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OPENSEQ.org
PCRA_RNAP1342_Ecoli
Genes: A B A+B
Length: 704 742 1411
Sequences: 260 1201 94
Seq/Len: 0.37 1.62 0.07
MirrorTree (Pazo et al. 2001) 0.41
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 0.10 0.00
2 0.01 0.10 0.00
5 0.01 0.10 0.00
10 0.01 0.10 0.00
20 0.01 0.10 0.00
100 0.02 0.10 0.00
∞ 0.05 0.10 0.07
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
542_T 476_I 1.40 0.14 0.00
533_V 512_I 1.36 0.13 0.00
274_A 14_Y 1.21 0.10 0.00
289_V 170_C 1.21 0.10 0.00
333_R 686_T 1.21 0.10 0.00
683_T 259_E 1.18 0.10 0.00
294_F 190_D 1.14 0.09 0.00
119_P 717_P 1.10 0.09 0.00
378_V 260_A 1.08 0.08 0.00
164_L 489_E 1.07 0.08 0.00
100_C 2_E 1.07 0.08 0.00
683_T 501_L 1.05 0.08 0.00
248_V 173_L 1.05 0.08 0.00
453_V 219_S 1.03 0.08 0.00
542_T 116_A 1.03 0.08 0.00
453_V 225_E 1.02 0.07 0.00
557_I 271_V 1.02 0.07 0.00
145_P 210_Y 1.00 0.07 0.00
274_A 86_Q 1.00 0.07 0.00
467_I 271_V 1.00 0.07 0.00
539_E 443_A 0.99 0.07 0.00
306_L 318_L 0.99 0.07 0.00
325_A 83_A 0.99 0.07 0.00
420_M 175_E 0.98 0.07 0.00
44_G 441_D 0.97 0.07 0.00
511_K 124_V 0.97 0.07 0.00
20_R 613_Y 0.97 0.07 0.00
174_E 179_R 0.96 0.07 0.00
366_P 319_R 0.96 0.07 0.00
311_T 68_I 0.96 0.07 0.00
538_G 153_L 0.95 0.07 0.00
10_L 136_V 0.95 0.07 0.00
247_L 188_S 0.95 0.07 0.00
149_I 175_E 0.94 0.07 0.00
274_A 522_K 0.94 0.07 0.00
255_P 716_E 0.94 0.07 0.00
383_V 279_G 0.93 0.07 0.00
480_I 529_N 0.93 0.07 0.00
375_Q 117_V 0.93 0.06 0.00
571_V 93_L 0.93 0.06 0.00
591_A 159_S 0.93 0.06 0.00
472_P 116_A 0.93 0.06 0.00
375_Q 488_D 0.93 0.06 0.00
556_M 24_D 0.92 0.06 0.00
431_A 512_I 0.92 0.06 0.00
279_Q 93_L 0.92 0.06 0.00
622_D 159_S 0.91 0.06 0.00
651_G 224_Q 0.91 0.06 0.00
560_A 247_P 0.91 0.06 0.00
31_E 4_H 0.91 0.06 0.00
378_V 116_A 0.91 0.06 0.00
646_V 611_R 0.90 0.06 0.00
413_F 128_D 0.90 0.06 0.00
467_I 260_A 0.90 0.06 0.00
465_T 170_C 0.90 0.06 0.00
150_D 134_I 0.90 0.06 0.00
122_E 512_I 0.90 0.06 0.00
464_F 194_L 0.89 0.06 0.00
591_A 501_L 0.89 0.06 0.00
26_Q 678_L 0.89 0.06 0.00
556_M 617_T 0.89 0.06 0.00
111_V 512_I 0.89 0.06 0.00
383_V 573_A 0.89 0.06 0.00
574_I 64_G 0.88 0.06 0.00
501_N 527_K 0.88 0.06 0.00
245_R 2_E 0.88 0.06 0.00
678_L 287_V 0.88 0.06 0.00
683_T 678_L 0.88 0.06 0.00
255_P 247_P 0.87 0.06 0.00
223_Q 3_I 0.87 0.06 0.00
476_N 67_L 0.87 0.06 0.00
110_Q 210_Y 0.87 0.06 0.00
20_R 49_Q 0.87 0.06 0.00
388_E 134_I 0.87 0.06 0.00
303_R 183_L 0.87 0.06 0.00
428_M 678_L 0.86 0.06 0.00
466_L 625_V 0.86 0.06 0.00
565_E 124_V 0.85 0.06 0.00
26_Q 675_V 0.85 0.06 0.00
143_G 253_D 0.85 0.06 0.00
538_G 175_E 0.85 0.06 0.00
451_I 512_I 0.85 0.06 0.00
499_G 235_E 0.85 0.06 0.00
58_V 717_P 0.85 0.06 0.00
467_I 52_Y 0.84 0.06 0.00
10_L 188_S 0.84 0.06 0.00
114_I 15_V 0.84 0.06 0.00
328_S 116_A 0.84 0.06 0.00
383_V 229_T 0.84 0.06 0.00
208_A 134_I 0.84 0.06 0.00
65_Q 271_V 0.83 0.06 0.00
415_E 617_T 0.83 0.05 0.00
197_D 116_A 0.83 0.05 0.00
177_H 496_I 0.83 0.05 0.00
447_P 630_M 0.83 0.05 0.00
502_V 443_A 0.83 0.05 0.00
351_C 24_D 0.83 0.05 0.00
388_E 168_M 0.83 0.05 0.00
472_P 3_I 0.83 0.05 0.00
501_N 175_E 0.83 0.05 0.00
538_G 521_A 0.82 0.05 0.00
630_A 489_E 0.82 0.05 0.00
528_L 262_L 0.82 0.05 0.00
520_T 10_E 0.82 0.05 0.00
276_W 99_L 0.82 0.05 0.00
407_A 441_D 0.82 0.05 0.00
26_Q 161_Q 0.82 0.05 0.00
521_R 210_Y 0.82 0.05 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)
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