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OPENSEQ.org
PcrAsubtilis_RNAP(4GZY)1119
Genes: A B A+B
Length: 739 619 1195
Sequences: 3698 1323 1039
Seq/Len: 5 2.14 0.87
MirrorTree (Pazo et al. 2001) 0.31
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 0.03
100 0.10 0.09 0.10
∞ 0.16 0.09 0.77
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
125_I 75_Q 1.17 0.45 0.00
220_I 300_V 1.11 0.40 0.00
430_I 29_V 1.08 0.38 0.00
331_G 245_I 1.07 0.36 0.00
148_I 34_V 0.99 0.30 0.00
95_M 360_H 0.97 0.29 0.00
558_D 31_F 0.96 0.28 0.00
336_V 245_I 0.94 0.27 0.00
618_L 6_N 0.94 0.26 0.00
211_E 482_P 0.90 0.24 0.00
173_V 314_E 0.89 0.23 0.00
335_F 27_E 0.88 0.23 0.00
246_L 31_F 0.88 0.23 0.00
130_K 367_V 0.88 0.22 0.00
99_I 349_V 0.87 0.22 0.00
642_I 26_P 0.87 0.22 0.00
205_R 487_I 0.87 0.22 0.00
557_K 197_R 0.86 0.21 0.00
313_T 111_I 0.86 0.21 0.00
484_T 76_A 0.85 0.21 0.00
131_E 367_V 0.85 0.21 0.00
482_E 245_I 0.84 0.20 0.00
471_L 154_L 0.84 0.20 0.00
512_I 552_M 0.84 0.20 0.00
377_N 104_A 0.83 0.20 0.00
22_T 111_I 0.83 0.19 0.00
556_G 382_L 0.82 0.19 0.00
465_R 29_V 0.82 0.19 0.00
434_A 197_R 0.81 0.19 0.00
356_I 473_V 0.81 0.19 0.00
641_E 166_L 0.81 0.19 0.00
462_D 245_I 0.81 0.19 0.00
290_K 245_I 0.80 0.18 0.00
106_R 352_I 0.80 0.18 0.00
58_N 78_V 0.80 0.18 0.00
581_L 10_A 0.79 0.18 0.00
358_Y 269_P 0.79 0.17 0.00
492_E 43_N 0.79 0.17 0.00
581_L 352_I 0.79 0.17 0.00
562_L 72_I 0.79 0.17 0.00
217_F 300_V 0.78 0.17 0.00
459_N 108_G 0.78 0.17 0.00
577_F 268_T 0.78 0.17 0.00
425_T 314_E 0.77 0.17 0.00
515_F 548_T 0.76 0.16 0.00
617_Y 100_D 0.76 0.16 0.00
239_L 140_R 0.76 0.16 0.00
427_L 300_V 0.76 0.16 0.00
176_V 316_K 0.76 0.16 0.00
122_L 111_I 0.76 0.16 0.00
356_I 482_P 0.76 0.16 0.00
482_E 175_A 0.76 0.16 0.00
341_H 579_P 0.75 0.16 0.00
371_L 352_I 0.75 0.15 0.00
579_M 349_V 0.75 0.15 0.00
196_I 560_I 0.74 0.15 0.00
466_Q 487_I 0.74 0.15 0.00
206_V 45_N 0.74 0.15 0.00
262_A 197_R 0.74 0.15 0.00
531_L 469_Q 0.74 0.15 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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