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OPENSEQ.org
cIV_B_40_cI_A_40_Pdenitr
Genes: A B A+B
Length: 252 121 362
Sequences: 4089 493 329
Seq/Len: 16.23 4.07 0.91
MirrorTree (Pazo et al. 2001) 0.20
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 0.06
10 0.00 0.00 0.18
20 0.01 0.00 0.24
100 0.01 0.00 0.31
∞ 0.03 0.00 0.88
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
174_V 18_A 1.45 0.70 0.01
231_V 67_S 1.41 0.68 0.01
95_F 94_A 1.33 0.61 0.00
238_K 31_V 1.32 0.60 0.00
117_I 11_I 1.22 0.51 0.00
70_R 67_S 1.20 0.49 0.00
176_A 38_D 1.18 0.47 0.00
33_W 50_N 1.14 0.44 0.00
206_V 104_V 1.14 0.43 0.00
225_A 86_S 1.12 0.42 0.00
80_I 61_V 1.11 0.41 0.00
94_A 13_V 1.08 0.39 0.00
174_V 119_E 1.08 0.39 0.00
170_V 36_N 1.07 0.38 0.00
53_L 55_A 1.05 0.36 0.00
10_I 14_F 1.00 0.32 0.00
231_V 54_D 1.00 0.32 0.00
223_N 77_V 1.00 0.32 0.00
61_N 14_F 0.99 0.31 0.00
116_A 36_N 0.98 0.30 0.00
84_V 31_V 0.97 0.30 0.00
91_A 11_I 0.96 0.29 0.00
84_V 55_A 0.96 0.29 0.00
25_S 24_V 0.95 0.28 0.00
223_N 87_F 0.94 0.27 0.00
38_V 20_A 0.93 0.27 0.00
86_V 94_A 0.93 0.27 0.00
110_P 26_I 0.93 0.26 0.00
168_K 7_E 0.92 0.26 0.00
128_P 77_V 0.92 0.26 0.00
194_A 24_V 0.91 0.25 0.00
208_Q 35_R 0.91 0.25 0.00
90_V 114_K 0.90 0.24 0.00
83_L 110_A 0.89 0.24 0.00
59_R 78_A 0.88 0.23 0.00
174_V 28_A 0.88 0.23 0.00
94_A 93_V 0.87 0.23 0.00
211_V 100_V 0.87 0.23 0.00
31_Q 110_A 0.87 0.23 0.00
134_F 110_A 0.87 0.23 0.00
191_K 63_F 0.87 0.22 0.00
112_L 53_D 0.86 0.22 0.00
100_L 63_F 0.86 0.22 0.00
167_G 37_P 0.86 0.22 0.00
145_A 84_A 0.85 0.22 0.00
117_I 22_A 0.85 0.22 0.00
45_V 89_S 0.85 0.21 0.00
201_Q 72_I 0.84 0.21 0.00
34_L 115_K 0.84 0.21 0.00
116_A 83_W 0.84 0.21 0.00
43_T 119_E 0.84 0.21 0.00
188_F 58_K 0.84 0.21 0.00
109_D 100_V 0.83 0.20 0.00
88_I 67_S 0.83 0.20 0.00
226_Y 66_V 0.83 0.20 0.00
87_L 20_A 0.83 0.20 0.00
102_R 22_A 0.82 0.20 0.00
90_V 27_L 0.82 0.20 0.00
97_L 21_L 0.82 0.20 0.00
133_A 119_E 0.82 0.20 0.00
114_I 19_S 0.82 0.20 0.00
44_A 17_M 0.81 0.19 0.00
55_I 25_L 0.81 0.19 0.00
91_A 61_V 0.81 0.19 0.00
111_D 119_E 0.81 0.19 0.00
190_V 86_S 0.80 0.19 0.00
129_N 33_A 0.80 0.19 0.00
34_L 12_L 0.80 0.19 0.00
225_A 93_V 0.80 0.18 0.00
47_I 77_V 0.79 0.18 0.00
233_A 22_A 0.79 0.18 0.00
177_T 55_A 0.79 0.18 0.00
188_F 97_G 0.79 0.18 0.00
24_S 40_E 0.79 0.18 0.00
157_A 103_A 0.78 0.18 0.00
116_A 71_I 0.78 0.18 0.00
57_I 38_D 0.78 0.17 0.00
67_V 32_I 0.78 0.17 0.00
41_I 86_S 0.78 0.17 0.00
35_D 104_V 0.77 0.17 0.00
70_R 119_E 0.77 0.17 0.00
196_P 65_L 0.77 0.17 0.00
234_V 20_A 0.77 0.17 0.00
89_L 119_E 0.77 0.17 0.00
29_H 32_I 0.76 0.17 0.00
87_L 107_V 0.76 0.17 0.00
34_L 52_F 0.76 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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