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OPENSEQ.org
cIV_B_2_cI_A_40_Pdenitr
Genes: A B A+B
Length: 252 121 362
Sequences: 4628 493 384
Seq/Len: 18.37 4.07 1.06
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 0.01
2 0.00 0.00 0.04
5 0.00 0.00 0.07
10 0.01 0.00 0.20
20 0.01 0.00 0.25
100 0.02 0.00 0.34
∞ 0.04 0.00 1.03
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
231_V 67_S 1.15 0.49 0.00
117_I 11_I 1.14 0.48 0.00
208_Q 35_R 1.11 0.45 0.00
70_R 67_S 1.04 0.39 0.00
238_K 31_V 1.03 0.38 0.00
87_L 20_A 1.03 0.38 0.00
225_A 86_S 1.02 0.37 0.00
174_V 18_A 1.02 0.37 0.00
45_V 61_V 1.01 0.36 0.00
91_A 11_I 1.01 0.36 0.00
174_V 28_A 1.00 0.35 0.00
176_A 38_D 1.00 0.35 0.00
231_V 35_R 0.99 0.34 0.00
80_I 61_V 0.98 0.33 0.00
43_T 119_E 0.96 0.32 0.00
212_Y 103_A 0.96 0.32 0.00
240_E 107_V 0.95 0.32 0.00
47_I 23_I 0.95 0.32 0.00
77_I 96_W 0.94 0.30 0.00
95_F 94_A 0.91 0.28 0.00
33_W 50_N 0.90 0.28 0.00
10_I 14_F 0.88 0.26 0.00
176_A 31_V 0.88 0.25 0.00
190_V 86_S 0.87 0.25 0.00
83_L 110_A 0.86 0.25 0.00
208_Q 24_V 0.85 0.23 0.00
223_N 77_V 0.84 0.23 0.00
54_L 32_I 0.84 0.23 0.00
172_V 28_A 0.84 0.23 0.00
41_I 119_E 0.83 0.22 0.00
39_L 114_K 0.83 0.22 0.00
212_Y 95_F 0.82 0.22 0.00
110_P 26_I 0.82 0.22 0.00
152_D 77_V 0.82 0.22 0.00
58_V 55_A 0.82 0.22 0.00
116_A 36_N 0.82 0.21 0.00
40_Y 25_L 0.81 0.21 0.00
35_D 104_V 0.81 0.21 0.00
177_T 28_A 0.81 0.21 0.00
245_G 107_V 0.81 0.21 0.00
94_A 93_V 0.80 0.21 0.00
167_G 37_P 0.80 0.20 0.00
29_H 32_I 0.80 0.20 0.00
116_A 83_W 0.79 0.20 0.00
189_A 109_F 0.79 0.20 0.00
174_V 119_E 0.79 0.20 0.00
59_R 78_A 0.78 0.19 0.00
88_I 67_S 0.78 0.19 0.00
61_N 14_F 0.78 0.19 0.00
183_W 19_S 0.77 0.19 0.00
34_L 52_F 0.76 0.18 0.00
189_A 55_A 0.76 0.18 0.00
31_Q 110_A 0.76 0.18 0.00
243_L 35_R 0.76 0.18 0.00
168_K 7_E 0.76 0.18 0.00
206_V 104_V 0.76 0.18 0.00
187_A 22_A 0.76 0.18 0.00
84_V 55_A 0.75 0.18 0.00
201_Q 97_G 0.75 0.17 0.00
176_A 35_R 0.75 0.17 0.00
58_V 119_E 0.75 0.17 0.00
245_G 55_A 0.75 0.17 0.00
86_V 94_A 0.74 0.17 0.00
249_E 63_F 0.74 0.17 0.00
41_I 86_S 0.74 0.17 0.00
34_L 12_L 0.74 0.17 0.00
217_S 6_Q 0.74 0.17 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
3230 8.06 cIV_B_4_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3229 8.65 cIV_B_20_cI_A_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3228 8.14 cIV_B_10_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3227 8.15 cIV_B_20_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3226 0.91 cIV_B_40_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3225 8.81 cIV_B_2_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3224 1.06 cIV_B_2_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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