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OPENSEQ.org
cIp_2_40_cIV_B_40
Genes: A B A+B
Length: 239 298 501
Sequences: 528 2549 147
Seq/Len: 2.21 8.55 0.29
MirrorTree (Pazo et al. 2001) 0.46
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 0.01 0.00
20 0.00 0.01 0.01
100 0.00 0.02 0.01
∞ 0.00 0.06 0.27
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
66_G 191_V 1.43 0.36 0.00
106_A 143_I 1.32 0.30 0.00
177_P 170_K 1.19 0.23 0.00
67_M 104_T 1.19 0.23 0.00
54_S 98_A 1.19 0.23 0.00
102_M 273_A 1.16 0.22 0.00
56_P 121_I 1.16 0.22 0.00
126_A 266_E 1.14 0.21 0.00
142_T 183_Y 1.14 0.21 0.00
68_P 63_L 1.14 0.21 0.00
169_F 54_S 1.14 0.21 0.00
165_L 63_L 1.12 0.20 0.00
61_C 143_I 1.09 0.19 0.00
36_Q 260_V 1.08 0.18 0.00
147_A 124_F 1.07 0.18 0.00
63_D 108_V 1.07 0.18 0.00
132_W 233_F 1.06 0.18 0.00
129_R 190_P 1.06 0.18 0.00
159_V 261_K 1.06 0.18 0.00
53_L 267_K 1.06 0.17 0.00
165_L 83_L 1.05 0.17 0.00
114_K 54_S 1.04 0.17 0.00
16_T 241_Y 1.04 0.17 0.00
167_D 234_S 1.04 0.17 0.00
158_T 168_L 1.04 0.17 0.00
42_V 224_V 1.03 0.17 0.00
16_T 199_V 1.01 0.16 0.00
181_N 199_V 1.01 0.16 0.00
54_S 90_N 1.01 0.15 0.00
21_E 161_V 0.99 0.15 0.00
70_I 203_V 0.97 0.14 0.00
153_F 212_W 0.96 0.14 0.00
109_L 233_F 0.95 0.14 0.00
93_I 205_A 0.94 0.13 0.00
132_W 254_A 0.93 0.13 0.00
106_A 247_E 0.93 0.13 0.00
42_V 267_K 0.92 0.13 0.00
17_P 211_A 0.92 0.13 0.00
53_L 104_T 0.92 0.13 0.00
154_Y 91_R 0.91 0.12 0.00
159_V 63_L 0.91 0.12 0.00
124_L 153_S 0.90 0.12 0.00
179_P 228_I 0.90 0.12 0.00
176_V 44_N 0.90 0.12 0.00
32_E 272_L 0.90 0.12 0.00
147_A 100_F 0.90 0.12 0.00
194_A 79_C 0.89 0.12 0.00
182_G 106_I 0.89 0.12 0.00
72_A 139_P 0.89 0.12 0.00
18_A 119_V 0.88 0.12 0.00
149_I 236_D 0.88 0.12 0.00
82_F 106_I 0.88 0.12 0.00
66_G 197_K 0.88 0.12 0.00
36_Q 119_V 0.88 0.12 0.00
106_A 184_L 0.88 0.12 0.00
160_E 88_R 0.87 0.12 0.00
44_W 90_N 0.87 0.11 0.00
17_P 201_V 0.87 0.11 0.00
57_A 126_L 0.87 0.11 0.00
169_F 75_T 0.87 0.11 0.00
120_E 112_L 0.86 0.11 0.00
72_A 120_A 0.86 0.11 0.00
125_S 202_Q 0.86 0.11 0.00
106_A 90_N 0.86 0.11 0.00
66_G 80_L 0.86 0.11 0.00
123_A 266_E 0.86 0.11 0.00
83_Q 176_A 0.85 0.11 0.00
66_G 86_I 0.85 0.11 0.00
154_Y 50_Q 0.85 0.11 0.00
61_C 231_L 0.85 0.11 0.00
18_A 216_A 0.85 0.11 0.00
159_V 263_V 0.84 0.11 0.00
82_F 120_A 0.84 0.11 0.00
104_C 200_L 0.84 0.10 0.00
80_F 221_Q 0.84 0.10 0.00
66_G 153_S 0.84 0.10 0.00
25_A 113_V 0.83 0.10 0.00
12_S 90_N 0.83 0.10 0.00
169_F 145_A 0.83 0.10 0.00
179_P 104_T 0.83 0.10 0.00
68_P 219_V 0.82 0.10 0.00
116_K 53_S 0.82 0.10 0.00
93_I 105_P 0.82 0.10 0.00
185_S 44_N 0.82 0.10 0.00
63_D 87_V 0.82 0.10 0.00
196_A 72_T 0.82 0.10 0.00
208_V 223_A 0.82 0.10 0.00
168_R 236_D 0.82 0.10 0.00
58_I 195_V 0.81 0.10 0.00
184_F 214_I 0.81 0.10 0.00
109_L 262_A 0.81 0.10 0.00
56_P 60_Q 0.81 0.10 0.00
234_A 161_V 0.81 0.10 0.00
148_Q 212_W 0.81 0.10 0.00
186_A 268_Y 0.81 0.10 0.00
68_P 80_L 0.81 0.10 0.00
134_E 271_W 0.81 0.10 0.00
233_L 89_F 0.81 0.10 0.00
25_A 238_E 0.81 0.10 0.00
94_Q 271_W 0.81 0.10 0.00
197_D 191_V 0.81 0.10 0.00
167_D 63_L 0.80 0.10 0.00
180_Q 124_F 0.80 0.10 0.00
119_P 120_A 0.80 0.10 0.00
176_V 72_T 0.80 0.10 0.00
58_I 41_K 0.80 0.10 0.00
56_P 45_G 0.80 0.10 0.00
25_A 106_I 0.80 0.10 0.00
68_P 88_R 0.80 0.10 0.00
69_Y 211_A 0.80 0.10 0.00
8_I 270_A 0.80 0.10 0.00
28_T 254_A 0.80 0.10 0.00
143_N 232_W 0.79 0.09 0.00
17_P 203_V 0.79 0.09 0.00
217_S 138_D 0.78 0.09 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
4027 0.49 cIp_2_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4026 0.29 cIp_2_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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