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OPENSEQ.org
cIV_C_4_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 273 263 515
Sequences: 2888 973 322
Seq/Len: 10.58 3.7 0.63
MirrorTree (Pazo et al. 2001) 0.33
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.00 0.01 0.01
100 0.00 0.01 0.08
∞ 0.01 0.01 0.60
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
27_M 105_R 1.28 0.46 0.00
55_L 137_Y 1.25 0.44 0.00
158_A 130_R 1.25 0.43 0.00
177_V 224_M 1.13 0.34 0.00
37_G 63_G 1.10 0.31 0.00
10_I 213_A 1.06 0.29 0.00
71_N 230_V 1.06 0.29 0.00
25_F 124_S 1.04 0.28 0.00
19_F 105_R 1.04 0.28 0.00
228_F 256_I 1.04 0.27 0.00
237_G 43_D 1.03 0.27 0.00
179_V 86_R 1.01 0.25 0.00
70_V 141_L 1.00 0.25 0.00
262_L 227_R 1.00 0.25 0.00
234_L 125_L 1.00 0.25 0.00
226_F 227_R 0.98 0.24 0.00
268_I 156_A 0.97 0.24 0.00
225_I 63_G 0.97 0.23 0.00
25_F 235_V 0.95 0.22 0.00
262_L 154_I 0.95 0.22 0.00
267_V 214_A 0.94 0.22 0.00
31_A 86_R 0.93 0.21 0.00
211_M 126_M 0.93 0.21 0.00
135_F 167_E 0.93 0.21 0.00
146_L 97_P 0.93 0.21 0.00
98_V 256_I 0.93 0.21 0.00
25_F 202_P 0.93 0.21 0.00
18_F 49_R 0.92 0.20 0.00
29_T 244_L 0.91 0.20 0.00
34_W 214_A 0.91 0.20 0.00
203_T 237_F 0.91 0.20 0.00
175_L 119_M 0.90 0.19 0.00
166_G 239_I 0.90 0.19 0.00
64_G 101_E 0.89 0.19 0.00
203_T 88_Y 0.89 0.19 0.00
21_A 207_Q 0.89 0.19 0.00
147_I 235_V 0.88 0.18 0.00
29_T 43_D 0.88 0.18 0.00
171_T 249_N 0.88 0.18 0.00
64_G 246_Y 0.88 0.18 0.00
29_T 86_R 0.87 0.18 0.00
265_F 250_K 0.87 0.18 0.00
88_Y 250_K 0.85 0.17 0.00
266_V 240_V 0.85 0.17 0.00
60_Y 130_R 0.85 0.17 0.00
169_K 241_L 0.84 0.17 0.00
250_A 177_A 0.84 0.17 0.00
18_F 177_A 0.84 0.16 0.00
237_G 244_L 0.84 0.16 0.00
190_A 254_Q 0.84 0.16 0.00
152_G 72_L 0.83 0.16 0.00
210_Y 122_D 0.83 0.16 0.00
21_A 203_A 0.83 0.16 0.00
19_F 63_G 0.83 0.16 0.00
140_L 43_D 0.82 0.16 0.00
187_G 256_I 0.82 0.16 0.00
23_G 130_R 0.82 0.16 0.00
28_L 249_N 0.81 0.15 0.00
222_I 217_M 0.81 0.15 0.00
83_R 154_I 0.81 0.15 0.00
146_L 216_L 0.81 0.15 0.00
246_G 238_L 0.81 0.15 0.00
138_W 65_R 0.81 0.15 0.00
13_P 218_W 0.80 0.15 0.00
226_F 186_M 0.80 0.15 0.00
10_I 65_R 0.80 0.15 0.00
49_W 85_V 0.80 0.15 0.00
245_V 165_E 0.79 0.15 0.00
71_N 200_G 0.79 0.14 0.00
58_V 229_Q 0.79 0.14 0.00
34_W 46_Q 0.79 0.14 0.00
208_A 148_I 0.79 0.14 0.00
31_A 131_A 0.79 0.14 0.00
120_S 71_T 0.79 0.14 0.00
190_A 205_V 0.79 0.14 0.00
109_I 131_A 0.79 0.14 0.00
262_L 124_S 0.79 0.14 0.00
262_L 244_L 0.79 0.14 0.00
29_T 102_D 0.79 0.14 0.00
152_G 80_L 0.79 0.14 0.00
263_F 64_L 0.79 0.14 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
3142 0.63 cIV_C_4_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3137 0.26 cIV_C_60_cIII_cyt1_60_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3136 0.26 cIV_C_60_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3135 0.34 cIV_C_40_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3134 0.26 cIV_C_40_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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