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OPENSEQ.org
cIV_C_4_cI_A_40_Pdenitr
Genes: A B A+B
Length: 273 121 382
Sequences: 2888 493 331
Seq/Len: 10.58 4.07 0.87
MirrorTree (Pazo et al. 2001) 0.14
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 0.03
2 0.00 0.00 0.04
5 0.00 0.00 0.10
10 0.00 0.00 0.19
20 0.00 0.00 0.25
100 0.00 0.00 0.31
∞ 0.01 0.00 0.84
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
137_P 4_L 1.36 0.62 0.00
184_C 62_R 1.27 0.54 0.00
210_Y 8_Y 1.26 0.53 0.00
138_W 33_A 1.21 0.48 0.00
29_T 28_A 1.20 0.48 0.00
88_Y 53_D 1.19 0.47 0.00
154_A 14_F 1.17 0.46 0.00
146_L 107_V 1.16 0.45 0.00
218_A 72_I 1.16 0.44 0.00
87_Q 54_D 1.13 0.41 0.00
208_A 18_A 1.11 0.40 0.00
175_L 40_E 1.11 0.40 0.00
36_K 21_L 1.10 0.40 0.00
109_I 98_L 1.09 0.38 0.00
270_I 62_R 1.09 0.38 0.00
85_G 29_A 1.07 0.37 0.00
19_F 28_A 1.07 0.36 0.00
150_L 110_A 1.06 0.36 0.00
150_L 15_L 1.03 0.34 0.00
182_G 58_K 1.02 0.33 0.00
120_S 20_A 1.01 0.32 0.00
266_V 12_L 1.01 0.32 0.00
83_R 67_S 1.01 0.32 0.00
71_N 20_A 1.01 0.32 0.00
210_Y 22_A 1.01 0.32 0.00
237_G 10_P 1.01 0.32 0.00
204_V 109_F 1.01 0.32 0.00
63_F 119_E 1.00 0.31 0.00
238_Q 71_I 1.00 0.31 0.00
143_I 104_V 1.00 0.31 0.00
231_L 26_I 1.00 0.31 0.00
266_V 79_F 0.99 0.30 0.00
179_V 15_L 0.99 0.30 0.00
51_F 87_F 0.98 0.30 0.00
268_I 43_S 0.98 0.29 0.00
237_G 84_A 0.97 0.29 0.00
140_L 10_P 0.97 0.29 0.00
58_V 104_V 0.96 0.28 0.00
13_P 95_F 0.96 0.28 0.00
239_M 84_A 0.95 0.27 0.00
18_F 78_A 0.95 0.27 0.00
179_V 27_L 0.95 0.27 0.00
180_I 31_V 0.95 0.27 0.00
121_P 10_P 0.93 0.26 0.00
228_F 20_A 0.93 0.26 0.00
180_I 110_A 0.93 0.26 0.00
150_L 27_L 0.93 0.26 0.00
71_N 40_E 0.92 0.25 0.00
55_L 67_S 0.92 0.25 0.00
243_Q 104_V 0.92 0.25 0.00
98_V 100_V 0.91 0.25 0.00
133_V 84_A 0.91 0.24 0.00
99_M 71_I 0.91 0.24 0.00
54_G 110_A 0.91 0.24 0.00
130_E 31_V 0.90 0.24 0.00
58_V 16_G 0.90 0.24 0.00
237_G 51_A 0.90 0.24 0.00
126_V 17_M 0.90 0.24 0.00
228_F 11_I 0.89 0.23 0.00
169_K 93_V 0.89 0.23 0.00
75_T 93_V 0.89 0.23 0.00
142_L 7_E 0.88 0.23 0.00
154_A 23_I 0.88 0.23 0.00
50_M 9_L 0.88 0.23 0.00
155_V 62_R 0.88 0.23 0.00
187_G 23_I 0.88 0.22 0.00
50_M 24_V 0.87 0.22 0.00
204_V 36_N 0.87 0.22 0.00
63_F 11_I 0.87 0.22 0.00
49_W 90_L 0.87 0.22 0.00
211_M 88_A 0.87 0.22 0.00
70_V 23_I 0.87 0.22 0.00
231_L 12_L 0.87 0.22 0.00
245_V 11_I 0.86 0.22 0.00
176_I 20_A 0.86 0.22 0.00
60_Y 26_I 0.86 0.22 0.00
147_I 93_V 0.86 0.22 0.00
57_G 109_F 0.86 0.21 0.00
164_L 77_V 0.85 0.21 0.00
4_K 78_A 0.85 0.21 0.00
8_Y 36_N 0.85 0.21 0.00
63_F 107_V 0.85 0.21 0.00
243_Q 99_M 0.85 0.21 0.00
115_P 21_L 0.85 0.21 0.00
95_M 15_L 0.85 0.21 0.00
250_A 106_T 0.84 0.20 0.00
32_V 19_S 0.84 0.20 0.00
79_T 63_F 0.84 0.20 0.00
137_P 24_V 0.84 0.20 0.00
26_V 12_L 0.84 0.20 0.00
236_K 12_L 0.84 0.20 0.00
21_A 67_S 0.83 0.20 0.00
118_P 32_I 0.83 0.20 0.00
70_V 36_N 0.83 0.19 0.00
200_L 10_P 0.82 0.19 0.00
110_K 29_A 0.82 0.19 0.00
25_F 31_V 0.82 0.19 0.00
252_W 83_W 0.82 0.19 0.00
140_L 66_V 0.82 0.19 0.00
157_W 43_S 0.81 0.19 0.00
60_Y 24_V 0.81 0.19 0.00
19_F 31_V 0.81 0.19 0.00
150_L 26_I 0.81 0.19 0.00
21_A 30_A 0.81 0.19 0.00
98_V 30_A 0.80 0.18 0.00
197_A 42_V 0.80 0.18 0.00
146_L 117_A 0.80 0.18 0.00
10_I 36_N 0.79 0.18 0.00
195_H 10_P 0.79 0.18 0.00
60_Y 119_E 0.79 0.18 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
3161 6.49 cIV_C_2_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
3160 6.88 cIV_C_4_cI_A_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.91 Done - Shared
3159 6.47 cIV_C_6_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
3158 0.87 cIV_C_4_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3157 6.47 cIV_C_4_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
3156 7.13 cIV_C_4_cI_A_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
3155 7.16 cIV_C_4_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
3154 0.82 cIV_C_40_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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