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OPENSEQ.org
cIp_3_4_cIV_2_4
Genes: A B A+B
Length: 727 227 905
Sequences: 1951 5082 789
Seq/Len: 2.68 22.39 0.87
MirrorTree (Pazo et al. 2001) 0.20
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 0.01
10 0.01 0.01 0.01
20 0.01 0.01 0.03
100 0.03 0.02 0.12
∞ 0.09 0.04 0.83
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
36_V 104_W 1.16 0.45 0.00
315_T 147_E 1.06 0.36 0.00
34_V 192_Y 0.96 0.28 0.00
609_A 14_S 0.95 0.28 0.00
60_I 217_K 0.94 0.27 0.00
49_V 74_V 0.91 0.24 0.00
583_I 36_F 0.90 0.24 0.00
36_V 95_L 0.89 0.23 0.00
206_V 152_M 0.89 0.23 0.00
40_S 192_Y 0.88 0.23 0.00
357_L 150_I 0.87 0.22 0.00
251_I 99_S 0.86 0.21 0.00
539_K 215_P 0.84 0.20 0.00
390_T 192_Y 0.82 0.19 0.00
436_V 218_I 0.82 0.19 0.00
55_K 219_F 0.81 0.19 0.00
545_L 71_I 0.81 0.18 0.00
567_I 93_P 0.80 0.18 0.00
535_E 71_I 0.79 0.17 0.00
424_H 71_I 0.79 0.17 0.00
164_N 224_V 0.78 0.17 0.00
110_K 224_V 0.78 0.17 0.00
361_V 97_I 0.78 0.17 0.00
600_E 219_F 0.77 0.17 0.00
551_D 166_P 0.75 0.16 0.00
341_I 165_V 0.75 0.15 0.00
49_V 203_N 0.74 0.15 0.00
471_K 188_R 0.74 0.15 0.00
609_A 205_S 0.74 0.15 0.00
41_V 147_E 0.73 0.15 0.00
468_E 150_I 0.73 0.15 0.00
286_I 73_L 0.72 0.14 0.00
560_L 218_I 0.72 0.14 0.00
622_I 44_L 0.72 0.14 0.00
544_V 146_I 0.71 0.14 0.00
450_K 67_I 0.71 0.14 0.00
543_K 131_G 0.71 0.14 0.00
329_M 99_S 0.71 0.14 0.00
318_S 163_W 0.71 0.14 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)
ID Seq/Len Name Options I_Prob Status
4191 0.87 cIp_3_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4190 0.66 cIp_3_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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