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OPENSEQ.org
cIV_C_6_cI_J_6_Pdenitr
Genes: A B A+B
Length: 273 200 429
Sequences: 2876 4916 2436
Seq/Len: 10.53 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 3.96
10 0.00 0.00 4.34
20 0.00 0.00 4.44
100 0.00 0.01 4.55
∞ 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 0.93 0.62
203_T 155_L 1.05 0.86 0.49
136_D 29_S 1.04 0.85 0.48
28_L 50_E 1.03 0.84 0.46
83_R 33_L 0.99 0.81 0.42
107_A 60_Y 0.97 0.80 0.41
225_I 43_L 0.97 0.80 0.41
103_A 67_L 0.96 0.79 0.40
231_L 164_L 0.96 0.79 0.39
174_G 53_A 0.96 0.79 0.39
125_G 49_A 0.95 0.78 0.38
210_Y 50_E 0.94 0.77 0.37
110_K 52_V 0.93 0.76 0.36
98_V 94_L 0.93 0.75 0.36
55_L 145_L 0.92 0.74 0.35
69_V 17_G 0.92 0.74 0.35
211_M 162_I 0.92 0.74 0.34
134_T 50_E 0.91 0.73 0.34
25_F 107_A 0.90 0.71 0.32
138_W 72_V 0.90 0.71 0.32
140_L 34_I 0.90 0.71 0.32
242_K 139_L 0.89 0.70 0.31
225_I 59_V 0.89 0.70 0.31
210_Y 148_Q 0.88 0.69 0.30
103_A 151_G 0.88 0.69 0.30
179_V 115_D 0.87 0.69 0.30
211_M 158_M 0.87 0.68 0.29
182_G 56_L 0.87 0.68 0.29
153_V 74_M 0.87 0.68 0.29
125_G 59_V 0.87 0.68 0.29
63_F 10_A 0.86 0.67 0.28
28_L 59_V 0.85 0.66 0.28
167_D 164_L 0.85 0.66 0.27
23_G 138_V 0.84 0.65 0.27
88_Y 79_F 0.84 0.64 0.27
61_V 147_F 0.84 0.64 0.27
57_G 10_A 0.84 0.64 0.26
23_G 149_L 0.84 0.64 0.26
134_T 74_M 0.83 0.63 0.25
4_K 147_F 0.82 0.62 0.25
153_V 58_V 0.82 0.62 0.25
70_V 148_Q 0.82 0.61 0.24
146_L 60_Y 0.82 0.61 0.24
201_A 141_D 0.82 0.61 0.24
238_Q 27_V 0.82 0.61 0.24
102_V 96_I 0.81 0.60 0.24
134_T 114_S 0.81 0.59 0.23
63_F 147_F 0.80 0.59 0.23
171_T 103_Q 0.80 0.59 0.23
8_Y 57_V 0.80 0.59 0.23
225_I 94_L 0.80 0.59 0.23
110_K 9_F 0.80 0.58 0.22
83_R 51_F 0.80 0.58 0.22
32_V 136_G 0.79 0.57 0.22
51_F 59_V 0.79 0.57 0.22
21_A 27_V 0.79 0.57 0.22
139_H 60_Y 0.79 0.57 0.21
110_K 49_A 0.79 0.56 0.21
205_Y 150_A 0.78 0.56 0.21
131_G 66_V 0.78 0.56 0.21
229_V 31_L 0.78 0.56 0.21
61_V 61_V 0.78 0.56 0.21
236_K 139_L 0.78 0.55 0.21
21_A 16_A 0.78 0.55 0.21
19_F 50_E 0.78 0.55 0.20
59_L 9_F 0.77 0.55 0.20
69_V 125_V 0.77 0.54 0.20
187_G 47_Q 0.77 0.54 0.20
56_V 95_V 0.77 0.54 0.20
8_Y 55_L 0.77 0.54 0.20
252_W 56_L 0.77 0.54 0.20
232_I 149_L 0.76 0.53 0.20
201_A 76_D 0.76 0.53 0.20
167_D 18_F 0.76 0.52 0.19
228_F 123_A 0.76 0.52 0.19
114_Y 13_A 0.76 0.52 0.19
138_W 158_M 0.75 0.52 0.19
139_H 29_S 0.75 0.52 0.19
158_A 15_V 0.75 0.52 0.19
107_A 33_L 0.75 0.52 0.19
37_G 147_F 0.75 0.52 0.18
150_L 50_E 0.75 0.51 0.18
22_I 60_Y 0.75 0.51 0.18
265_F 26_P 0.75 0.51 0.18
154_A 140_Y 0.75 0.51 0.18
52_L 34_I 0.75 0.51 0.18
146_L 160_G 0.74 0.50 0.18
177_V 143_Y 0.74 0.50 0.18
103_A 29_S 0.74 0.50 0.18
155_V 168_H 0.74 0.50 0.18
161_A 15_V 0.74 0.50 0.18
48_P 100_L 0.74 0.50 0.18
73_G 160_G 0.74 0.50 0.18
81_V 131_N 0.74 0.50 0.18
60_Y 157_A 0.73 0.49 0.17
150_L 82_L 0.73 0.49 0.17
168_R 147_F 0.73 0.48 0.17
229_V 144_V 0.73 0.48 0.17
161_A 56_L 0.73 0.48 0.17
203_T 153_V 0.73 0.48 0.17
170_T 158_M 0.73 0.48 0.17
63_F 34_I 0.72 0.48 0.17
147_I 69_L 0.72 0.48 0.17
34_W 65_A 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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