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OPENSEQ.org
cIp_4_4_cIV_D_4
Genes: A B A+B
Length: 412 50 443
Sequences: 3488 202 67
Seq/Len: 8.47 4.04 0.15
MirrorTree (Pazo et al. 2001) -0.02
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.03 0.00 0.00
10 0.04 0.00 0.00
20 0.05 0.00 0.00
100 0.06 0.01 0.01
∞ 0.13 0.01 0.15
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
122_S 42_L 1.37 0.21 0.00
131_L 16_D 1.34 0.20 0.00
371_A 20_Q 1.23 0.17 0.00
279_C 9_D 1.21 0.16 0.00
285_R 36_I 1.21 0.16 0.00
71_M 20_Q 1.18 0.15 0.00
279_C 20_Q 1.16 0.14 0.00
207_T 41_V 1.14 0.14 0.00
273_C 32_T 1.12 0.13 0.00
371_A 24_F 1.11 0.13 0.00
365_T 48_A 1.10 0.13 0.00
112_R 46_A 1.09 0.13 0.00
74_R 39_I 1.09 0.13 0.00
277_Y 42_L 1.09 0.12 0.00
26_N 35_S 1.06 0.12 0.00
410_V 1_M 1.06 0.12 0.00
245_L 17_I 1.04 0.12 0.00
223_G 15_M 1.01 0.11 0.00
316_R 36_I 1.01 0.11 0.00
205_L 46_A 1.01 0.11 0.00
279_C 17_I 1.01 0.11 0.00
307_L 47_L 1.00 0.11 0.00
201_L 47_L 0.96 0.10 0.00
305_D 32_T 0.96 0.10 0.00
28_N 19_H 0.94 0.09 0.00
199_P 17_I 0.94 0.09 0.00
277_Y 33_W 0.94 0.09 0.00
278_L 42_L 0.94 0.09 0.00
281_M 30_G 0.93 0.09 0.00
199_P 13_G 0.92 0.09 0.00
71_M 13_G 0.92 0.09 0.00
305_D 24_F 0.92 0.09 0.00
251_R 25_A 0.92 0.09 0.00
252_S 36_I 0.91 0.09 0.00
74_R 26_G 0.90 0.09 0.00
402_T 32_T 0.90 0.09 0.00
296_Q 48_A 0.90 0.09 0.00
186_D 31_A 0.90 0.09 0.00
306_V 43_V 0.90 0.09 0.00
139_M 16_D 0.90 0.09 0.00
386_W 17_I 0.89 0.09 0.00
79_N 20_Q 0.89 0.08 0.00
129_N 13_G 0.88 0.08 0.00
106_T 24_F 0.88 0.08 0.00
389_R 26_G 0.87 0.08 0.00
99_C 32_T 0.87 0.08 0.00
29_I 3_S 0.87 0.08 0.00
186_D 40_A 0.87 0.08 0.00
302_P 41_V 0.86 0.08 0.00
28_N 34_V 0.86 0.08 0.00
273_C 42_L 0.85 0.08 0.00
261_F 33_W 0.84 0.08 0.00
71_M 12_H 0.84 0.08 0.00
169_L 44_F 0.84 0.08 0.00
29_I 45_L 0.84 0.08 0.00
294_A 1_M 0.83 0.07 0.00
115_S 32_T 0.83 0.07 0.00
104_R 47_L 0.83 0.07 0.00
297_K 3_S 0.83 0.07 0.00
286_E 30_G 0.82 0.07 0.00
200_K 28_I 0.82 0.07 0.00
104_R 36_I 0.82 0.07 0.00
28_N 41_V 0.82 0.07 0.00
265_I 41_V 0.82 0.07 0.00
400_I 24_F 0.81 0.07 0.00
270_N 42_L 0.81 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)
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