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OPENSEQ.org
cIp_2_4_cIV_B_4
Genes: A B A+B
Length: 239 298 503
Sequences: 755 3243 247
Seq/Len: 3.16 10.88 0.49
MirrorTree (Pazo et al. 2001) 0.24
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 0.01 0.00
20 0.01 0.01 0.01
100 0.01 0.03 0.04
∞ 0.04 0.06 0.46
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
59_E 196_G 1.26 0.37 0.00
54_S 90_N 1.14 0.30 0.00
85_Q 160_G 1.11 0.28 0.00
106_A 143_I 1.09 0.26 0.00
21_E 273_A 1.07 0.25 0.00
17_P 49_F 1.07 0.25 0.00
27_M 241_Y 1.05 0.24 0.00
93_I 235_V 1.04 0.24 0.00
109_L 262_A 0.97 0.20 0.00
169_F 54_S 0.97 0.20 0.00
62_A 141_L 0.94 0.18 0.00
51_G 209_I 0.92 0.17 0.00
69_Y 211_A 0.92 0.17 0.00
171_A 73_A 0.91 0.17 0.00
160_E 88_R 0.91 0.17 0.00
153_F 212_W 0.91 0.17 0.00
103_I 66_F 0.91 0.17 0.00
131_S 268_Y 0.90 0.17 0.00
66_G 266_E 0.90 0.17 0.00
114_K 54_S 0.90 0.16 0.00
77_T 191_V 0.88 0.16 0.00
142_T 183_Y 0.88 0.16 0.00
36_Q 260_V 0.88 0.16 0.00
77_T 267_K 0.87 0.15 0.00
197_D 165_A 0.87 0.15 0.00
194_A 79_C 0.86 0.15 0.00
125_S 190_P 0.86 0.15 0.00
64_L 76_I 0.86 0.15 0.00
40_I 262_A 0.86 0.15 0.00
61_C 211_A 0.86 0.15 0.00
34_R 160_G 0.86 0.15 0.00
165_L 69_Y 0.85 0.15 0.00
121_P 199_V 0.84 0.14 0.00
110_I 266_E 0.83 0.14 0.00
192_P 88_R 0.83 0.14 0.00
177_P 170_K 0.83 0.14 0.00
66_G 153_S 0.83 0.14 0.00
175_P 265_Q 0.82 0.14 0.00
147_A 100_F 0.82 0.14 0.00
71_R 196_G 0.82 0.14 0.00
68_P 63_L 0.82 0.14 0.00
53_L 67_V 0.81 0.13 0.00
64_L 145_A 0.81 0.13 0.00
53_L 212_W 0.80 0.13 0.00
125_S 211_A 0.80 0.13 0.00
77_T 60_Q 0.80 0.13 0.00
67_M 205_A 0.80 0.13 0.00
126_A 237_Q 0.80 0.13 0.00
57_A 254_A 0.80 0.13 0.00
12_S 90_N 0.80 0.13 0.00
66_G 191_V 0.79 0.13 0.00
163_A 108_V 0.79 0.13 0.00
21_E 270_A 0.79 0.12 0.00
169_F 75_T 0.79 0.12 0.00
159_V 261_K 0.79 0.12 0.00
61_C 206_T 0.79 0.12 0.00
112_V 205_A 0.79 0.12 0.00
20_L 120_A 0.79 0.12 0.00
75_V 260_V 0.79 0.12 0.00
110_I 187_T 0.78 0.12 0.00
154_Y 83_L 0.78 0.12 0.00
115_E 97_P 0.78 0.12 0.00
93_I 74_V 0.78 0.12 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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