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OPENSEQ.org
cIV_B_6_cI_K_20_Pdenitr
Genes: A B A+B
Length: 252 101 344
Sequences: 4627 1319 898
Seq/Len: 18.36 13.06 2.61
MirrorTree (Pazo et al. 2001) 0.35
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 0.05
2 0.00 0.00 0.07
5 0.00 0.00 0.16
10 0.01 0.01 0.30
20 0.01 0.01 0.43
100 0.02 0.02 0.64
∞ 0.04 0.03 2.54
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
239_Y 38_L 0.97 0.56 0.00
65_N 30_I 0.92 0.51 0.00
130_D 17_T 0.91 0.50 0.00
112_L 38_L 0.91 0.50 0.00
186_P 79_A 0.91 0.50 0.00
46_T 99_M 0.89 0.47 0.00
164_V 11_G 0.86 0.44 0.00
247_K 2_I 0.82 0.39 0.00
239_Y 43_V 0.81 0.38 0.00
89_L 27_K 0.81 0.38 0.00
60_F 30_I 0.80 0.37 0.00
39_L 10_V 0.80 0.36 0.00
72_T 7_Y 0.79 0.36 0.00
23_A 94_E 0.79 0.35 0.00
117_I 48_V 0.78 0.35 0.00
31_Q 64_M 0.78 0.35 0.00
80_I 80_I 0.78 0.35 0.00
54_L 11_G 0.77 0.33 0.00
77_I 28_N 0.77 0.33 0.00
34_L 20_F 0.76 0.32 0.00
73_H 56_D 0.76 0.32 0.00
52_L 48_V 0.75 0.31 0.00
179_V 78_L 0.75 0.31 0.00
132_V 17_T 0.74 0.30 0.00
84_V 12_A 0.74 0.30 0.00
108_N 63_T 0.73 0.29 0.00
121_W 78_L 0.73 0.29 0.00
92_I 91_I 0.72 0.29 0.00
117_I 69_V 0.72 0.29 0.00
116_A 100_K 0.72 0.29 0.00
18_M 42_A 0.72 0.28 0.00
83_L 36_I 0.72 0.28 0.00
182_A 29_V 0.72 0.28 0.00
239_Y 64_M 0.71 0.28 0.00
111_D 53_H 0.71 0.28 0.00
98_P 33_L 0.71 0.27 0.00
204_F 7_Y 0.70 0.27 0.00
122_Y 76_I 0.70 0.27 0.00
60_F 31_V 0.70 0.27 0.00
162_V 54_L 0.70 0.27 0.00
173_Q 66_V 0.69 0.26 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
3301 8.31 cIV_B_10_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
3300 8.28 cIV_B_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
3299 2.61 cIV_B_6_cI_K_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3297 7.24 cIV_B_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3296 7.26 cIV_B_4_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3295 8.33 cIV_B_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3294 8.64 cIV_B_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3239 0.62 cIV_B_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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