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OPENSEQ.org
cIV_B_60_cI_L_80_2_human
Genes: A B A+B
Length: 227 603 825
Sequences: 2677 4961 2987
Seq/Len: 11.79 8.23 3.62
MirrorTree (Pazo et al. 2001) 0.81
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 0.05
2 0.00 0.00 0.13
5 0.00 0.00 1.49
10 0.00 0.00 3.27
20 0.00 0.00 3.35
100 0.00 0.01 3.37
∞ 0.00 0.02 3.60
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
82_R 337_A 1.25 0.90 0.26
76_I 152_F 1.24 0.89 0.25
170_L 57_L 1.18 0.85 0.21
193_Y 341_M 1.15 0.84 0.20
156_S 394_H 1.11 0.81 0.17
99_S 298_I 1.06 0.76 0.15
129_E 496_L 1.05 0.76 0.15
9_L 74_T 1.04 0.74 0.14
76_I 231_P 1.04 0.74 0.14
9_L 341_M 1.03 0.74 0.14
170_L 394_H 1.00 0.71 0.13
28_L 567_S 1.00 0.70 0.13
21_I 379_A 0.99 0.69 0.12
137_D 544_T 0.98 0.68 0.12
95_L 587_Y 0.98 0.68 0.12
123_L 206_A 0.97 0.67 0.11
156_S 67_H 0.96 0.66 0.11
99_S 153_L 0.96 0.66 0.11
140_N 104_S 0.95 0.65 0.11
160_L 119_K 0.95 0.65 0.11
7_V 319_I 0.95 0.65 0.11
100_I 529_Y 0.95 0.64 0.10
9_L 132_V 0.94 0.63 0.10
86_M 396_I 0.94 0.63 0.10
61_M 316_T 0.93 0.62 0.10
156_S 434_Q 0.92 0.61 0.10
36_F 80_F 0.92 0.60 0.09
67_I 54_F 0.91 0.60 0.09
187_T 473_S 0.91 0.59 0.09
175_I 584_I 0.90 0.58 0.09
96_T 532_I 0.88 0.56 0.08
143_V 495_F 0.88 0.56 0.08
99_S 587_Y 0.87 0.55 0.08
88_D 454_I 0.87 0.55 0.08
88_D 111_D 0.87 0.55 0.08
34_I 356_I 0.87 0.54 0.08
126_L 276_L 0.86 0.53 0.08
156_S 277_T 0.86 0.53 0.08
26_H 150_M 0.86 0.53 0.08
160_L 188_W 0.85 0.52 0.07
225_F 566_I 0.85 0.52 0.07
130_P 46_I 0.85 0.52 0.07
156_S 76_L 0.85 0.52 0.07
210_V 356_I 0.85 0.52 0.07
211_L 430_T 0.84 0.51 0.07
107_T 352_N 0.84 0.51 0.07
191_V 87_M 0.84 0.50 0.07
155_T 201_M 0.84 0.50 0.07
71_I 532_I 0.84 0.50 0.07
7_V 202_A 0.84 0.50 0.07
41_A 296_N 0.83 0.50 0.07
55_I 574_S 0.83 0.49 0.07
192_Y 555_L 0.83 0.49 0.07
217_K 543_L 0.83 0.49 0.07
149_P 152_F 0.83 0.49 0.07
105_Y 243_V 0.83 0.49 0.07
107_T 389_F 0.82 0.48 0.07
41_A 584_I 0.82 0.48 0.07
137_D 260_L 0.82 0.47 0.06
43_F 410_S 0.82 0.47 0.06
214_I 536_T 0.82 0.47 0.06
163_W 194_N 0.81 0.47 0.06
175_I 412_T 0.81 0.47 0.06
221_M 210_L 0.81 0.47 0.06
84_L 345_S 0.81 0.46 0.06
95_L 497_G 0.80 0.46 0.06
97_I 7_M 0.80 0.46 0.06
149_P 582_G 0.80 0.46 0.06
16_I 475_A 0.80 0.45 0.06
107_T 95_F 0.80 0.45 0.06
181_Q 487_K 0.80 0.45 0.06
126_L 592_F 0.80 0.45 0.06
8_G 371_T 0.80 0.45 0.06
156_S 80_F 0.80 0.45 0.06
38_V 467_L 0.79 0.45 0.06
23_F 315_V 0.79 0.44 0.06
217_K 576_I 0.79 0.44 0.06
57_D 150_M 0.79 0.44 0.06
191_V 504_L 0.79 0.44 0.06
15_P 360_G 0.79 0.43 0.06
86_M 561_L 0.78 0.43 0.06
160_L 383_M 0.78 0.43 0.06
72_I 364_K 0.78 0.42 0.05
9_L 473_S 0.78 0.42 0.05
175_I 443_I 0.78 0.42 0.05
29_M 387_T 0.78 0.42 0.05
219_F 314_M 0.78 0.42 0.05
97_I 592_F 0.78 0.42 0.05
110_Y 596_I 0.77 0.42 0.05
87_T 74_T 0.77 0.42 0.05
90_V 281_G 0.77 0.42 0.05
12_A 46_I 0.77 0.42 0.05
76_I 491_L 0.77 0.42 0.05
87_T 302_V 0.77 0.41 0.05
54_N 261_I 0.77 0.41 0.05
36_F 543_L 0.77 0.41 0.05
29_M 375_I 0.77 0.41 0.05
143_V 203_L 0.76 0.41 0.05
152_M 68_W 0.76 0.41 0.05
156_S 387_T 0.76 0.41 0.05
160_L 218_L 0.76 0.41 0.05
64_V 565_T 0.76 0.41 0.05
28_L 69_A 0.76 0.40 0.05
137_D 131_L 0.76 0.40 0.05
213_L 426_M 0.76 0.40 0.05
218_I 590_S 0.76 0.40 0.05
113_Y 139_Q 0.75 0.40 0.05
81_L 526_L 0.75 0.39 0.05
199_I 146_G 0.75 0.39 0.05
83_I 527_G 0.75 0.39 0.05
156_S 474_P 0.75 0.39 0.05
116_L 47_S 0.75 0.39 0.05
219_F 468_I 0.75 0.39 0.05
143_V 90_I 0.74 0.38 0.05
61_M 101_M 0.74 0.38 0.05
88_D 458_A 0.74 0.38 0.05
156_S 135_N 0.74 0.38 0.05
170_L 596_I 0.74 0.38 0.05
167_T 523_S 0.74 0.38 0.05
86_M 416_T 0.74 0.38 0.05
142_V 502_L 0.74 0.38 0.05
38_V 327_L 0.74 0.38 0.05
96_T 68_W 0.74 0.38 0.05
95_L 468_I 0.74 0.38 0.05
144_L 486_L 0.74 0.37 0.05
15_P 339_L 0.74 0.37 0.05
38_V 337_A 0.73 0.37 0.05
186_A 588_F 0.73 0.37 0.04
95_L 555_L 0.73 0.37 0.04
67_I 311_G 0.73 0.37 0.04
88_D 261_I 0.73 0.37 0.04
67_I 485_Y 0.73 0.37 0.04
150_I 514_K 0.73 0.37 0.04
170_L 424_T 0.73 0.37 0.04
221_M 600_L 0.73 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
4657 2.9 cIV_B_60_cI_L_80_2_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.24 Done - Shared
4656 3.62 cIV_B_60_cI_L_80_2_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 2) msa: Jackhmmer (2015_06) 0.26 Done - Shared
4655 3.34 cIV_B_80_cI_L_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 2) msa: Jackhmmer (2015_06) 0.46 Done - Shared
4449 2.05 cIV_B_60_cI_L_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4448 2.88 cIV_B_80_cI_L_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.35 Done - Shared
4447 2.04 cIV_B_80_cI_L_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.91 Done - Shared
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