F 49_T 1.66 0.67 0.06
81_Y 42_V 1.54 0.58 0.04
88_L 67_T 1.47 0.53 0.04
13_V 86_G 1.36 0.45 0.03
70_N 71_I 1.29 0.39 0.02
69_S 23_F 1.27 0.38 0.02
61_S 75_V 1.26 0.37 0.02
93_K 35_E 1.25 0.36 0.02
70_N 60_H 1.21 0.34 0.02
111_I 67_T 1.20 0.33 0.02
115_V 57_V 1.16 0.30 0.01
96_I 55_S 1.15 0.30 0.01
93_K 39_D 1.15 0.29 0.01
124_E 18_I 1.14 0.29 0.01
90_S 43_K 1.12 0.28 0.01
87_H 55_S 1.11 0.27 0.01
78_L 45_F 1.10 0.26 0.01
92_E 43_K 1.09 0.26 0.01
83_V 56_G 1.08 0.26 0.01
27_V 80_A 1.08 0.26 0.01
127_K 8_S 1.08 0.25 0.01
11_Q 82_N 1.07 0.25 0.01
111_I 64_G 1.06 0.24 0.01
75_S 8_S 1.05 0.23 0.01
57_S 73_K 1.04 0.23 0.01
104_S 59_F 1.03 0.23 0.01
87_H 46_E 1.02 0.22 0.01
116_I 85_P 0.99 0.21 0.01
93_K 41_L 0.99 0.20 0.01
19_A 89_A 0.98 0.20 0.01
81_Y 35_E 0.98 0.20 0.01
32_Q 81_A 0.96 0.19 0.01
79_A 72_V 0.95 0.18 0.01
94_F 18_I 0.94 0.18 0.01
93_K 42_V 0.94 0.18 0.01
79_A 42_V 0.93 0.18 0.01
64_E 73_K 0.93 0.18 0.01
12_P 81_A 0.93 0.18 0.01
27_V 27_S 0.93 0.17 0.01
110_N 43_K 0.93 0.17 0.01
6_A 80_A 0.92 0.17 0.01
73_F 42_V 0.92 0.17 0.01
55_A 50_S 0.92 0.17 0.01
51_Q 69_E 0.92 0.17 0.01
36_Q 81_A 0.91 0.17 0.01
12_P 84_L 0.91 0.17 0.01
38_R 76_K 0.88 0.16 0.01
94_F 22_F 0.88 0.16 0.01
100_V 84_L 0.87 0.15 0.01
123_S 70_G 0.86 0.15 0.00
37_L 83_G 0.86 0.15 0.00
96_I 31_G 0.86 0.15 0.00
83_V 42_V 0.86 0.15 0.00
95_E 67_T 0.85 0.14 0.00
15_G 84_L 0.85 0.14 0.00
3_P 48_V 0.84 0.14 0.00
41_E 20_E 0.84 0.14 0.00
79_A 6_N 0.84 0.14 0.00
124_E 6_N 0.84 0.14 0.00
24_G 1_M 0.84 0.14 0.00
95_E 70_G 0.84 0.14 0.00
102_L 59_F 0.83 0.14 0.00
33_I 86_G 0.83 0.14 0.00
43_K 80_A 0.83 0.14 0.00
116_I 17_Q 0.82 0.14 0.00
31_S 77_E 0.82 0.13 0.00
117_V 84_L 0.81 0.13 0.00
124_E 63_P 0.81 0.13 0.00
103_E 81_A 0.81 0.13 0.00
104_S 8_S 0.80 0.13 0.00
24_G 81_A 0.80 0.13 0.00
19_A 84_L 0.80 0.13 0.00
120_K 34_L 0.80 0.12 0.00
114_L 4_K 0.79 0.12 0.00
94_F 67_T 0.79 0.12 0.00
81_Y 38_M 0.79 0.12 0.00
47_D 77_E 0.79 0.12 0.00
40_K 40_K 0.78 0.12 0.00
68_P 21_E 0.78 0.12 0.00
29_I 80_A 0.78 0.12 0.00
59_D 86_G 0.78 0.12 0.00
11_Q 80_A 0.78 0.12 0.00
60_P 9_D 0.78 0.12 0.00
63_L 86_G 0.77 0.12 0.00
33_I 77_E 0.77 0.12 0.00
40_K 43_K 0.76 0.12 0.00
82_A 63_P 0.76 0.11 0.00
9_N 72_V 0.76 0.11 0.00
39_G 18_I 0.76 0.11 0.00
78_L 26_K 0.76 0.11 0.00
38_R 12_E 0.75 0.11 0.00
42_F 16_L 0.75 0.11 0.00
94_F 41_L 0.74 0.11 0.00
20_G 81_A 0.74 0.11 0.00
127_K 6_N 0.74 0.11 0.00
125_I 69_E 0.74 0.11 0.00
104_S 22_F 0.73 0.10 0.00
13_V 89_A 0.73 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.44 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
1837 0.48 CAPRI T104 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.14 Done - Shared
1820 0.34 CAPRI T104 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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