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cIV_B_4_cI_Ld500_560_20_1_Pdenitr
Genes: A B A+B
Length: 252 642 870
Sequences: 4637 2007 987
Seq/Len: 18.4 3.13 1.13
MirrorTree (Pazo et al. 2001) 0.42
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 0.02
2 0.00 0.00 0.05
5 0.00 0.00 0.15
10 0.01 0.00 0.28
20 0.01 0.00 0.34
100 0.02 0.01 0.41
∞ 0.04 0.03 1.10
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
170_V 18_L 1.22 0.58 0.00
77_I 47_F 1.10 0.46 0.00
209_E 74_I 1.04 0.40 0.00
212_Y 106_D 0.98 0.35 0.00
170_V 70_A 0.95 0.32 0.00
195_V 617_Y 0.93 0.31 0.00
51_L 295_I 0.92 0.30 0.00
176_A 86_V 0.89 0.28 0.00
22_P 76_L 0.89 0.27 0.00
242_W 443_W 0.88 0.27 0.00
132_V 87_V 0.87 0.26 0.00
103_S 280_P 0.87 0.26 0.00
59_R 97_Y 0.86 0.25 0.00
212_Y 220_D 0.86 0.25 0.00
44_A 86_V 0.82 0.23 0.00
23_A 629_I 0.81 0.22 0.00
236_Q 18_L 0.81 0.22 0.00
167_G 559_N 0.81 0.22 0.00
192_Q 536_Y 0.80 0.22 0.00
239_Y 608_R 0.80 0.21 0.00
79_V 340_A 0.80 0.21 0.00
239_Y 515_A 0.80 0.21 0.00
176_A 141_M 0.79 0.21 0.00
32_Q 186_G 0.79 0.21 0.00
92_I 432_V 0.79 0.21 0.00
170_V 226_L 0.79 0.21 0.00
167_G 607_T 0.79 0.20 0.00
131_G 487_M 0.79 0.20 0.00
204_F 14_L 0.79 0.20 0.00
91_A 394_A 0.78 0.20 0.00
25_S 99_L 0.77 0.20 0.00
48_F 366_H 0.77 0.20 0.00
91_A 424_S 0.77 0.20 0.00
167_G 417_I 0.76 0.19 0.00
90_V 615_S 0.76 0.19 0.00
54_L 61_D 0.76 0.19 0.00
139_L 479_A 0.76 0.19 0.00
94_A 185_L 0.75 0.18 0.00
114_I 138_L 0.75 0.18 0.00
227_M 252_M 0.75 0.18 0.00
117_I 49_S 0.75 0.18 0.00
175_T 449_T 0.75 0.18 0.00
182_A 135_A 0.74 0.18 0.00
73_H 471_M 0.74 0.18 0.00
77_I 446_I 0.73 0.17 0.00
84_V 237_G 0.73 0.17 0.00
128_P 311_N 0.73 0.17 0.00
45_V 574_P 0.73 0.17 0.00
166_V 31_L 0.73 0.17 0.00
49_V 72_W 0.73 0.17 0.00
45_V 289_K 0.73 0.17 0.00
212_Y 389_M 0.72 0.17 0.00
130_D 523_V 0.72 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
3320 1.13 cIV_B_4_cI_Ld500_560_4_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3319 1.13 cIV_B_4_cI_Ld500_560_10_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3318 1.13 cIV_B_4_cI_Ld500_560_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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