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OPENSEQ.org
cIp_9_4_cIV_D_4
Genes: A B A+B
Length: 163 50 204
Sequences: 2843 202 78
Seq/Len: 17.44 4.04 0.38
MirrorTree (Pazo et al. 2001) 0.05
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 0.03 0.00 0.00
5 0.04 0.00 0.00
10 0.04 0.00 0.00
20 0.05 0.00 0.01
100 0.07 0.01 0.08
∞ 0.16 0.01 0.37
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
129_E 34_V 1.30 0.34 0.00
22_G 20_Q 1.29 0.34 0.00
20_G 35_S 1.12 0.24 0.00
46_P 26_G 1.10 0.23 0.00
112_A 48_A 1.04 0.20 0.00
88_D 20_Q 1.02 0.19 0.00
15_W 36_I 1.01 0.18 0.00
157_Q 3_S 0.96 0.17 0.00
10_K 13_G 0.96 0.17 0.00
42_G 42_L 0.96 0.16 0.00
52_H 34_V 0.95 0.16 0.00
66_A 24_F 0.95 0.16 0.00
90_S 20_Q 0.91 0.14 0.00
25_M 33_W 0.90 0.14 0.00
9_T 40_A 0.90 0.14 0.00
35_L 17_I 0.87 0.13 0.00
10_K 36_I 0.85 0.13 0.00
84_E 20_Q 0.83 0.12 0.00
140_K 2_A 0.82 0.12 0.00
132_E 33_W 0.82 0.12 0.00
124_F 24_F 0.81 0.11 0.00
25_M 25_A 0.80 0.11 0.00
24_G 9_D 0.80 0.11 0.00
19_K 46_A 0.79 0.11 0.00
22_G 17_I 0.79 0.11 0.00
43_P 28_I 0.78 0.11 0.00
139_Q 21_Q 0.78 0.10 0.00
112_A 46_A 0.78 0.10 0.00
16_D 13_G 0.77 0.10 0.00
94_T 28_I 0.77 0.10 0.00
88_D 17_I 0.76 0.10 0.00
46_P 35_S 0.75 0.10 0.00
83_A 46_A 0.75 0.10 0.00
140_K 35_S 0.75 0.10 0.00
49_R 36_I 0.74 0.10 0.00
73_V 40_A 0.74 0.10 0.00
52_H 15_M 0.74 0.10 0.00
128_T 19_H 0.73 0.09 0.00
59_N 40_A 0.72 0.09 0.00
69_L 20_Q 0.72 0.09 0.00
41_K 36_I 0.72 0.09 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
3954 0.38 cIp_9_4_cIV_D_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3934 0 cIp_9_40_cIV_D_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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