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OPENSEQ.org
cIV_C_4_cIII_isp_4_Pdenitr
Genes: A B A+B
Length: 273 190 452
Sequences: 2888 1692 377
Seq/Len: 10.58 8.91 0.83
MirrorTree (Pazo et al. 2001) 0.36
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 0.02
5 0.00 0.01 0.02
10 0.00 0.01 0.03
20 0.00 0.01 0.03
100 0.00 0.01 0.14
∞ 0.01 0.05 0.81
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
184_C 176_I 1.18 0.45 0.00
107_A 72_L 1.09 0.37 0.00
188_L 34_A 1.04 0.33 0.00
146_L 43_N 1.02 0.31 0.00
22_I 87_Q 1.01 0.31 0.00
164_L 25_G 0.99 0.29 0.00
111_N 129_I 0.98 0.28 0.00
9_Q 166_R 0.97 0.28 0.00
171_T 67_L 0.97 0.28 0.00
268_I 26_A 0.94 0.26 0.00
62_M 184_D 0.94 0.26 0.00
109_I 23_T 0.93 0.25 0.00
143_I 84_D 0.93 0.25 0.00
127_W 71_W 0.93 0.25 0.00
197_A 28_T 0.92 0.25 0.00
197_A 186_T 0.92 0.25 0.00
91_I 28_T 0.92 0.24 0.00
187_G 189_L 0.90 0.23 0.00
177_V 186_T 0.89 0.22 0.00
234_L 67_L 0.88 0.22 0.00
143_I 32_G 0.88 0.22 0.00
18_F 34_A 0.88 0.22 0.00
130_E 183_D 0.87 0.21 0.00
180_I 94_L 0.87 0.21 0.00
207_G 167_R 0.87 0.21 0.00
155_V 61_V 0.87 0.21 0.00
201_A 98_I 0.86 0.21 0.00
225_I 62_E 0.86 0.21 0.00
194_S 78_I 0.85 0.20 0.00
210_Y 19_L 0.85 0.20 0.00
104_W 41_Q 0.84 0.20 0.00
204_V 30_A 0.84 0.20 0.00
210_Y 34_A 0.82 0.19 0.00
199_G 62_E 0.82 0.18 0.00
210_Y 66_Q 0.81 0.18 0.00
184_C 87_Q 0.81 0.18 0.00
251_A 187_I 0.81 0.18 0.00
228_F 32_G 0.81 0.18 0.00
177_V 162_S 0.80 0.18 0.00
12_P 32_G 0.80 0.18 0.00
62_M 74_K 0.80 0.18 0.00
225_I 31_A 0.80 0.17 0.00
187_G 83_E 0.80 0.17 0.00
22_I 83_E 0.79 0.17 0.00
116_M 47_D 0.78 0.17 0.00
102_V 151_F 0.78 0.17 0.00
25_F 87_Q 0.78 0.16 0.00
21_A 9_G 0.78 0.16 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
3153 0.83 cIV_C_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3152 0.63 cIV_C_40_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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