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OPENSEQ.org
cIp_2_4_cIV_2_4
Genes: A B A+B
Length: 249 227 428
Sequences: 509 5082 148
Seq/Len: 2.04 22.39 0.35
MirrorTree (Pazo et al. 2001) 0.13
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 0.03
∞ 0.00 0.04 0.31
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
76_A 211_L 1.51 0.47 0.00
61_K 144_L 1.08 0.21 0.00
148_I 213_L 1.05 0.19 0.00
93_L 176_P 1.04 0.19 0.00
61_K 224_V 1.03 0.18 0.00
107_V 59_Q 1.03 0.18 0.00
193_Y 97_I 1.02 0.18 0.00
192_Y 163_W 1.00 0.17 0.00
101_V 162_S 1.00 0.17 0.00
181_V 134_R 0.98 0.17 0.00
132_I 125_P 0.96 0.16 0.00
65_A 61_M 0.96 0.15 0.00
214_P 147_E 0.94 0.15 0.00
115_V 95_L 0.94 0.15 0.00
186_V 79_P 0.94 0.15 0.00
155_K 56_S 0.94 0.15 0.00
145_S 97_I 0.94 0.15 0.00
48_N 167_T 0.93 0.14 0.00
208_L 95_L 0.93 0.14 0.00
112_V 192_Y 0.92 0.14 0.00
220_S 224_V 0.91 0.14 0.00
169_F 82_R 0.91 0.14 0.00
141_M 148_A 0.90 0.14 0.00
186_V 55_I 0.89 0.13 0.00
130_Y 131_G 0.88 0.13 0.00
94_P 6_Q 0.88 0.13 0.00
218_P 219_F 0.88 0.13 0.00
225_C 99_S 0.88 0.13 0.00
48_N 221_M 0.88 0.13 0.00
123_N 131_G 0.87 0.13 0.00
155_K 112_D 0.86 0.12 0.00
186_V 45_A 0.85 0.12 0.00
143_R 180_N 0.85 0.12 0.00
99_N 147_E 0.84 0.12 0.00
76_A 187_T 0.84 0.12 0.00
221_G 61_M 0.84 0.12 0.00
235_T 36_F 0.83 0.11 0.00
154_K 156_S 0.83 0.11 0.00
145_S 39_L 0.83 0.11 0.00
193_Y 47_T 0.82 0.11 0.00
169_F 127_F 0.82 0.11 0.00
108_P 32_F 0.81 0.11 0.00
56_T 60_E 0.81 0.11 0.00
206_D 44_L 0.80 0.11 0.00
147_S 154_I 0.80 0.11 0.00
127_V 188_R 0.80 0.11 0.00
218_P 224_V 0.80 0.11 0.00
164_T 162_S 0.79 0.10 0.00
94_P 61_M 0.79 0.10 0.00
94_P 169_G 0.78 0.10 0.00
198_A 211_L 0.78 0.10 0.00
208_L 93_P 0.78 0.10 0.00
233_S 42_L 0.78 0.10 0.00
145_S 218_I 0.77 0.10 0.00
155_K 144_L 0.77 0.10 0.00
159_K 188_R 0.77 0.10 0.00
236_E 72_I 0.77 0.10 0.00
102_A 93_P 0.77 0.10 0.00
64_E 219_F 0.77 0.10 0.00
145_S 215_P 0.77 0.10 0.00
142_L 223_P 0.77 0.10 0.00
181_V 150_I 0.76 0.10 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
4181 0.35 cIp_2_4_cIV_2_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4180 0.47 cIp_2_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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