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OPENSEQ.org
cIV_C_4_cI_J_6_Pdenitr
Genes: A B A+B
Length: 273 200 429
Sequences: 2888 4916 2437
Seq/Len: 10.58 24.58 5.68
MirrorTree (Pazo et al. 2001) 0.52
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 0.10
2 0.00 0.00 0.20
5 0.00 0.00 3.94
10 0.00 0.00 4.32
20 0.00 0.00 4.46
100 0.00 0.01 4.53
∞ 0.01 0.02 5.15
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
13_P 59_V 1.52 0.99 0.86
138_W 74_M 1.17 0.92 0.61
225_I 43_L 1.03 0.84 0.46
28_L 50_E 1.00 0.82 0.43
203_T 155_L 0.99 0.82 0.43
107_A 60_Y 0.99 0.81 0.42
83_R 33_L 0.99 0.81 0.42
140_L 34_I 0.98 0.81 0.41
103_A 67_L 0.98 0.81 0.41
136_D 29_S 0.97 0.80 0.40
174_G 53_A 0.95 0.78 0.38
125_G 49_A 0.95 0.77 0.38
110_K 52_V 0.94 0.76 0.36
242_K 139_L 0.93 0.75 0.35
98_V 94_L 0.92 0.74 0.34
210_Y 50_E 0.91 0.73 0.34
103_A 151_G 0.91 0.73 0.33
211_M 162_I 0.91 0.73 0.33
179_V 115_D 0.91 0.73 0.33
167_D 164_L 0.90 0.72 0.33
134_T 74_M 0.90 0.72 0.32
182_G 56_L 0.90 0.72 0.32
225_I 59_V 0.89 0.71 0.32
134_T 50_E 0.89 0.71 0.31
138_W 72_V 0.89 0.70 0.31
153_V 58_V 0.88 0.70 0.31
55_L 145_L 0.88 0.70 0.31
153_V 74_M 0.88 0.70 0.30
69_V 17_G 0.88 0.69 0.30
125_G 59_V 0.88 0.69 0.30
25_F 107_A 0.86 0.67 0.28
211_M 158_M 0.85 0.66 0.28
59_L 9_F 0.85 0.66 0.27
210_Y 148_Q 0.85 0.66 0.27
201_A 141_D 0.85 0.65 0.27
155_V 168_H 0.84 0.64 0.26
231_L 164_L 0.84 0.64 0.26
63_F 10_A 0.83 0.64 0.26
238_Q 27_V 0.83 0.63 0.26
171_T 103_Q 0.83 0.63 0.25
110_K 9_F 0.83 0.62 0.25
21_A 16_A 0.82 0.62 0.24
225_I 94_L 0.82 0.61 0.24
23_G 149_L 0.81 0.61 0.24
23_G 138_V 0.81 0.60 0.23
83_R 51_F 0.81 0.60 0.23
21_A 27_V 0.81 0.60 0.23
146_L 60_Y 0.81 0.59 0.23
88_Y 79_F 0.81 0.59 0.23
56_V 95_V 0.80 0.59 0.23
61_V 61_V 0.80 0.58 0.22
8_Y 57_V 0.80 0.58 0.22
158_A 15_V 0.80 0.58 0.22
4_K 147_F 0.80 0.58 0.22
19_F 50_E 0.79 0.58 0.22
125_G 28_H 0.79 0.57 0.22
131_G 66_V 0.79 0.57 0.21
61_V 147_F 0.79 0.57 0.21
187_G 47_Q 0.79 0.57 0.21
32_V 136_G 0.78 0.56 0.21
154_A 140_Y 0.78 0.55 0.20
22_I 60_Y 0.78 0.55 0.20
110_K 49_A 0.78 0.55 0.20
63_F 147_F 0.77 0.55 0.20
57_G 10_A 0.77 0.55 0.20
51_F 59_V 0.77 0.55 0.20
28_L 59_V 0.77 0.54 0.20
236_K 139_L 0.76 0.53 0.19
139_H 29_S 0.76 0.53 0.19
252_W 56_L 0.76 0.53 0.19
139_H 60_Y 0.76 0.53 0.19
107_A 33_L 0.76 0.53 0.19
210_Y 55_L 0.76 0.53 0.19
37_G 147_F 0.76 0.52 0.19
203_T 153_V 0.76 0.52 0.19
69_V 125_V 0.75 0.52 0.18
229_V 144_V 0.75 0.52 0.18
29_T 15_V 0.75 0.51 0.18
161_A 15_V 0.75 0.51 0.18
146_L 160_G 0.74 0.51 0.18
34_W 65_A 0.74 0.50 0.18
150_L 50_E 0.74 0.50 0.18
205_Y 150_A 0.74 0.50 0.17
138_W 158_M 0.74 0.50 0.17
147_I 69_L 0.74 0.50 0.17
201_A 76_D 0.74 0.49 0.17
81_V 131_N 0.74 0.49 0.17
134_T 114_S 0.74 0.49 0.17
70_V 148_Q 0.73 0.49 0.17
8_Y 55_L 0.73 0.49 0.17
27_M 22_I 0.73 0.48 0.17
52_L 34_I 0.73 0.48 0.17
265_F 26_P 0.72 0.47 0.16
103_A 29_S 0.72 0.47 0.16
13_P 155_L 0.72 0.47 0.16
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
3179 5.65 cIV_C_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
3178 5.68 cIV_C_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3177 5.65 cIV_C_2_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
3176 5.68 cIV_C_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3175 1.26 cIV_C_4_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3174 1.24 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3173 6.66 cIV_C_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
3172 6.66 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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