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OPENSEQ.org
RNAP_MFD
Genes: A B A+B
Length: 180 160 305
Sequences: 1823 2106 853
Seq/Len: 10.13 13.16 2.8
MirrorTree (Pazo et al. 2001) 0.64
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 0.09 0.00 0.01
2 0.09 0.00 0.01
5 0.09 0.00 0.01
10 0.09 0.00 0.01
20 0.09 0.00 0.05
100 0.09 0.00 0.39
∞ 0.09 0.01 2.51
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
111_D 67_A 1.85 0.99 0.95
99_Q 49_L 1.73 0.98 0.93
140_I 117_E 1.57 0.96 0.88
115_L 123_A 1.44 0.93 0.81
173_D 140_Y 1.40 0.92 0.79
89_T 61_L 1.33 0.89 0.74
109_K 49_L 1.21 0.82 0.63
69_L 49_L 1.20 0.81 0.62
172_I 81_R 1.19 0.81 0.61
26_Y 80_S 1.17 0.79 0.59
20_E 102_R 1.15 0.78 0.57
98_L 110_K 1.10 0.73 0.52
136_I 133_F 1.07 0.70 0.48
114_F 64_A 1.05 0.69 0.46
125_G 118_L 1.05 0.68 0.46
46_A 157_Q 1.04 0.67 0.45
64_L 37_E 1.04 0.67 0.44
21_I 126_A 1.02 0.65 0.42
172_I 93_H 1.01 0.64 0.41
91_Q 119_L 1.00 0.63 0.40
136_I 47_T 1.00 0.62 0.40
100_L 45_G 0.99 0.61 0.39
104_D 150_E 0.99 0.61 0.39
73_L 80_S 0.98 0.60 0.38
17_P 113_D 0.98 0.60 0.37
162_I 73_V 0.97 0.59 0.37
3_I 43_Y 0.97 0.59 0.37
158_Y 61_L 0.97 0.59 0.37
98_L 80_S 0.96 0.58 0.36
129_I 50_E 0.95 0.57 0.35
45_Q 40_V 0.94 0.56 0.34
55_E 124_Q 0.93 0.54 0.32
173_D 136_D 0.92 0.53 0.32
175_E 58_Y 0.92 0.53 0.31
48_F 97_G 0.92 0.53 0.31
75_E 48_T 0.92 0.52 0.31
146_V 113_D 0.91 0.52 0.30
7_G 59_L 0.91 0.52 0.30
19_T 76_L 0.91 0.51 0.30
44_I 122_Y 0.90 0.51 0.29
168_R 78_L 0.90 0.51 0.29
162_I 47_T 0.90 0.51 0.29
128_I 97_G 0.90 0.50 0.29
113_V 111_V 0.90 0.50 0.29
95_Y 55_T 0.89 0.49 0.28
20_E 59_L 0.88 0.49 0.28
27_R 43_Y 0.88 0.48 0.27
48_F 57_E 0.88 0.48 0.27
26_Y 143_F 0.88 0.48 0.27
160_A 120_D 0.87 0.47 0.26
168_R 34_V 0.86 0.46 0.26
44_I 78_L 0.86 0.45 0.25
104_D 29_I 0.85 0.45 0.25
97_R 93_H 0.85 0.45 0.25
155_P 62_T 0.85 0.45 0.24
97_R 45_G 0.85 0.44 0.24
118_I 71_V 0.85 0.44 0.24
83_C 70_Y 0.85 0.44 0.24
158_Y 105_Q 0.84 0.44 0.24
162_I 119_L 0.84 0.44 0.24
4_K 48_T 0.84 0.43 0.23
95_Y 103_A 0.84 0.43 0.23
146_V 114_V 0.83 0.43 0.23
126_S 34_V 0.83 0.43 0.23
27_R 105_Q 0.83 0.43 0.23
136_I 49_L 0.83 0.42 0.23
114_F 130_G 0.83 0.42 0.23
159_I 109_E 0.83 0.42 0.22
7_G 148_P 0.83 0.42 0.22
89_T 45_G 0.83 0.42 0.22
97_R 63_Y 0.83 0.42 0.22
146_V 81_R 0.82 0.41 0.22
44_I 110_K 0.82 0.41 0.22
177_E 76_L 0.82 0.41 0.22
118_I 83_A 0.82 0.41 0.22
47_A 104_R 0.82 0.41 0.22
26_Y 21_I 0.82 0.41 0.22
69_L 104_R 0.82 0.41 0.21
136_I 124_Q 0.82 0.40 0.21
113_V 48_T 0.81 0.40 0.21
51_T 149_F 0.81 0.40 0.21
116_G 118_L 0.81 0.40 0.21
90_Y 77_H 0.81 0.40 0.21
69_L 103_A 0.81 0.40 0.20
24_E 87_E 0.81 0.40 0.20
9_I 119_L 0.81 0.39 0.20
81_D 42_R 0.81 0.39 0.20
116_G 147_F 0.80 0.39 0.20
101_I 51_A 0.80 0.39 0.20
140_I 74_S 0.80 0.38 0.19
67_D 91_P 0.78 0.37 0.18
89_T 43_Y 0.78 0.36 0.18
41_N 40_V 0.78 0.36 0.18
107_L 136_D 0.78 0.36 0.18
140_I 43_Y 0.78 0.36 0.18
70_E 121_I 0.78 0.36 0.18
24_E 156_A 0.78 0.36 0.18
52_F 73_V 0.78 0.36 0.18
132_A 140_Y 0.78 0.36 0.18
14_P 65_N 0.78 0.36 0.18
67_D 31_Q 0.78 0.36 0.18
49_R 23_N 0.78 0.36 0.18
17_P 112_R 0.77 0.36 0.18
123_E 153_P 0.77 0.35 0.17
106_G 130_G 0.77 0.35 0.17
51_T 54_I 0.77 0.35 0.17
26_Y 120_D 0.77 0.35 0.17
6_F 19_T 0.76 0.34 0.17
124_D 111_V 0.76 0.34 0.17
47_A 114_V 0.76 0.34 0.17
63_G 150_E 0.76 0.34 0.17
162_I 60_M 0.76 0.34 0.17
50_E 143_F 0.76 0.34 0.17
146_V 101_S 0.76 0.34 0.17
96_A 148_P 0.76 0.34 0.17
8_R 105_Q 0.75 0.33 0.16
14_P 102_R 0.75 0.33 0.16
73_L 60_M 0.75 0.33 0.16
124_D 43_Y 0.75 0.33 0.16
94_L 95_L 0.74 0.32 0.15
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
5374 2.8 RNAP_MFD Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.95 Done - Shared
5365 0.06 MFDecoliRNAPthermus Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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