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OPENSEQ.org
cIp_4_4_cIV_2_4
Genes: A B A+B
Length: 463 227 618
Sequences: 3147 5082 902
Seq/Len: 6.8 22.39 1.46
MirrorTree (Pazo et al. 2001) 0.15
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 0.01
2 0.01 0.00 0.02
5 0.02 0.00 0.04
10 0.02 0.01 0.06
20 0.03 0.01 0.11
100 0.05 0.02 0.28
∞ 0.11 0.04 1.31
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
400_I 162_S 0.89 0.32 0.00
447_V 76_I 0.86 0.30 0.00
162_R 74_V 0.80 0.25 0.00
280_A 150_I 0.80 0.25 0.00
400_I 64_V 0.80 0.25 0.00
250_N 147_E 0.80 0.25 0.00
106_V 97_I 0.79 0.24 0.00
453_T 44_L 0.78 0.24 0.00
365_P 33_L 0.78 0.23 0.00
345_A 150_I 0.76 0.22 0.00
106_V 191_V 0.75 0.22 0.00
259_E 218_I 0.75 0.22 0.00
154_A 190_G 0.75 0.21 0.00
320_V 40_Y 0.75 0.21 0.00
160_N 183_T 0.74 0.21 0.00
102_S 91_N 0.73 0.20 0.00
356_I 77_A 0.72 0.20 0.00
249_K 217_K 0.72 0.20 0.00
296_S 192_Y 0.72 0.20 0.00
246_Q 162_S 0.71 0.19 0.00
253_L 224_V 0.70 0.18 0.00
173_L 36_F 0.70 0.18 0.00
105_M 156_S 0.69 0.18 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
4507 1 cIp_4_80_cIV_2_60 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4506 0.43 cIp_4_80_cIV_2_60 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4505 0.16 cIp_4_80_cIV_2_80 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4294 1.04 cIp_4_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4293 1.46 cIp_4_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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