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OPENSEQ.org
RimPRsmA
Genes: A B A+B
Length: 150 273 411
Sequences: 2642 3757 1248
Seq/Len: 17.61 13.76 3.04
MirrorTree (Pazo et al. 2001) 0.58
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 0.07 0.00
2 0.10 0.07 0.00
5 0.10 0.07 0.01
10 0.10 0.07 0.01
20 0.10 0.07 0.04
100 0.10 0.07 0.23
∞ 0.10 0.08 2.95
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
24_V 249_A 1.61 0.97 0.86
83_R 114_L 1.08 0.73 0.42
149_H 18_N 0.98 0.62 0.32
21_F 14_R 0.94 0.58 0.28
36_L 165_Q 0.92 0.56 0.26
21_F 63_T 0.91 0.54 0.25
136_F 76_Q 0.89 0.52 0.24
77_S 194_L 0.89 0.52 0.23
59_S 114_L 0.89 0.52 0.23
46_I 254_V 0.87 0.50 0.22
49_D 240_G 0.83 0.45 0.19
98_E 210_L 0.81 0.42 0.17
131_G 118_I 0.80 0.41 0.16
66_D 148_L 0.80 0.40 0.16
29_I 87_I 0.79 0.40 0.16
117_I 206_D 0.79 0.39 0.15
39_Y 71_L 0.78 0.38 0.15
25_G 48_L 0.76 0.36 0.14
56_H 176_V 0.76 0.36 0.14
19_L 196_P 0.75 0.35 0.13
31_G 127_F 0.75 0.35 0.13
135_V 10_L 0.75 0.35 0.13
28_F 110_V 0.74 0.34 0.13
102_V 97_F 0.74 0.34 0.13
103_L 191_V 0.74 0.33 0.12
10_E 154_S 0.73 0.33 0.12
86_F 168_C 0.73 0.33 0.12
23_L 247_M 0.73 0.32 0.12
91_Y 219_N 0.72 0.32 0.12
90_H 138_F 0.72 0.32 0.11
71_A 31_S 0.71 0.31 0.11
39_Y 22_D 0.71 0.30 0.11
50_D 65_I 0.70 0.30 0.11
101_L 258_C 0.70 0.29 0.10
122_G 239_T 0.70 0.29 0.10
17_E 239_T 0.70 0.29 0.10
58_V 119_S 0.70 0.29 0.10
79_P 149_V 0.69 0.28 0.10
101_L 57_E 0.69 0.28 0.10
143_K 162_V 0.69 0.28 0.10
119_A 169_N 0.69 0.28 0.10
89_E 229_L 0.68 0.27 0.10
119_A 260_M 0.68 0.27 0.09
15_P 148_L 0.68 0.27 0.09
23_L 32_A 0.67 0.26 0.09
44_D 51_L 0.67 0.26 0.09
148_P 180_A 0.67 0.26 0.09
11_M 260_M 0.67 0.26 0.09
42_S 210_L 0.67 0.26 0.09
50_D 110_V 0.66 0.26 0.09
30_R 94_T 0.66 0.26 0.09
46_I 23_Q 0.66 0.26 0.09
38_I 86_T 0.66 0.25 0.08
127_V 252_I 0.66 0.25 0.08
62_L 25_V 0.65 0.24 0.08
84_P 12_R 0.65 0.24 0.08
101_L 73_A 0.65 0.24 0.08
46_I 219_N 0.65 0.24 0.08
13_T 260_M 0.65 0.24 0.08
92_A 208_R 0.64 0.24 0.08
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
10951 3.04 RimPRsmA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.86 Done - Shared
10947 0.23 RimPRsmA Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10943 0.05 RimPRsmA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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