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OPENSEQ.org
cIp_2_4_cIV_A_4
Genes: A B A+B
Length: 239 558 769
Sequences: 755 4375 304
Seq/Len: 3.16 7.84 0.4
MirrorTree (Pazo et al. 2001) 0.08
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.02 0.00
10 0.01 0.03 0.01
20 0.01 0.03 0.01
100 0.01 0.05 0.09
∞ 0.04 0.08 0.38
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
89_S 40_G 1.11 0.24 0.00
68_P 394_S 1.08 0.23 0.00
127_D 314_A 1.04 0.21 0.00
21_E 508_F 1.00 0.19 0.00
85_Q 37_F 0.98 0.18 0.00
196_A 151_A 0.96 0.17 0.00
85_Q 44_L 0.93 0.16 0.00
23_A 409_V 0.92 0.15 0.00
82_F 314_A 0.91 0.15 0.00
53_L 56_E 0.91 0.15 0.00
93_I 251_F 0.91 0.15 0.00
165_L 377_F 0.90 0.15 0.00
158_T 208_R 0.89 0.14 0.00
51_G 438_R 0.89 0.14 0.00
109_L 507_V 0.88 0.14 0.00
14_E 346_T 0.88 0.14 0.00
54_S 441_P 0.87 0.14 0.00
165_L 179_M 0.86 0.13 0.00
170_A 301_P 0.85 0.13 0.00
53_L 232_L 0.85 0.13 0.00
93_I 115_F 0.85 0.13 0.00
23_A 314_A 0.84 0.13 0.00
122_H 444_A 0.84 0.12 0.00
14_E 405_T 0.84 0.12 0.00
158_T 491_I 0.83 0.12 0.00
170_A 314_A 0.82 0.12 0.00
216_D 33_I 0.81 0.12 0.00
106_A 497_F 0.81 0.12 0.00
93_I 219_L 0.80 0.11 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
4029 0.2 cIp_2_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4028 0.4 cIp_2_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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