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OPENSEQ.org
CAPRI T105
Genes: A B A+B
Length: 131 87 217
Sequences: 144 197 106
Seq/Len: 1.1 2.26 0.49
MirrorTree (Pazo et al. 2001) 0.35
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 0.48
2 0.01 0.43 0.48
5 0.01 0.44 0.49
10 0.01 0.44 0.49
20 0.01 0.44 0.49
100 0.01 0.44 0.49
∞ 0.01 0.45 0.49
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
77_V 31_E 1.88 0.80 0.06
88_E 52_D 1.84 0.78 0.05
88_E 42_K 1.82 0.77 0.05
98_I 45_T 1.71 0.70 0.04
85_Y 38_V 1.65 0.66 0.03
96_I 39_L 1.59 0.62 0.03
127_I 64_S 1.49 0.55 0.02
74_S 56_Y 1.47 0.53 0.02
17_V 83_G 1.38 0.47 0.01
100_I 51_S 1.38 0.46 0.01
92_A 64_S 1.34 0.43 0.01
73_G 21_Y 1.28 0.39 0.01
15_Q 79_K 1.22 0.35 0.01
97_K 31_E 1.20 0.34 0.01
97_K 35_I 1.20 0.33 0.01
74_S 68_V 1.19 0.33 0.01
71_N 63_D 1.11 0.28 0.01
87_R 52_D 1.10 0.27 0.01
65_E 72_V 1.07 0.25 0.01
83_A 38_V 1.07 0.25 0.01
91_Q 51_S 1.06 0.25 0.01
31_A 77_A 1.05 0.24 0.01
82_G 41_F 1.02 0.23 0.01
97_K 38_V 1.02 0.22 0.01
119_V 53_L 1.00 0.21 0.00
91_Q 42_K 1.00 0.21 0.00
108_D 55_Y 0.99 0.21 0.00
128_E 16_F 0.99 0.21 0.00
61_A 70_K 0.98 0.20 0.00
68_K 70_K 0.98 0.20 0.00
115_M 60_N 0.96 0.20 0.00
114_N 39_L 0.96 0.19 0.00
94_G 39_L 0.96 0.19 0.00
59_A 46_E 0.96 0.19 0.00
97_K 37_A 0.95 0.19 0.00
77_V 38_V 0.95 0.19 0.00
55_Q 66_A 0.94 0.19 0.00
16_P 81_L 0.94 0.18 0.00
98_I 16_F 0.93 0.18 0.00
16_P 78_S 0.93 0.18 0.00
87_R 38_V 0.93 0.18 0.00
42_R 10_E 0.92 0.18 0.00
106_I 55_Y 0.91 0.17 0.00
128_E 4_K 0.90 0.17 0.00
79_R 6_S 0.90 0.17 0.00
19_G 45_T 0.90 0.17 0.00
115_M 64_S 0.90 0.16 0.00
3_P 81_L 0.89 0.16 0.00
120_A 82_P 0.87 0.15 0.00
3_P 79_K 0.87 0.15 0.00
35_S 74_E 0.86 0.15 0.00
37_I 83_G 0.86 0.15 0.00
11_T 55_Y 0.86 0.15 0.00
15_Q 77_A 0.85 0.15 0.00
23_G 86_A 0.85 0.15 0.00
10_A 77_A 0.85 0.14 0.00
13_K 69_V 0.84 0.14 0.00
108_D 6_S 0.83 0.14 0.00
36_Q 78_S 0.83 0.14 0.00
96_I 35_I 0.82 0.14 0.00
67_S 83_G 0.82 0.14 0.00
23_G 74_E 0.82 0.14 0.00
90_E 11_K 0.82 0.13 0.00
47_K 77_A 0.81 0.13 0.00
41_L 80_G 0.81 0.13 0.00
40_K 78_S 0.81 0.13 0.00
120_A 15_E 0.81 0.13 0.00
131_K 59_E 0.81 0.13 0.00
129_I 66_A 0.81 0.13 0.00
93_G 64_S 0.80 0.13 0.00
85_Y 31_E 0.80 0.13 0.00
98_I 20_I 0.80 0.13 0.00
107_A 79_K 0.80 0.13 0.00
104_V 81_L 0.79 0.12 0.00
55_Q 52_D 0.79 0.12 0.00
45_T 18_K 0.79 0.12 0.00
100_I 27_K 0.79 0.12 0.00
17_V 86_A 0.79 0.12 0.00
111_G 53_L 0.78 0.12 0.00
33_I 77_A 0.78 0.12 0.00
83_A 69_V 0.77 0.12 0.00
128_E 59_E 0.76 0.12 0.00
65_E 31_E 0.76 0.12 0.00
18_S 44_L 0.76 0.12 0.00
54_E 17_V 0.76 0.12 0.00
131_K 6_S 0.76 0.11 0.00
99_E 64_S 0.76 0.11 0.00
16_P 74_E 0.76 0.11 0.00
58_I 68_V 0.75 0.11 0.00
24_A 78_S 0.75 0.11 0.00
131_K 4_K 0.75 0.11 0.00
32_P 12_E 0.75 0.11 0.00
111_G 67_G 0.74 0.11 0.00
5_D 69_V 0.73 0.11 0.00
68_K 53_L 0.73 0.11 0.00
43_G 16_F 0.73 0.11 0.00
61_A 5_I 0.73 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)
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
1836 0.49 CAPRI T105 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.06 Done - Shared
1821 0.33 CAPRI T105 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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