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OPENSEQ.org
cIV_C_40_cIII_isp_40_Pdenitr
Genes: A B A+B
Length: 273 190 453
Sequences: 2504 1013 287
Seq/Len: 9.17 5.33 0.63
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.00 0.01 0.01
100 0.00 0.01 0.09
∞ 0.00 0.02 0.62
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
107_A 72_L 1.56 0.68 0.00
25_F 87_Q 1.55 0.67 0.00
62_M 74_K 1.38 0.54 0.00
208_A 72_L 1.36 0.52 0.00
9_Q 166_R 1.35 0.51 0.00
22_I 87_Q 1.34 0.51 0.00
104_W 41_Q 1.32 0.49 0.00
262_L 33_A 1.30 0.48 0.00
108_F 70_K 1.26 0.44 0.00
85_G 47_D 1.19 0.38 0.00
146_L 43_N 1.18 0.38 0.00
62_M 24_A 1.16 0.36 0.00
270_I 182_L 1.15 0.36 0.00
245_V 72_L 1.15 0.35 0.00
265_F 60_G 1.15 0.35 0.00
194_S 78_I 1.12 0.34 0.00
66_W 17_D 1.12 0.33 0.00
210_Y 151_F 1.12 0.33 0.00
143_I 32_G 1.10 0.32 0.00
186_T 98_I 1.08 0.31 0.00
251_A 57_D 1.07 0.30 0.00
132_I 187_I 1.07 0.30 0.00
164_L 25_G 1.06 0.29 0.00
232_I 181_F 1.05 0.28 0.00
152_G 42_M 1.04 0.27 0.00
16_W 15_R 1.03 0.27 0.00
225_I 31_A 1.03 0.27 0.00
208_A 23_T 1.03 0.27 0.00
191_Y 69_V 1.02 0.27 0.00
115_P 38_L 1.02 0.27 0.00
47_G 124_E 1.02 0.26 0.00
10_I 70_K 1.01 0.26 0.00
246_G 128_M 1.00 0.25 0.00
59_L 52_A 1.00 0.25 0.00
127_W 71_W 1.00 0.25 0.00
265_F 168_G 0.98 0.24 0.00
84_I 42_M 0.98 0.24 0.00
222_I 183_D 0.98 0.24 0.00
137_P 108_P 0.96 0.23 0.00
165_E 115_E 0.96 0.23 0.00
246_G 131_V 0.95 0.22 0.00
236_K 45_S 0.95 0.22 0.00
180_I 95_G 0.95 0.22 0.00
111_N 129_I 0.94 0.22 0.00
140_L 63_T 0.94 0.21 0.00
246_G 159_Y 0.93 0.21 0.00
195_H 55_Q 0.93 0.21 0.00
36_K 48_V 0.93 0.21 0.00
37_G 61_V 0.92 0.21 0.00
32_V 52_A 0.92 0.20 0.00
135_F 182_L 0.91 0.20 0.00
166_G 184_D 0.91 0.20 0.00
134_T 175_H 0.91 0.20 0.00
82_V 46_A 0.91 0.20 0.00
177_V 162_S 0.90 0.20 0.00
89_G 65_T 0.90 0.20 0.00
89_G 18_F 0.90 0.19 0.00
245_V 175_H 0.90 0.19 0.00
7_D 41_Q 0.90 0.19 0.00
226_F 141_G 0.89 0.19 0.00
246_G 87_Q 0.89 0.19 0.00
226_F 187_I 0.89 0.19 0.00
242_K 185_T 0.89 0.19 0.00
123_K 47_D 0.89 0.19 0.00
187_G 175_H 0.88 0.18 0.00
35_M 145_G 0.88 0.18 0.00
199_G 62_E 0.88 0.18 0.00
85_G 51_L 0.87 0.18 0.00
85_G 45_S 0.87 0.18 0.00
191_Y 127_V 0.86 0.17 0.00
271_W 166_R 0.86 0.17 0.00
178_A 179_A 0.86 0.17 0.00
69_V 43_N 0.86 0.17 0.00
236_K 62_E 0.86 0.17 0.00
27_M 32_G 0.85 0.17 0.00
78_H 158_H 0.85 0.17 0.00
153_V 19_L 0.85 0.17 0.00
89_G 15_R 0.85 0.17 0.00
115_P 48_V 0.85 0.17 0.00
69_V 168_G 0.85 0.17 0.00
172_I 60_G 0.84 0.17 0.00
16_W 19_L 0.84 0.17 0.00
184_C 176_I 0.84 0.17 0.00
108_F 138_V 0.84 0.17 0.00
245_V 52_A 0.84 0.17 0.00
25_F 174_L 0.84 0.17 0.00
201_A 69_V 0.84 0.16 0.00
207_G 106_N 0.83 0.16 0.00
86_L 148_G 0.83 0.16 0.00
121_P 19_L 0.83 0.16 0.00
168_R 153_P 0.83 0.16 0.00
98_V 31_A 0.83 0.16 0.00
57_G 58_V 0.83 0.16 0.00
251_A 185_T 0.83 0.16 0.00
210_Y 166_R 0.83 0.16 0.00
249_A 65_T 0.83 0.16 0.00
184_C 58_V 0.83 0.16 0.00
156_T 148_G 0.82 0.16 0.00
12_P 71_W 0.82 0.16 0.00
25_F 92_V 0.82 0.16 0.00
201_A 118_T 0.82 0.15 0.00
188_L 49_Q 0.82 0.15 0.00
28_L 30_A 0.82 0.15 0.00
240_T 74_K 0.82 0.15 0.00
110_K 45_S 0.82 0.15 0.00
210_Y 19_L 0.81 0.15 0.00
38_I 184_D 0.81 0.15 0.00
178_A 72_L 0.81 0.15 0.00
157_W 42_M 0.81 0.15 0.00
106_W 53_S 0.81 0.15 0.00
36_K 21_Y 0.81 0.15 0.00
142_L 138_V 0.81 0.15 0.00
188_L 34_A 0.80 0.15 0.00
221_I 25_G 0.80 0.15 0.00
51_F 9_G 0.80 0.15 0.00
147_I 96_Q 0.80 0.15 0.00
231_L 22_A 0.80 0.15 0.00
154_A 72_L 0.80 0.15 0.00
225_I 19_L 0.80 0.15 0.00
132_I 140_I 0.80 0.15 0.00
62_M 184_D 0.79 0.15 0.00
51_F 58_V 0.79 0.15 0.00
27_M 33_A 0.79 0.14 0.00
129_P 159_Y 0.79 0.14 0.00
154_A 179_A 0.79 0.14 0.00
167_D 127_V 0.79 0.14 0.00
196_A 72_L 0.79 0.14 0.00
263_F 146_D 0.79 0.14 0.00
238_Q 27_G 0.78 0.14 0.00
86_L 161_T 0.78 0.14 0.00
178_A 55_Q 0.78 0.14 0.00
16_W 18_F 0.78 0.14 0.00
130_E 26_A 0.78 0.14 0.00
26_V 184_D 0.78 0.14 0.00
86_L 165_I 0.78 0.14 0.00
123_K 45_S 0.78 0.14 0.00
162_F 45_S 0.78 0.14 0.00
7_D 168_G 0.78 0.14 0.00
22_I 140_I 0.78 0.14 0.00
78_H 147_F 0.78 0.14 0.00
11_L 48_V 0.78 0.14 0.00
228_F 46_A 0.78 0.14 0.00
200_L 95_G 0.77 0.14 0.00
34_W 34_A 0.77 0.14 0.00
160_H 104_N 0.77 0.14 0.00
116_M 45_S 0.77 0.14 0.00
222_I 28_T 0.77 0.14 0.00
161_A 66_Q 0.77 0.13 0.00
230_C 78_I 0.77 0.13 0.00
123_K 178_V 0.77 0.13 0.00
231_L 90_R 0.77 0.13 0.00
175_L 50_A 0.77 0.13 0.00
172_I 176_I 0.77 0.13 0.00
66_W 49_Q 0.76 0.13 0.00
187_G 98_I 0.76 0.13 0.00
114_Y 27_G 0.76 0.13 0.00
224_T 67_L 0.76 0.13 0.00
11_L 45_S 0.76 0.13 0.00
238_Q 187_I 0.76 0.13 0.00
109_I 23_T 0.76 0.13 0.00
75_T 122_A 0.76 0.13 0.00
88_Y 68_T 0.76 0.13 0.00
103_A 23_T 0.76 0.13 0.00
120_S 45_S 0.76 0.13 0.00
160_H 159_Y 0.76 0.13 0.00
52_L 122_A 0.76 0.13 0.00
125_G 68_T 0.76 0.13 0.00
102_V 180_E 0.76 0.13 0.00
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
3153 0.83 cIV_C_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3152 0.63 cIV_C_40_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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