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OPENSEQ.org
cIV_C_4_cI_Ld500_560_10_1_Pdenitr
Genes: A B A+B
Length: 273 642 864
Sequences: 2888 7818 3309
Seq/Len: 10.58 12.18 3.83
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 0.03 1.09
5 0.00 0.05 2.73
10 0.00 0.05 3.05
20 0.00 0.06 3.13
100 0.00 0.06 3.21
∞ 0.01 0.10 3.62
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 1.21 0.89 0.20
265_F 260_A 1.14 0.84 0.17
63_F 597_G 1.09 0.80 0.14
166_G 472_T 1.05 0.77 0.13
55_L 515_A 0.98 0.70 0.10
27_M 185_L 0.95 0.67 0.09
56_V 531_T 0.94 0.66 0.09
132_I 196_S 0.94 0.64 0.09
121_P 443_W 0.92 0.63 0.08
188_L 41_L 0.91 0.61 0.08
6_H 135_A 0.90 0.61 0.08
50_M 534_T 0.89 0.59 0.07
180_I 44_W 0.89 0.59 0.07
251_A 122_L 0.88 0.58 0.07
55_L 585_G 0.87 0.57 0.07
225_I 578_L 0.87 0.56 0.07
53_I 515_A 0.87 0.56 0.07
203_T 437_F 0.85 0.54 0.07
8_Y 437_F 0.85 0.53 0.06
266_V 452_G 0.84 0.52 0.06
32_V 168_A 0.83 0.51 0.06
60_Y 229_F 0.83 0.50 0.06
187_G 433_I 0.83 0.50 0.06
51_F 529_L 0.82 0.49 0.06
88_Y 187_I 0.82 0.49 0.06
69_V 23_I 0.82 0.49 0.06
48_P 40_C 0.82 0.49 0.06
232_I 626_V 0.81 0.48 0.05
126_V 88_T 0.80 0.47 0.05
236_K 433_I 0.80 0.46 0.05
242_K 131_M 0.80 0.46 0.05
29_T 624_A 0.80 0.46 0.05
123_K 555_R 0.79 0.46 0.05
183_V 553_L 0.79 0.46 0.05
21_A 614_Q 0.79 0.45 0.05
210_Y 175_V 0.79 0.45 0.05
59_L 531_T 0.78 0.45 0.05
180_I 476_G 0.78 0.45 0.05
172_I 367_H 0.78 0.44 0.05
154_A 602_L 0.77 0.43 0.05
201_A 291_F 0.77 0.43 0.05
197_A 622_A 0.77 0.43 0.05
164_L 619_F 0.77 0.43 0.05
225_I 40_C 0.76 0.41 0.04
201_A 167_A 0.76 0.41 0.04
204_V 185_L 0.76 0.41 0.04
108_F 341_M 0.75 0.41 0.04
270_I 234_G 0.75 0.41 0.04
21_A 625_M 0.75 0.41 0.04
238_Q 358_A 0.75 0.41 0.04
108_F 175_V 0.75 0.41 0.04
69_V 65_T 0.75 0.40 0.04
123_K 74_I 0.75 0.40 0.04
59_L 631_G 0.75 0.40 0.04
21_A 628_G 0.75 0.40 0.04
221_I 473_I 0.74 0.40 0.04
83_R 296_G 0.74 0.40 0.04
87_Q 410_F 0.74 0.39 0.04
56_V 517_V 0.74 0.39 0.04
150_L 329_F 0.74 0.39 0.04
218_A 159_Y 0.74 0.39 0.04
250_A 153_Y 0.73 0.39 0.04
196_A 175_V 0.73 0.39 0.04
147_I 345_L 0.73 0.38 0.04
61_V 393_F 0.73 0.38 0.04
21_A 193_L 0.73 0.38 0.04
25_F 89_T 0.73 0.38 0.04
59_L 570_I 0.73 0.38 0.04
183_V 229_F 0.73 0.38 0.04
114_Y 133_V 0.73 0.38 0.04
73_G 160_Y 0.73 0.37 0.04
50_M 233_V 0.72 0.37 0.04
83_R 183_F 0.72 0.37 0.04
51_F 526_V 0.72 0.37 0.04
18_F 70_A 0.72 0.37 0.04
231_L 70_A 0.72 0.36 0.04
12_P 451_Y 0.72 0.36 0.04
88_Y 168_A 0.72 0.36 0.04
201_A 510_A 0.72 0.36 0.04
210_Y 278_M 0.72 0.36 0.04
13_P 246_T 0.72 0.36 0.04
224_T 386_W 0.72 0.36 0.04
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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