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OPENSEQ.org
cIp_9_40_cIV_A_40
Genes: A B A+B
Length: 163 558 693
Sequences: 644 3242 465
Seq/Len: 3.95 5.81 0.67
MirrorTree (Pazo et al. 2001) 0.23
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 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.00 0.02 0.02
100 0.00 0.03 0.09
∞ 0.01 0.06 0.64
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
35_L 507_V 1.27 0.47 0.00
139_Q 232_L 1.19 0.40 0.00
31_P 505_G 1.02 0.28 0.00
108_F 346_T 1.02 0.27 0.00
33_P 426_A 0.99 0.26 0.00
108_F 97_L 0.99 0.26 0.00
30_S 301_P 0.97 0.24 0.00
7_R 302_I 0.95 0.23 0.00
108_F 445_G 0.94 0.22 0.00
159_D 39_A 0.92 0.21 0.00
5_F 219_L 0.91 0.21 0.00
108_F 498_A 0.91 0.21 0.00
108_F 207_M 0.90 0.20 0.00
4_D 55_M 0.90 0.20 0.00
10_K 421_V 0.90 0.20 0.00
58_P 394_S 0.89 0.20 0.00
73_V 505_G 0.87 0.19 0.00
29_V 118_L 0.87 0.19 0.00
21_F 90_M 0.86 0.18 0.00
134_L 176_G 0.86 0.18 0.00
143_A 223_S 0.85 0.18 0.00
15_W 293_V 0.85 0.18 0.00
24_G 421_V 0.85 0.17 0.00
23_L 83_N 0.85 0.17 0.00
10_K 488_I 0.84 0.17 0.00
17_F 90_M 0.84 0.17 0.00
139_Q 130_L 0.83 0.17 0.00
44_L 314_A 0.82 0.16 0.00
31_P 139_V 0.82 0.16 0.00
112_A 380_L 0.82 0.16 0.00
11_Y 349_V 0.81 0.16 0.00
94_T 369_F 0.80 0.15 0.00
151_E 522_Y 0.80 0.15 0.00
24_G 179_M 0.80 0.15 0.00
21_F 372_P 0.79 0.15 0.00
30_S 150_L 0.79 0.15 0.00
84_E 342_L 0.79 0.15 0.00
36_N 188_V 0.78 0.15 0.00
143_A 55_M 0.78 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
3681 1.75 cIp_9_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3680 0.67 cIp_9_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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