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OPENSEQ.org
cIV_B_4_cI_N_40_1_Pdenitr
Genes: A B A+B
Length: 252 499 701
Sequences: 4637 1784 781
Seq/Len: 18.4 3.58 1.11
MirrorTree (Pazo et al. 2001) 0.34
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 0.00 0.00 0.02
5 0.00 0.00 0.04
10 0.01 0.00 0.09
20 0.01 0.02 0.16
100 0.02 0.02 0.25
∞ 0.04 0.04 1.04
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
212_Y 234_S 1.69 0.89 0.27
116_A 120_M 1.18 0.54 0.07
176_A 221_V 1.14 0.49 0.06
80_I 175_A 1.07 0.43 0.04
239_Y 435_E 1.01 0.37 0.03
237_E 189_G 0.97 0.33 0.03
209_E 374_V 0.93 0.30 0.03
40_Y 412_I 0.91 0.29 0.02
239_Y 433_E 0.89 0.27 0.02
112_L 153_S 0.86 0.25 0.02
212_Y 252_A 0.86 0.25 0.02
172_V 390_A 0.85 0.24 0.02
25_S 246_P 0.84 0.24 0.02
94_A 175_A 0.83 0.23 0.02
96_S 232_E 0.83 0.23 0.02
241_A 106_F 0.81 0.22 0.02
114_I 10_L 0.81 0.21 0.01
25_S 374_V 0.81 0.21 0.01
80_I 341_F 0.81 0.21 0.01
47_I 432_G 0.80 0.21 0.01
239_Y 394_V 0.80 0.21 0.01
243_L 48_V 0.79 0.20 0.01
87_L 38_L 0.79 0.20 0.01
237_E 79_V 0.79 0.20 0.01
88_I 389_F 0.78 0.20 0.01
184_T 136_Q 0.78 0.20 0.01
116_A 157_G 0.78 0.20 0.01
33_W 206_G 0.78 0.20 0.01
25_S 52_M 0.78 0.20 0.01
88_I 138_L 0.77 0.19 0.01
118_G 408_V 0.77 0.19 0.01
92_I 297_L 0.77 0.19 0.01
172_V 63_A 0.76 0.19 0.01
180_I 316_G 0.76 0.18 0.01
22_P 41_V 0.76 0.18 0.01
237_E 298_M 0.76 0.18 0.01
212_Y 13_V 0.76 0.18 0.01
142_E 379_L 0.75 0.18 0.01
162_V 90_A 0.75 0.18 0.01
94_A 241_F 0.74 0.18 0.01
180_I 209_F 0.74 0.17 0.01
87_L 213_G 0.73 0.17 0.01
92_I 170_L 0.73 0.17 0.01
86_V 92_S 0.73 0.17 0.01
185_I 44_A 0.73 0.17 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
3315 1.12 cIV_B_2_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.26 Done - Shared
3314 1.11 cIV_B_4_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.27 Done - Shared
3313 0.83 cIV_B_6_cI_N_60_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3312 1.12 cIV_B_6_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3311 1.65 cIV_B_6_cI_N_10_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3308 1.24 cIV_B_6_cI_N_20_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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