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OPENSEQ.org
cI_I_4_cIII_cytb_4_Pdenitr
Genes: A B A+B
Length: 163 263 404
Sequences: 2843 973 414
Seq/Len: 17.44 3.7 1.02
MirrorTree (Pazo et al. 2001) 0.19
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 0.01 0.00
2 0.03 0.01 0.00
5 0.04 0.01 0.00
10 0.04 0.01 0.01
20 0.05 0.01 0.02
100 0.07 0.01 0.09
∞ 0.16 0.01 0.97
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
18_I 236_I 1.11 0.44 0.00
28_F 226_D 1.00 0.34 0.00
139_Q 195_V 0.99 0.33 0.00
44_L 216_L 0.95 0.31 0.00
101_T 257_K 0.91 0.28 0.00
155_N 241_L 0.89 0.26 0.00
9_T 161_Y 0.88 0.25 0.00
90_S 124_S 0.86 0.24 0.00
35_L 220_A 0.85 0.23 0.00
12_F 220_A 0.84 0.22 0.00
89_G 241_L 0.83 0.22 0.00
155_N 130_R 0.82 0.21 0.00
84_E 203_A 0.82 0.21 0.00
140_K 154_I 0.81 0.21 0.00
155_N 214_A 0.81 0.20 0.00
54_L 81_P 0.80 0.20 0.00
82_D 235_V 0.80 0.20 0.00
157_Q 135_G 0.78 0.19 0.00
35_L 30_D 0.78 0.19 0.00
139_Q 201_T 0.78 0.19 0.00
35_L 237_F 0.78 0.18 0.00
21_F 125_L 0.77 0.18 0.00
139_Q 246_Y 0.76 0.18 0.00
84_E 239_I 0.76 0.17 0.00
161_P 216_L 0.75 0.17 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
3057 0.35 cI_I_60_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3056 1.02 cI_I_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3055 0.36 cI_I_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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