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OPENSEQ.org
cIp_3_40_cIV_3_40
Genes: A B A+B
Length: 727 261 945
Sequences: 1907 2465 352
Seq/Len: 2.62 9.44 0.37
MirrorTree (Pazo et al. 2001) 0.29
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 0.01 0.00 0.01
10 0.01 0.00 0.01
20 0.01 0.00 0.02
100 0.03 0.00 0.05
∞ 0.09 0.00 0.36
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
36_V 258_W 1.40 0.40 0.00
251_I 35_F 1.35 0.37 0.00
259_S 53_T 1.35 0.37 0.00
98_K 23_S 1.30 0.34 0.00
102_I 31_L 1.28 0.32 0.00
195_L 192_I 1.20 0.28 0.00
49_V 27_M 1.19 0.27 0.00
326_V 168_L 1.17 0.26 0.00
429_V 179_S 1.16 0.26 0.00
630_A 62_T 1.10 0.22 0.00
57_G 199_V 1.08 0.21 0.00
35_F 198_F 1.04 0.20 0.00
106_S 256_I 1.03 0.19 0.00
206_V 23_S 1.03 0.19 0.00
622_I 174_T 1.02 0.19 0.00
593_S 167_I 1.01 0.18 0.00
217_E 166_T 1.00 0.18 0.00
403_V 19_T 0.99 0.18 0.00
654_V 47_L 0.99 0.17 0.00
567_I 154_N 0.99 0.17 0.00
99_G 191_G 0.98 0.17 0.00
211_E 12_K 0.98 0.17 0.00
384_N 132_L 0.98 0.17 0.00
242_P 155_N 0.98 0.17 0.00
153_F 91_V 0.98 0.17 0.00
468_E 228_T 0.97 0.17 0.00
217_E 143_S 0.96 0.16 0.00
456_A 126_P 0.96 0.16 0.00
174_T 18_L 0.96 0.16 0.00
41_V 26_L 0.96 0.16 0.00
384_N 123_P 0.95 0.16 0.00
588_A 31_L 0.94 0.16 0.00
642_V 217_I 0.94 0.16 0.00
307_V 25_L 0.94 0.15 0.00
165_I 20_G 0.94 0.15 0.00
536_A 171_L 0.93 0.15 0.00
217_E 83_M 0.93 0.15 0.00
37_D 172_Y 0.92 0.15 0.00
352_V 159_M 0.92 0.15 0.00
317_T 42_L 0.92 0.15 0.00
579_I 167_I 0.92 0.15 0.00
100_W 97_F 0.91 0.14 0.00
474_V 256_I 0.91 0.14 0.00
575_V 43_L 0.91 0.14 0.00
105_N 26_L 0.90 0.14 0.00
552_G 213_T 0.90 0.14 0.00
115_G 162_A 0.89 0.14 0.00
567_I 210_I 0.89 0.14 0.00
701_S 97_F 0.89 0.14 0.00
268_G 32_T 0.89 0.14 0.00
491_A 198_F 0.89 0.14 0.00
499_K 195_S 0.89 0.14 0.00
706_T 200_A 0.88 0.14 0.00
335_G 154_N 0.88 0.13 0.00
261_I 162_A 0.88 0.13 0.00
213_M 237_A 0.88 0.13 0.00
311_K 182_F 0.88 0.13 0.00
346_V 95_A 0.88 0.13 0.00
421_S 65_S 0.88 0.13 0.00
31_L 189_S 0.87 0.13 0.00
545_L 198_F 0.87 0.13 0.00
609_A 160_I 0.87 0.13 0.00
560_L 96_G 0.87 0.13 0.00
153_F 18_L 0.87 0.13 0.00
189_I 129_V 0.86 0.13 0.00
459_S 62_T 0.86 0.13 0.00
428_K 25_L 0.86 0.13 0.00
106_S 25_L 0.86 0.13 0.00
352_V 154_N 0.86 0.13 0.00
270_V 192_I 0.86 0.13 0.00
49_V 136_V 0.85 0.12 0.00
169_V 220_I 0.85 0.12 0.00
286_I 60_D 0.85 0.12 0.00
107_E 26_L 0.85 0.12 0.00
98_K 53_T 0.85 0.12 0.00
250_S 176_L 0.85 0.12 0.00
41_V 189_S 0.85 0.12 0.00
199_G 23_S 0.85 0.12 0.00
286_I 209_I 0.85 0.12 0.00
73_G 133_N 0.85 0.12 0.00
641_Q 234_G 0.84 0.12 0.00
681_A 171_L 0.84 0.12 0.00
259_S 192_I 0.84 0.12 0.00
496_I 206_L 0.84 0.12 0.00
34_V 19_T 0.83 0.12 0.00
225_I 162_A 0.83 0.12 0.00
88_V 30_G 0.83 0.12 0.00
286_I 229_S 0.83 0.12 0.00
120_L 145_T 0.83 0.12 0.00
434_S 61_V 0.83 0.12 0.00
391_I 132_L 0.83 0.12 0.00
206_V 206_L 0.83 0.12 0.00
146_F 191_G 0.82 0.12 0.00
352_V 62_T 0.82 0.12 0.00
644_N 213_T 0.82 0.11 0.00
616_A 126_P 0.81 0.11 0.00
287_S 239_A 0.81 0.11 0.00
617_R 196_T 0.81 0.11 0.00
628_E 114_G 0.81 0.11 0.00
401_L 49_T 0.81 0.11 0.00
331_Q 171_L 0.81 0.11 0.00
447_D 192_I 0.81 0.11 0.00
98_K 167_I 0.80 0.11 0.00
35_F 196_T 0.80 0.11 0.00
460_H 210_I 0.80 0.11 0.00
111_K 238_A 0.80 0.11 0.00
646_L 167_I 0.80 0.11 0.00
338_V 12_K 0.80 0.11 0.00
640_D 25_L 0.80 0.11 0.00
97_M 195_S 0.80 0.11 0.00
466_L 193_Y 0.80 0.11 0.00
49_V 21_A 0.80 0.11 0.00
222_I 210_I 0.80 0.11 0.00
384_N 231_H 0.80 0.11 0.00
622_I 210_I 0.80 0.11 0.00
628_E 126_P 0.80 0.11 0.00
222_I 206_L 0.80 0.11 0.00
382_R 168_L 0.80 0.11 0.00
189_I 14_S 0.80 0.11 0.00
102_I 34_W 0.80 0.11 0.00
32_I 23_S 0.80 0.11 0.00
502_M 22_L 0.79 0.11 0.00
55_K 192_I 0.79 0.11 0.00
315_T 154_N 0.79 0.11 0.00
171_T 253_Y 0.79 0.11 0.00
251_I 199_V 0.79 0.11 0.00
574_D 23_S 0.79 0.11 0.00
333_F 25_L 0.79 0.11 0.00
153_F 84_I 0.79 0.11 0.00
292_F 23_S 0.79 0.10 0.00
429_V 171_L 0.79 0.10 0.00
318_S 124_L 0.78 0.10 0.00
45_P 34_W 0.78 0.10 0.00
102_I 21_A 0.78 0.10 0.00
259_S 196_T 0.78 0.10 0.00
97_M 168_L 0.78 0.10 0.00
52_A 25_L 0.78 0.10 0.00
50_L 256_I 0.78 0.10 0.00
324_S 175_L 0.78 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
4189 0.45 cIp_3_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4188 0.37 cIp_3_40_cIV_3_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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