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OPENSEQ.org
PcrA(3PJR)_RNAP1190(geobacillus)
Genes: A B A+B
Length: 724 590 1182
Sequences: 4096 1433 1150
Seq/Len: 5.66 2.43 0.97
MirrorTree (Pazo et al. 2001) 0.20
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
∞ 0.17 0.09 0.88
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
148_I 13_V 1.06 0.38 0.00
335_F 6_D 1.02 0.35 0.00
220_I 287_V 1.00 0.33 0.00
331_D 232_I 0.97 0.31 0.00
484_V 55_A 0.94 0.29 0.00
246_I 10_Y 0.93 0.28 0.00
430_L 8_V 0.91 0.27 0.00
340_I 136_V 0.91 0.27 0.00
95_M 346_F 0.91 0.26 0.00
577_L 355_I 0.90 0.26 0.00
640_E 153_L 0.89 0.25 0.00
515_F 371_V 0.88 0.24 0.00
371_L 338_I 0.88 0.24 0.00
239_L 127_R 0.87 0.23 0.00
559_V 223_N 0.86 0.23 0.00
557_D 10_Y 0.86 0.23 0.00
99_I 335_I 0.85 0.23 0.00
392_I 338_I 0.85 0.22 0.00
333_A 336_S 0.85 0.22 0.00
74_E 416_V 0.84 0.22 0.00
531_L 412_D 0.84 0.22 0.00
643_A 8_V 0.83 0.21 0.00
106_R 371_V 0.81 0.20 0.00
555_E 368_I 0.81 0.20 0.00
160_Q 226_E 0.81 0.20 0.00
641_I 5_R 0.80 0.19 0.00
574_V 21_A 0.80 0.19 0.00
176_V 62_M 0.80 0.19 0.00
57_W 355_I 0.80 0.19 0.00
402_I 190_I 0.79 0.19 0.00
215_Y 5_R 0.79 0.19 0.00
611_A 348_P 0.79 0.19 0.00
58_N 57_I 0.79 0.19 0.00
358_Y 256_A 0.78 0.18 0.00
195_L 238_D 0.78 0.18 0.00
165_A 232_I 0.77 0.18 0.00
494_R 371_V 0.77 0.18 0.00
125_M 54_E 0.77 0.18 0.00
377_P 83_E 0.77 0.18 0.00
465_R 300_E 0.77 0.17 0.00
616_V 79_R 0.76 0.17 0.00
459_G 87_A 0.76 0.17 0.00
220_I 41_A 0.76 0.17 0.00
356_V 307_Q 0.76 0.17 0.00
518_V 41_A 0.76 0.17 0.00
94_S 312_Y 0.75 0.17 0.00
612_E 136_V 0.75 0.17 0.00
380_I 313_I 0.75 0.17 0.00
130_K 353_I 0.75 0.17 0.00
322_L 24_A 0.75 0.17 0.00
211_H 425_P 0.75 0.17 0.00
313_T 90_I 0.75 0.16 0.00
612_E 93_R 0.75 0.16 0.00
577_L 319_I 0.74 0.16 0.00
205_R 430_V 0.74 0.16 0.00
94_S 41_A 0.74 0.16 0.00
334_Q 52_E 0.74 0.16 0.00
356_V 425_P 0.74 0.16 0.00
234_T 533_K 0.73 0.16 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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