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OPENSEQ.org
cIp_1_40_cIV_3_40
Genes: A B A+B
Length: 455 261 690
Sequences: 2247 2465 297
Seq/Len: 4.94 9.44 0.43
MirrorTree (Pazo et al. 2001) 0.26
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.00
20 0.02 0.00 0.01
100 0.04 0.00 0.04
∞ 0.12 0.00 0.41
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
266_L 43_L 1.26 0.35 0.00
149_I 139_A 1.13 0.26 0.00
441_M 21_A 1.03 0.21 0.00
169_E 52_L 1.02 0.21 0.00
285_V 129_V 1.01 0.20 0.00
320_K 165_I 1.00 0.20 0.00
286_P 238_A 0.98 0.19 0.00
246_C 43_L 0.98 0.19 0.00
130_L 41_A 0.96 0.18 0.00
172_L 198_F 0.96 0.18 0.00
186_V 24_A 0.95 0.17 0.00
170_A 168_L 0.94 0.17 0.00
430_I 32_T 0.94 0.17 0.00
194_A 219_F 0.93 0.16 0.00
43_R 129_V 0.92 0.16 0.00
181_G 228_T 0.92 0.16 0.00
242_S 45_L 0.92 0.16 0.00
104_L 224_M 0.91 0.16 0.00
224_V 209_I 0.91 0.16 0.00
149_I 33_M 0.91 0.16 0.00
194_A 163_L 0.91 0.16 0.00
350_R 65_S 0.90 0.15 0.00
186_V 212_S 0.90 0.15 0.00
65_D 47_L 0.89 0.15 0.00
210_K 219_F 0.89 0.15 0.00
162_V 37_F 0.88 0.15 0.00
228_G 133_N 0.88 0.14 0.00
307_A 19_T 0.88 0.14 0.00
48_L 42_L 0.87 0.14 0.00
238_T 129_V 0.87 0.14 0.00
428_G 131_L 0.87 0.14 0.00
275_H 189_S 0.86 0.14 0.00
44_L 179_S 0.86 0.14 0.00
404_W 101_F 0.86 0.14 0.00
61_L 192_I 0.85 0.13 0.00
61_L 48_L 0.85 0.13 0.00
233_V 237_A 0.84 0.13 0.00
164_I 109_T 0.84 0.13 0.00
116_C 219_F 0.84 0.13 0.00
69_G 65_S 0.84 0.13 0.00
255_G 23_S 0.84 0.13 0.00
201_T 131_L 0.83 0.13 0.00
250_G 26_L 0.83 0.13 0.00
45_K 159_M 0.83 0.13 0.00
173_I 85_L 0.83 0.13 0.00
45_K 164_L 0.83 0.13 0.00
149_I 255_S 0.83 0.13 0.00
292_E 48_L 0.83 0.13 0.00
65_D 175_L 0.82 0.13 0.00
65_D 9_H 0.82 0.12 0.00
45_K 22_L 0.82 0.12 0.00
233_V 253_Y 0.81 0.12 0.00
403_L 178_A 0.81 0.12 0.00
356_K 141_G 0.81 0.12 0.00
130_L 39_S 0.81 0.12 0.00
291_I 210_I 0.81 0.12 0.00
137_G 213_T 0.81 0.12 0.00
63_G 153_E 0.81 0.12 0.00
67_I 238_A 0.80 0.12 0.00
73_T 131_L 0.80 0.12 0.00
202_A 19_T 0.80 0.12 0.00
289_E 126_P 0.80 0.12 0.00
68_L 25_L 0.80 0.12 0.00
285_V 125_N 0.80 0.12 0.00
431_R 32_T 0.80 0.12 0.00
99_G 62_T 0.79 0.12 0.00
249_G 89_S 0.79 0.12 0.00
73_T 153_E 0.79 0.12 0.00
334_V 27_M 0.79 0.12 0.00
248_R 20_G 0.79 0.12 0.00
275_H 223_L 0.79 0.11 0.00
251_T 136_V 0.79 0.11 0.00
344_A 228_T 0.78 0.11 0.00
45_K 27_M 0.78 0.11 0.00
345_V 220_I 0.78 0.11 0.00
64_P 198_F 0.78 0.11 0.00
111_G 65_S 0.78 0.11 0.00
45_K 45_L 0.78 0.11 0.00
256_F 111_Q 0.77 0.11 0.00
318_I 79_L 0.77 0.11 0.00
318_I 193_Y 0.77 0.11 0.00
141_G 174_T 0.77 0.11 0.00
45_K 33_M 0.77 0.11 0.00
48_L 59_R 0.77 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
4165 0.43 cIp_1_40_cIV_3_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4163 0.62 cIp_1_4_cIV_3_2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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