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OPENSEQ.org
cIV_A_4_cI_K_4_Pdenitr
Genes: A B A+B
Length: 538 101 611
Sequences: 4477 4825 2200
Seq/Len: 8.32 47.77 3.6
MirrorTree (Pazo et al. 2001) 0.16
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 0.04
2 0.01 0.00 0.08
5 0.02 0.01 0.29
10 0.03 0.01 1.41
20 0.03 0.02 1.55
100 0.05 0.03 1.95
∞ 0.08 0.07 3.44
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
196_M 34_M 1.04 0.74 0.02
438_I 29_V 0.93 0.62 0.02
273_I 34_M 0.90 0.59 0.01
438_I 81_L 0.90 0.58 0.01
408_I 38_L 0.88 0.56 0.01
186_T 75_A 0.84 0.51 0.01
308_A 69_V 0.83 0.50 0.01
21_F 56_D 0.83 0.49 0.01
200_K 28_N 0.83 0.49 0.01
354_K 23_F 0.82 0.48 0.01
385_V 25_N 0.82 0.47 0.01
21_F 81_L 0.81 0.46 0.01
279_S 76_I 0.80 0.45 0.01
81_L 68_T 0.80 0.45 0.01
278_I 19_I 0.79 0.43 0.01
383_D 78_L 0.78 0.43 0.01
491_V 27_K 0.78 0.42 0.01
284_K 80_I 0.76 0.40 0.01
491_V 16_V 0.74 0.38 0.01
195_G 25_N 0.74 0.38 0.01
507_W 60_Q 0.74 0.38 0.01
346_M 99_M 0.74 0.37 0.01
22_T 42_A 0.73 0.37 0.01
409_F 63_T 0.73 0.37 0.01
29_I 30_I 0.73 0.36 0.01
5_R 70_A 0.73 0.36 0.01
23_A 36_I 0.72 0.36 0.01
282_A 18_G 0.72 0.35 0.01
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
3364 2.98 cIV_A_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3362 2.97 cIV_A_10_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3359 3.4 cIV_A_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3358 3.42 cIV_A_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3356 0.36 cIV_A_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3355 3.6 cIV_A_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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