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OPENSEQ.org
cIV_C_2_cI_J_6_Pdenitr
Genes: A B A+B
Length: 273 200 429
Sequences: 2897 4916 2424
Seq/Len: 10.61 24.58 5.65
MirrorTree (Pazo et al. 2001) 0.51
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 4.33
20 0.00 0.00 4.44
100 0.00 0.01 4.54
∞ 0.01 0.02 5.12
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 1.51 0.99 0.85
138_W 74_M 1.18 0.93 0.62
203_T 155_L 1.03 0.84 0.46
136_D 29_S 1.02 0.84 0.45
103_A 67_L 0.98 0.80 0.41
83_R 33_L 0.98 0.80 0.41
174_G 53_A 0.98 0.80 0.41
225_I 43_L 0.98 0.80 0.40
107_A 60_Y 0.97 0.80 0.40
28_L 50_E 0.97 0.79 0.39
125_G 49_A 0.96 0.79 0.39
69_V 17_G 0.96 0.78 0.38
55_L 145_L 0.95 0.77 0.37
134_T 50_E 0.94 0.76 0.36
56_V 95_V 0.94 0.76 0.36
125_G 59_V 0.94 0.76 0.36
98_V 94_L 0.93 0.76 0.35
211_M 162_I 0.93 0.75 0.35
110_K 52_V 0.92 0.74 0.34
138_W 72_V 0.92 0.74 0.34
231_L 164_L 0.91 0.73 0.33
140_L 34_I 0.91 0.73 0.33
210_Y 50_E 0.91 0.72 0.32
242_K 139_L 0.89 0.71 0.31
225_I 59_V 0.88 0.69 0.30
211_M 158_M 0.88 0.69 0.30
153_V 74_M 0.88 0.69 0.29
182_G 56_L 0.87 0.68 0.29
167_D 164_L 0.87 0.68 0.29
134_T 74_M 0.87 0.68 0.28
103_A 151_G 0.86 0.66 0.28
210_Y 148_Q 0.85 0.66 0.27
4_K 147_F 0.84 0.65 0.26
25_F 107_A 0.84 0.65 0.26
88_Y 79_F 0.84 0.65 0.26
8_Y 57_V 0.84 0.65 0.26
23_G 138_V 0.83 0.63 0.25
153_V 58_V 0.83 0.63 0.25
110_K 9_F 0.83 0.62 0.25
63_F 147_F 0.82 0.61 0.24
150_L 50_E 0.82 0.61 0.24
236_K 139_L 0.82 0.61 0.24
28_L 59_V 0.82 0.61 0.24
171_T 103_Q 0.82 0.61 0.24
201_A 141_D 0.82 0.61 0.24
155_V 168_H 0.81 0.60 0.23
146_L 60_Y 0.81 0.60 0.23
57_G 10_A 0.81 0.59 0.23
238_Q 27_V 0.81 0.59 0.23
32_V 136_G 0.81 0.59 0.23
21_A 27_V 0.80 0.59 0.22
138_W 158_M 0.80 0.58 0.22
131_G 66_V 0.79 0.58 0.22
23_G 149_L 0.79 0.58 0.22
63_F 10_A 0.79 0.57 0.21
51_F 59_V 0.79 0.57 0.21
146_L 160_G 0.79 0.56 0.21
205_Y 150_A 0.79 0.56 0.21
158_A 15_V 0.78 0.56 0.20
61_V 147_F 0.78 0.56 0.20
83_R 51_F 0.78 0.56 0.20
52_L 34_I 0.78 0.55 0.20
19_F 50_E 0.78 0.55 0.20
139_H 60_Y 0.78 0.55 0.20
110_K 49_A 0.77 0.55 0.20
60_Y 157_A 0.77 0.55 0.20
179_V 115_D 0.77 0.55 0.20
125_G 28_H 0.77 0.54 0.20
21_A 16_A 0.77 0.54 0.20
252_W 56_L 0.77 0.53 0.19
201_A 76_D 0.76 0.53 0.19
167_D 18_F 0.76 0.53 0.19
27_M 22_I 0.76 0.53 0.19
236_K 38_L 0.76 0.52 0.19
134_T 114_S 0.76 0.52 0.19
70_V 148_Q 0.75 0.52 0.18
228_F 123_A 0.75 0.52 0.18
265_F 26_P 0.75 0.52 0.18
59_L 9_F 0.75 0.52 0.18
203_T 153_V 0.75 0.51 0.18
22_I 60_Y 0.75 0.51 0.18
177_V 143_Y 0.75 0.51 0.18
107_A 33_L 0.75 0.51 0.18
8_Y 55_L 0.75 0.51 0.18
61_V 61_V 0.75 0.51 0.18
175_L 53_A 0.74 0.50 0.18
34_W 65_A 0.74 0.50 0.17
69_V 125_V 0.74 0.50 0.17
37_G 147_F 0.74 0.49 0.17
168_R 147_F 0.73 0.49 0.17
86_L 160_G 0.73 0.49 0.17
210_Y 77_V 0.73 0.48 0.17
53_I 140_Y 0.73 0.48 0.17
103_A 29_S 0.73 0.48 0.17
13_P 155_L 0.73 0.48 0.16
29_T 15_V 0.73 0.48 0.16
229_V 144_V 0.73 0.48 0.16
139_H 29_S 0.73 0.48 0.16
225_I 94_L 0.72 0.47 0.16
170_T 158_M 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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