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OPENSEQ.org
cIV_C_4_cI_Ld500_560_20_8_Pdenitr
Genes: A B A+B
Length: 273 642 864
Sequences: 2888 7796 3288
Seq/Len: 10.58 12.14 3.81
MirrorTree (Pazo et al. 2001) 0.70
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 0.03 0.09
2 0.00 0.04 1.09
5 0.00 0.05 2.72
10 0.00 0.06 3.06
20 0.00 0.06 3.10
100 0.00 0.07 3.20
∞ 0.01 0.10 3.59
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
265_F 352_A 1.29 0.92 0.38
265_F 260_A 1.13 0.83 0.25
63_F 597_G 1.02 0.74 0.19
55_L 585_G 1.02 0.74 0.18
166_G 472_T 1.00 0.72 0.17
55_L 515_A 0.92 0.62 0.13
121_P 443_W 0.91 0.61 0.12
27_M 185_L 0.91 0.61 0.12
56_V 531_T 0.90 0.60 0.12
251_A 122_L 0.90 0.60 0.12
231_L 38_L 0.89 0.58 0.12
60_Y 229_F 0.88 0.57 0.11
8_Y 437_F 0.87 0.56 0.11
228_F 537_I 0.87 0.56 0.11
132_I 196_S 0.87 0.56 0.11
6_H 135_A 0.86 0.55 0.11
242_K 131_M 0.86 0.55 0.11
183_V 45_Y 0.86 0.54 0.10
172_I 367_H 0.86 0.54 0.10
201_A 291_F 0.85 0.53 0.10
73_G 160_Y 0.84 0.53 0.10
21_A 625_M 0.83 0.51 0.09
50_M 534_T 0.83 0.51 0.09
123_K 74_I 0.83 0.51 0.09
21_A 628_G 0.81 0.48 0.09
210_Y 278_M 0.81 0.48 0.09
154_A 602_L 0.81 0.48 0.08
114_Y 133_V 0.80 0.47 0.08
32_V 168_A 0.80 0.47 0.08
221_I 473_I 0.80 0.46 0.08
210_Y 175_V 0.79 0.46 0.08
232_I 626_V 0.79 0.46 0.08
21_A 614_Q 0.79 0.45 0.08
88_Y 187_I 0.79 0.45 0.08
10_I 384_T 0.79 0.45 0.08
183_V 36_L 0.79 0.45 0.08
188_L 41_L 0.78 0.44 0.07
169_K 598_V 0.78 0.44 0.07
56_V 571_F 0.78 0.44 0.07
29_T 624_A 0.78 0.43 0.07
108_F 175_V 0.77 0.43 0.07
83_R 296_G 0.77 0.43 0.07
28_L 390_I 0.77 0.43 0.07
150_L 388_M 0.77 0.42 0.07
180_I 516_W 0.77 0.42 0.07
123_K 555_R 0.77 0.42 0.07
91_I 494_F 0.76 0.42 0.07
53_I 515_A 0.76 0.42 0.07
183_V 553_L 0.76 0.42 0.07
238_Q 358_A 0.76 0.41 0.07
126_V 88_T 0.76 0.41 0.07
207_G 597_G 0.76 0.41 0.07
201_A 167_A 0.75 0.41 0.07
203_T 437_F 0.75 0.41 0.07
59_L 570_I 0.75 0.40 0.07
187_G 433_I 0.75 0.40 0.07
236_K 433_I 0.75 0.40 0.07
232_I 44_W 0.74 0.40 0.07
69_V 33_T 0.74 0.40 0.06
134_T 582_L 0.74 0.39 0.06
18_F 479_A 0.74 0.39 0.06
225_I 578_L 0.74 0.39 0.06
49_W 13_S 0.74 0.39 0.06
8_Y 621_Y 0.74 0.39 0.06
204_V 185_L 0.74 0.39 0.06
52_L 629_I 0.73 0.38 0.06
270_I 234_G 0.73 0.38 0.06
207_G 620_H 0.73 0.38 0.06
180_I 627_L 0.73 0.38 0.06
73_G 338_S 0.73 0.38 0.06
61_V 393_F 0.73 0.37 0.06
50_M 233_V 0.73 0.37 0.06
59_L 531_T 0.72 0.37 0.06
69_V 65_T 0.72 0.37 0.06
204_V 449_T 0.72 0.37 0.06
224_T 597_G 0.72 0.37 0.06
197_A 622_A 0.72 0.37 0.06
237_G 303_A 0.72 0.37 0.06
218_A 159_Y 0.72 0.37 0.06
180_I 476_G 0.72 0.37 0.06
50_M 553_L 0.72 0.37 0.06
177_V 130_L 0.72 0.36 0.06
87_Q 410_F 0.72 0.36 0.06
187_G 626_V 0.72 0.36 0.06
80_P 552_A 0.72 0.36 0.06
190_A 557_L 0.72 0.36 0.06
70_V 42_I 0.72 0.36 0.06
237_G 554_Y 0.71 0.36 0.06
108_F 341_M 0.71 0.36 0.06
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
3203 3.81 cIV_C_4_cI_Ld500_560_20_8_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
3202 3.83 cIV_C_4_cI_Ld500_560_10_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
3198 0.66 cIV_C_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
3197 0.66 cIV_C_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
3196 0.65 cIV_C_4_cI_Ld500_560_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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