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OPENSEQ.org
cIp_2_4_cIV_3_4
Genes: A B A+B
Length: 249 261 465
Sequences: 509 2963 118
Seq/Len: 2.04 11.35 0.25
MirrorTree (Pazo et al. 2001) 0.10
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.02
∞ 0.00 0.01 0.23
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
101_V 198_F 1.67 0.48 0.00
51_T 176_L 1.44 0.34 0.00
106_Q 19_T 1.42 0.32 0.00
226_E 32_T 1.36 0.29 0.00
169_F 124_L 1.34 0.28 0.00
145_S 220_I 1.34 0.28 0.00
218_P 165_I 1.27 0.25 0.00
220_S 20_G 1.23 0.23 0.00
165_P 174_T 1.18 0.20 0.00
169_F 50_N 1.17 0.20 0.00
181_V 49_T 1.17 0.20 0.00
120_T 28_T 1.17 0.20 0.00
136_T 7_A 1.12 0.18 0.00
155_K 10_M 1.11 0.18 0.00
218_P 47_L 1.11 0.18 0.00
189_N 143_S 1.10 0.17 0.00
143_R 83_M 1.09 0.17 0.00
139_P 83_M 1.09 0.17 0.00
120_T 83_M 1.07 0.17 0.00
72_E 127_L 1.07 0.16 0.00
120_T 10_M 1.07 0.16 0.00
204_I 41_A 1.07 0.16 0.00
136_T 258_W 1.07 0.16 0.00
106_Q 2_T 1.06 0.16 0.00
236_E 121_I 1.05 0.16 0.00
218_P 176_L 1.05 0.16 0.00
108_P 122_T 1.03 0.15 0.00
120_T 15_P 1.02 0.15 0.00
215_K 187_T 1.02 0.15 0.00
82_V 259_W 1.01 0.14 0.00
205_I 157_N 1.00 0.14 0.00
202_E 196_T 1.00 0.14 0.00
206_D 198_F 1.00 0.14 0.00
98_M 195_S 0.99 0.14 0.00
181_V 39_S 0.99 0.14 0.00
108_P 18_L 0.99 0.14 0.00
214_P 209_I 0.99 0.14 0.00
170_T 97_F 0.99 0.14 0.00
54_D 25_L 0.99 0.14 0.00
197_T 18_L 0.99 0.14 0.00
205_I 42_L 0.98 0.14 0.00
142_L 116_W 0.98 0.14 0.00
192_Y 78_G 0.98 0.13 0.00
224_S 47_L 0.98 0.13 0.00
219_R 259_W 0.98 0.13 0.00
101_V 18_L 0.97 0.13 0.00
214_P 73_P 0.97 0.13 0.00
101_V 153_E 0.96 0.13 0.00
120_T 166_T 0.96 0.13 0.00
94_P 76_Q 0.96 0.13 0.00
80_L 22_L 0.96 0.13 0.00
76_A 206_L 0.94 0.12 0.00
108_P 226_H 0.94 0.12 0.00
130_Y 40_M 0.93 0.12 0.00
155_K 175_L 0.92 0.12 0.00
91_G 34_W 0.92 0.12 0.00
143_R 15_P 0.92 0.12 0.00
231_L 261_S 0.92 0.12 0.00
50_D 96_G 0.91 0.12 0.00
97_A 96_G 0.91 0.12 0.00
112_V 101_F 0.90 0.11 0.00
226_E 118_P 0.90 0.11 0.00
101_V 139_A 0.90 0.11 0.00
120_T 116_W 0.89 0.11 0.00
72_E 40_M 0.89 0.11 0.00
93_L 190_D 0.88 0.11 0.00
162_E 160_I 0.88 0.11 0.00
56_T 50_N 0.88 0.11 0.00
197_T 43_L 0.88 0.11 0.00
228_A 142_V 0.88 0.11 0.00
204_I 176_L 0.88 0.11 0.00
94_P 56_Q 0.88 0.11 0.00
80_L 210_I 0.87 0.11 0.00
153_Q 68_Q 0.87 0.10 0.00
202_E 105_S 0.87 0.10 0.00
205_I 188_I 0.87 0.10 0.00
145_S 179_S 0.86 0.10 0.00
95_I 158_Q 0.86 0.10 0.00
203_E 171_L 0.86 0.10 0.00
233_S 61_V 0.86 0.10 0.00
229_G 3_H 0.85 0.10 0.00
189_N 49_T 0.85 0.10 0.00
171_L 194_G 0.85 0.10 0.00
214_P 70_H 0.85 0.10 0.00
204_I 123_P 0.85 0.10 0.00
94_P 179_S 0.84 0.10 0.00
156_L 194_G 0.84 0.10 0.00
120_T 143_S 0.83 0.10 0.00
59_N 259_W 0.83 0.10 0.00
121_M 132_L 0.83 0.10 0.00
122_Y 22_L 0.83 0.10 0.00
198_A 178_A 0.83 0.10 0.00
123_N 27_M 0.83 0.10 0.00
156_L 97_F 0.82 0.09 0.00
205_I 216_T 0.82 0.09 0.00
123_N 43_L 0.82 0.09 0.00
143_R 166_T 0.82 0.09 0.00
170_T 195_S 0.82 0.09 0.00
91_G 22_L 0.82 0.09 0.00
228_A 230_K 0.81 0.09 0.00
143_R 107_A 0.81 0.09 0.00
143_R 143_S 0.81 0.09 0.00
149_L 258_W 0.81 0.09 0.00
108_P 55_Y 0.81 0.09 0.00
131_H 5_S 0.81 0.09 0.00
120_T 11_V 0.81 0.09 0.00
201_I 193_Y 0.81 0.09 0.00
132_I 168_L 0.81 0.09 0.00
94_P 68_Q 0.81 0.09 0.00
121_M 85_L 0.81 0.09 0.00
208_L 47_L 0.80 0.09 0.00
109_P 190_D 0.80 0.09 0.00
189_N 61_V 0.80 0.09 0.00
132_I 174_T 0.80 0.09 0.00
186_V 111_Q 0.80 0.09 0.00
228_A 154_N 0.80 0.09 0.00
109_P 97_F 0.80 0.09 0.00
74_H 129_V 0.80 0.09 0.00
72_E 6_H 0.80 0.09 0.00
131_H 23_S 0.79 0.09 0.00
181_V 198_F 0.79 0.09 0.00
208_L 36_H 0.79 0.09 0.00
57_P 47_L 0.79 0.09 0.00
69_N 132_L 0.79 0.09 0.00
75_K 39_S 0.79 0.09 0.00
76_A 209_I 0.78 0.09 0.00
150_E 47_L 0.78 0.09 0.00
113_Y 195_S 0.78 0.09 0.00
66_I 256_I 0.78 0.09 0.00
202_E 233_F 0.78 0.09 0.00
170_T 43_L 0.78 0.09 0.00
141_M 124_L 0.78 0.09 0.00
208_L 20_G 0.78 0.09 0.00
129_K 83_M 0.78 0.09 0.00
231_L 66_T 0.78 0.08 0.00
147_S 124_L 0.78 0.08 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
4187 0.22 cIp_2_40_cIV_3_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4184 0.25 cIp_2_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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