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OPENSEQ.org
cIp_3_4_cIV_D_4
Genes: A B A+B
Length: 674 50 715
Sequences: 1936 202 82
Seq/Len: 2.87 4.04 0.11
MirrorTree (Pazo et al. 2001) 0.09
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.00
100 0.03 0.01 0.02
∞ 0.09 0.01 0.11
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
255_I 22_A 1.27 0.15 0.00
440_A 14_E 1.26 0.14 0.00
375_I 45_L 1.20 0.13 0.00
232_S 29_K 1.19 0.13 0.00
169_T 42_L 1.18 0.12 0.00
299_S 35_S 1.08 0.10 0.00
403_V 28_I 1.08 0.10 0.00
487_A 34_V 1.08 0.10 0.00
658_L 12_H 1.05 0.10 0.00
7_I 43_V 1.04 0.10 0.00
345_C 15_M 1.03 0.10 0.00
33_V 40_A 1.02 0.09 0.00
607_A 33_W 1.02 0.09 0.00
248_K 20_Q 1.00 0.09 0.00
10_D 20_Q 0.98 0.09 0.00
179_Q 38_S 0.98 0.09 0.00
400_G 35_S 0.98 0.09 0.00
261_D 36_I 0.98 0.09 0.00
374_M 20_Q 0.96 0.08 0.00
33_V 4_H 0.95 0.08 0.00
315_K 13_G 0.95 0.08 0.00
570_A 43_V 0.95 0.08 0.00
14_I 33_W 0.94 0.08 0.00
248_K 24_F 0.94 0.08 0.00
575_K 34_V 0.94 0.08 0.00
262_G 46_A 0.93 0.08 0.00
619_Q 3_S 0.93 0.08 0.00
508_V 39_I 0.91 0.07 0.00
567_A 24_F 0.90 0.07 0.00
12_T 45_L 0.90 0.07 0.00
408_E 48_A 0.90 0.07 0.00
588_L 45_L 0.89 0.07 0.00
554_F 22_A 0.89 0.07 0.00
536_H 19_H 0.89 0.07 0.00
506_E 39_I 0.88 0.07 0.00
263_V 16_D 0.88 0.07 0.00
475_L 20_Q 0.88 0.07 0.00
589_G 36_I 0.88 0.07 0.00
571_P 36_I 0.88 0.07 0.00
225_W 24_F 0.88 0.07 0.00
404_G 28_I 0.87 0.07 0.00
380_T 21_Q 0.87 0.07 0.00
460_V 15_M 0.86 0.07 0.00
398_S 45_L 0.86 0.07 0.00
403_V 25_A 0.86 0.07 0.00
186_S 35_S 0.86 0.07 0.00
135_Y 25_A 0.86 0.07 0.00
190_S 11_K 0.85 0.07 0.00
628_F 47_L 0.85 0.07 0.00
56_V 41_V 0.85 0.07 0.00
442_P 37_L 0.85 0.07 0.00
72_D 39_I 0.84 0.07 0.00
214_V 39_I 0.84 0.07 0.00
261_D 44_F 0.84 0.07 0.00
25_A 36_I 0.84 0.07 0.00
313_G 45_L 0.84 0.07 0.00
603_K 21_Q 0.84 0.07 0.00
665_R 39_I 0.84 0.07 0.00
177_M 3_S 0.83 0.07 0.00
169_T 19_H 0.83 0.07 0.00
312_K 45_L 0.83 0.07 0.00
405_L 5_H 0.83 0.07 0.00
506_E 31_A 0.83 0.07 0.00
459_A 41_V 0.83 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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