OPENSEQ.org
PcrA_CT_conserved vs RNAP beta 1st half

Genes: A B A+B
Length: 49 600 590
Sequences: 430 1432 66
Seq/Len: 8.78 2.39 0.11
MirrorTree (Pazo et al. 2001) 0.16
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 0.00 0.09 0.00
2 0.00 0.09 0.00
5 0.00 0.09 0.00
10 0.00 0.09 0.00
20 0.00 0.09 0.00
100 0.00 0.09 0.02
0.00 0.09 0.10
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
28_I 579_A 1.62 0.26 0.00
28_I 26_L 1.24 0.14 0.00
41_A 390_N 1.19 0.13 0.00
14_V 84_R 1.17 0.12 0.00
46_I 501_M 1.17 0.12 0.00
37_K 594_A 1.16 0.12 0.00
28_I 582_D 1.11 0.11 0.00
15_V 108_D 1.07 0.10 0.00
2_D 58_F 1.04 0.10 0.00
4_A 134_I 1.04 0.10 0.00
2_D 186_R 1.02 0.09 0.00
17_V 427_M 1.02 0.09 0.00
14_V 42_D 1.01 0.09 0.00
28_I 532_S 1.00 0.09 0.00
28_I 153_N 1.00 0.09 0.00
7_K 180_V 0.99 0.09 0.00
7_K 497_E 0.99 0.09 0.00
9_W 162_V 0.97 0.09 0.00
7_K 249_E 0.97 0.09 0.00
14_V 126_I 0.96 0.08 0.00
4_A 534_Y 0.96 0.08 0.00
28_I 244_E 0.96 0.08 0.00
31_P 121_D 0.95 0.08 0.00
3_K 563_Y 0.94 0.08 0.00
28_I 454_V 0.94 0.08 0.00
45_P 49_F 0.93 0.08 0.00
28_I 459_K 0.93 0.08 0.00
39_L 409_L 0.92 0.08 0.00
26_L 162_V 0.92 0.08 0.00
28_I 249_E 0.92 0.08 0.00
1_G 81_S 0.91 0.08 0.00
29_A 110_D 0.90 0.07 0.00
21_G 594_A 0.90 0.07 0.00
2_D 482_H 0.90 0.07 0.00
46_I 58_F 0.89 0.07 0.00
9_W 540_F 0.89 0.07 0.00
31_P 126_I 0.89 0.07 0.00
14_V 23_V 0.88 0.07 0.00
2_D 162_V 0.88 0.07 0.00
2_D 193_T 0.88 0.07 0.00
41_A 436_S 0.88 0.07 0.00
16_S 497_E 0.87 0.07 0.00
13_T 383_S 0.86 0.07 0.00
9_W 158_F 0.85 0.07 0.00
31_P 540_F 0.84 0.07 0.00
44_A 88_Y 0.84 0.07 0.00
29_A 464_S 0.84 0.07 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
8206 0.11 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, ∞) A:(1E-04, 2) B:(1E-10, 2) msa: HHblits (2015_06) 0.00 Done - Shared
8205 0.11 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, ∞) A:(1E-04, 2) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8204 0 PcrA_CT_conserved vs RNAP beta 1st half Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared

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