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OPENSEQ.org
PcrA_RNAP500bsubtilis
Genes: A B A+B
Length: 739 500 1098
Sequences: 3698 1293 1042
Seq/Len: 5 2.59 0.95
MirrorTree (Pazo et al. 2001) 0.29
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 0.09 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.01
10 0.09 0.09 0.03
20 0.09 0.09 0.04
100 0.10 0.09 0.11
∞ 0.16 0.09 0.84
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
613_E 126_I 1.07 0.39 0.00
323_Y 127_I 1.05 0.37 0.00
323_Y 126_I 0.99 0.32 0.00
375_G 88_Y 0.98 0.31 0.00
190_L 162_V 0.96 0.29 0.00
498_K 126_I 0.94 0.28 0.00
352_S 68_D 0.93 0.28 0.00
427_L 199_L 0.93 0.27 0.00
371_L 88_Y 0.92 0.27 0.00
174_S 262_P 0.92 0.27 0.00
89_I 231_K 0.92 0.27 0.00
598_M 31_E 0.91 0.26 0.00
421_G 459_K 0.91 0.26 0.00
339_K 25_E 0.90 0.26 0.00
95_M 126_I 0.88 0.24 0.00
618_L 375_N 0.88 0.24 0.00
509_L 257_S 0.86 0.23 0.00
595_E 249_E 0.86 0.23 0.00
536_T 454_V 0.86 0.22 0.00
184_L 162_V 0.84 0.22 0.00
246_L 478_A 0.84 0.22 0.00
55_A 192_V 0.84 0.21 0.00
367_I 441_N 0.83 0.21 0.00
281_L 456_A 0.83 0.21 0.00
74_E 18_A 0.83 0.21 0.00
185_L 385_I 0.83 0.21 0.00
74_E 88_Y 0.83 0.21 0.00
125_I 179_V 0.83 0.21 0.00
578_L 134_I 0.82 0.20 0.00
188_Q 249_E 0.82 0.20 0.00
355_A 375_N 0.81 0.20 0.00
81_G 49_F 0.81 0.20 0.00
522_F 195_L 0.81 0.20 0.00
557_K 436_S 0.81 0.20 0.00
632_M 158_F 0.81 0.20 0.00
356_I 88_Y 0.80 0.19 0.00
558_D 213_E 0.80 0.19 0.00
534_F 38_Q 0.80 0.19 0.00
59_I 127_I 0.80 0.19 0.00
108_G 127_I 0.80 0.19 0.00
443_Q 89_S 0.80 0.19 0.00
41_L 459_K 0.79 0.19 0.00
29_L 77_P 0.79 0.19 0.00
74_E 458_I 0.79 0.19 0.00
376_L 126_I 0.79 0.18 0.00
159_E 454_V 0.78 0.18 0.00
96_C 182_V 0.78 0.18 0.00
191_D 66_F 0.77 0.18 0.00
512_I 37_Y 0.77 0.18 0.00
195_L 442_T 0.77 0.18 0.00
178_A 221_L 0.77 0.17 0.00
229_N 162_V 0.77 0.17 0.00
42_T 432_R 0.77 0.17 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)
ID Seq/Len Name Options I_Prob Status
5571 0.95 PcrA_RNAP500bsubtilis Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5561 0.95 PcrA_RNAP500bsubtilis Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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