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OPENSEQ.org
RimP-S12
Genes: A B A+B
Length: 124 150 271
Sequences: 1157 2642 1045
Seq/Len: 9.33 17.61 3.86
MirrorTree (Pazo et al. 2001) 0.33
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 0.10 0.10 0.00
2 0.10 0.10 0.00
5 0.10 0.10 0.00
10 0.10 0.10 0.01
20 0.10 0.10 0.04
100 0.10 0.10 0.30
∞ 0.10 0.10 3.81
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
8_V 12_I 1.31 0.93 0.43
2_A 25_G 1.29 0.92 0.41
5_N 83_R 1.23 0.90 0.36
2_A 86_F 1.06 0.79 0.23
8_V 97_E 1.03 0.76 0.21
79_V 146_L 0.95 0.66 0.16
68_G 86_F 0.92 0.63 0.14
59_N 65_E 0.91 0.61 0.14
4_V 47_N 0.90 0.60 0.13
70_E 136_F 0.88 0.58 0.12
79_V 22_E 0.86 0.55 0.12
113_A 90_H 0.84 0.53 0.11
65_S 64_V 0.84 0.52 0.11
111_K 135_V 0.83 0.52 0.10
98_V 34_S 0.83 0.52 0.10
11_P 29_I 0.82 0.50 0.10
98_V 18_A 0.82 0.50 0.10
82_I 39_Y 0.82 0.49 0.10
24_L 135_V 0.82 0.49 0.10
2_A 60_A 0.82 0.49 0.10
102_L 55_S 0.81 0.49 0.10
58_T 39_Y 0.81 0.48 0.09
113_A 40_I 0.80 0.47 0.09
88_K 16_V 0.80 0.47 0.09
11_P 93_R 0.79 0.45 0.09
58_T 48_V 0.78 0.45 0.08
70_E 90_H 0.77 0.43 0.08
96_H 24_V 0.76 0.42 0.08
97_T 38_I 0.76 0.41 0.08
11_P 60_A 0.76 0.41 0.07
81_L 46_I 0.76 0.41 0.07
20_N 30_R 0.75 0.40 0.07
119_V 127_V 0.74 0.40 0.07
8_V 32_R 0.74 0.39 0.07
22_P 37_R 0.74 0.39 0.07
119_V 12_I 0.74 0.39 0.07
21_V 143_K 0.73 0.39 0.07
64_T 83_R 0.73 0.38 0.07
104_C 98_E 0.73 0.38 0.07
26_A 69_T 0.73 0.38 0.07
82_I 68_I 0.72 0.37 0.07
40_T 49_D 0.72 0.37 0.06
121_R 24_V 0.71 0.36 0.06
64_T 94_F 0.69 0.33 0.06
14_R 118_K 0.69 0.33 0.06
101_A 57_Q 0.69 0.33 0.06
119_V 60_A 0.68 0.32 0.05
56_R 11_M 0.68 0.32 0.05
59_N 48_V 0.68 0.32 0.05
70_E 41_D 0.68 0.32 0.05
105_S 52_A 0.68 0.32 0.05
116_K 48_V 0.67 0.31 0.05
68_G 26_I 0.67 0.31 0.05
16_V 13_T 0.66 0.30 0.05
119_V 49_D 0.66 0.30 0.05
25_E 56_H 0.66 0.29 0.05
111_K 115_G 0.66 0.29 0.05
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
10972 3.86 RimP-S12 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.43 Done - Shared
10971 0.04 RimP-S12 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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