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OPENSEQ.org
cIp_2_4_cIV_C_4
Genes: A B A+B
Length: 239 274 505
Sequences: 755 2893 188
Seq/Len: 3.16 10.56 0.37
MirrorTree (Pazo et al. 2001) 0.17
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 0.01 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.00 0.04
∞ 0.04 0.01 0.37
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
21_E 197_A 1.27 0.32 0.00
54_S 192_Y 1.23 0.29 0.00
159_V 19_F 1.11 0.23 0.00
68_P 49_P 1.05 0.20 0.00
166_I 170_K 1.03 0.19 0.00
27_M 167_G 1.03 0.19 0.00
61_C 166_E 1.02 0.19 0.00
60_Y 178_V 1.02 0.18 0.00
52_W 178_V 1.00 0.18 0.00
142_T 58_G 1.00 0.18 0.00
53_L 188_G 0.98 0.17 0.00
20_L 144_I 0.98 0.17 0.00
66_G 20_F 0.98 0.17 0.00
166_I 201_L 0.97 0.17 0.00
51_G 35_W 0.96 0.16 0.00
20_L 180_V 0.95 0.16 0.00
166_I 53_L 0.94 0.16 0.00
111_R 56_L 0.94 0.16 0.00
130_F 136_F 0.94 0.16 0.00
169_F 56_L 0.94 0.15 0.00
160_E 68_A 0.93 0.15 0.00
171_A 11_I 0.93 0.15 0.00
54_S 70_V 0.93 0.15 0.00
68_P 91_F 0.92 0.14 0.00
20_L 197_A 0.91 0.14 0.00
68_P 167_G 0.90 0.14 0.00
196_A 226_I 0.90 0.14 0.00
40_I 23_I 0.90 0.14 0.00
73_L 208_G 0.90 0.14 0.00
126_A 187_T 0.89 0.14 0.00
54_S 76_T 0.88 0.14 0.00
107_E 49_P 0.88 0.13 0.00
110_I 242_Q 0.88 0.13 0.00
158_T 52_F 0.88 0.13 0.00
66_G 3_H 0.88 0.13 0.00
53_L 170_K 0.88 0.13 0.00
175_P 222_I 0.87 0.13 0.00
179_P 59_V 0.87 0.13 0.00
175_P 235_L 0.87 0.13 0.00
93_I 74_G 0.87 0.13 0.00
93_I 171_T 0.87 0.13 0.00
99_T 151_L 0.87 0.13 0.00
77_T 50_W 0.87 0.13 0.00
125_S 169_R 0.86 0.13 0.00
106_A 233_I 0.86 0.13 0.00
158_T 141_L 0.86 0.13 0.00
93_I 181_I 0.85 0.12 0.00
11_D 189_L 0.85 0.12 0.00
95_I 179_A 0.85 0.12 0.00
117_I 105_W 0.85 0.12 0.00
53_L 192_Y 0.84 0.12 0.00
106_A 148_I 0.84 0.12 0.00
95_I 222_I 0.84 0.12 0.00
104_C 91_F 0.83 0.12 0.00
61_C 19_F 0.83 0.12 0.00
7_P 273_G 0.83 0.12 0.00
28_T 188_G 0.82 0.12 0.00
58_I 208_G 0.82 0.12 0.00
186_A 192_Y 0.81 0.11 0.00
80_F 90_G 0.81 0.11 0.00
194_A 68_A 0.81 0.11 0.00
132_W 207_A 0.81 0.11 0.00
150_G 155_A 0.80 0.11 0.00
66_G 2_A 0.80 0.11 0.00
54_S 246_V 0.80 0.11 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
4025 0.22 cIp_2_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4018 0.37 cIp_2_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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