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OPENSEQ.org
mxij_spa24
Genes: A B A+B
Length: 241 216 425
Sequences: 3945 3130 2994
Seq/Len: 16.37 14.49 7.04
MirrorTree (Pazo et al. 2001) 0.74
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 0.00 0.01
2 0.00 0.00 0.11
5 0.00 0.00 1.04
10 0.00 0.00 3.07
20 0.00 0.00 5.74
100 0.01 0.01 6.09
∞ 0.06 0.06 6.55
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
101_A 36_M 1.26 0.97 0.46
177_V 37_V 0.90 0.78 0.17
17_G 34_F 0.89 0.77 0.16
103_K 11_L 0.86 0.73 0.14
101_A 184_T 0.84 0.71 0.14
140_I 123_A 0.83 0.70 0.13
148_S 40_A 0.82 0.68 0.12
109_A 186_S 0.82 0.68 0.12
96_V 152_K 0.81 0.67 0.12
26_S 174_A 0.81 0.66 0.12
119_V 174_A 0.81 0.66 0.12
73_M 35_V 0.80 0.66 0.12
49_K 56_A 0.77 0.61 0.10
99_P 156_Y 0.76 0.59 0.10
131_V 181_S 0.75 0.58 0.09
24_L 153_I 0.75 0.58 0.09
73_M 32_I 0.74 0.56 0.09
104_A 36_M 0.73 0.55 0.09
36_I 159_L 0.73 0.55 0.09
205_S 157_L 0.73 0.55 0.09
18_C 191_L 0.73 0.54 0.08
102_E 17_L 0.72 0.54 0.08
136_E 162_V 0.72 0.54 0.08
144_P 52_L 0.70 0.51 0.08
39_V 181_S 0.70 0.50 0.07
46_T 138_L 0.70 0.50 0.07
173_T 55_I 0.70 0.50 0.07
97_S 44_Q 0.70 0.49 0.07
140_I 129_E 0.69 0.49 0.07
6_G 117_R 0.69 0.49 0.07
137_E 109_L 0.69 0.48 0.07
60_Q 187_V 0.69 0.48 0.07
182_I 143_A 0.68 0.47 0.07
27_N 13_F 0.68 0.47 0.07
162_L 22_A 0.68 0.47 0.07
95_L 152_K 0.68 0.47 0.07
73_M 45_Q 0.68 0.47 0.07
131_V 167_V 0.68 0.46 0.07
90_F 39_N 0.68 0.46 0.07
188_P 105_K 0.67 0.46 0.07
96_V 149_D 0.67 0.46 0.07
6_G 152_K 0.67 0.45 0.06
170_L 144_L 0.67 0.45 0.06
128_K 206_A 0.67 0.45 0.06
11_L 131_N 0.66 0.44 0.06
149_V 163_V 0.66 0.44 0.06
42_R 168_I 0.66 0.44 0.06
174_F 163_V 0.66 0.44 0.06
124_V 113_R 0.66 0.43 0.06
111_E 205_K 0.66 0.43 0.06
106_L 204_S 0.65 0.43 0.06
136_E 113_R 0.65 0.42 0.06
132_S 210_Q 0.65 0.42 0.06
101_A 39_N 0.65 0.42 0.06
211_E 79_P 0.65 0.41 0.06
102_E 181_S 0.64 0.41 0.06
73_M 164_V 0.64 0.41 0.06
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
8982 6.14 mxij spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.16 Done
7087 7.04 mxij_spa24 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.46 Done
6868 0.52 jp Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
6862 mxij_spa24_jackhammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Running
6829 0.63 mxij_spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
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