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OPENSEQ.org
cIV_C_4_cI_N_60_1_Pdenitr
Genes: A B A+B
Length: 273 499 727
Sequences: 2888 1133 349
Seq/Len: 10.58 2.27 0.48
MirrorTree (Pazo et al. 2001) 0.25
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 0.02
2 0.00 0.00 0.02
5 0.00 0.00 0.04
10 0.00 0.00 0.09
20 0.00 0.02 0.10
100 0.00 0.03 0.14
∞ 0.01 0.03 0.45
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
211_M 342_I 1.50 0.55 0.00
56_V 424_I 1.38 0.46 0.00
188_L 150_S 1.25 0.36 0.00
146_L 234_S 1.24 0.35 0.00
125_G 425_V 1.22 0.34 0.00
234_L 234_S 1.20 0.33 0.00
204_V 374_V 1.20 0.33 0.00
166_G 424_I 1.16 0.30 0.00
25_F 67_M 1.12 0.28 0.00
23_G 115_L 1.11 0.27 0.00
241_Q 245_A 1.11 0.27 0.00
18_F 341_F 1.08 0.26 0.00
51_F 43_V 1.08 0.25 0.00
231_L 110_V 1.06 0.24 0.00
190_A 110_V 1.06 0.24 0.00
30_G 288_G 1.05 0.24 0.00
143_I 42_T 1.03 0.23 0.00
268_I 304_A 1.03 0.23 0.00
127_W 414_S 1.02 0.22 0.00
175_L 398_A 1.02 0.22 0.00
91_I 422_L 1.01 0.22 0.00
95_M 124_G 1.00 0.21 0.00
222_I 306_M 1.00 0.21 0.00
179_V 203_V 0.99 0.21 0.00
179_V 126_L 0.99 0.20 0.00
51_F 139_A 0.98 0.20 0.00
172_I 82_L 0.98 0.20 0.00
225_I 401_A 0.97 0.20 0.00
31_A 358_L 0.97 0.20 0.00
207_G 18_Y 0.97 0.20 0.00
107_A 411_V 0.97 0.20 0.00
107_A 127_L 0.97 0.20 0.00
204_V 127_L 0.96 0.19 0.00
165_E 281_M 0.96 0.19 0.00
241_Q 278_V 0.95 0.19 0.00
234_L 221_V 0.94 0.18 0.00
183_V 47_L 0.94 0.18 0.00
222_I 416_I 0.94 0.18 0.00
135_F 131_M 0.93 0.18 0.00
26_V 287_A 0.93 0.18 0.00
50_M 79_V 0.93 0.18 0.00
135_F 46_F 0.93 0.18 0.00
19_F 277_A 0.93 0.17 0.00
7_D 205_F 0.93 0.17 0.00
25_F 342_I 0.92 0.17 0.00
56_V 412_I 0.92 0.17 0.00
225_I 205_F 0.92 0.17 0.00
186_T 260_D 0.92 0.17 0.00
178_A 426_Y 0.92 0.17 0.00
21_A 111_A 0.91 0.17 0.00
235_L 360_R 0.91 0.17 0.00
245_V 416_I 0.91 0.17 0.00
125_G 169_G 0.91 0.17 0.00
266_V 345_M 0.90 0.17 0.00
167_D 379_L 0.90 0.17 0.00
150_L 120_M 0.90 0.17 0.00
166_G 370_L 0.90 0.16 0.00
68_D 419_F 0.89 0.16 0.00
153_V 83_V 0.89 0.16 0.00
57_G 74_S 0.89 0.16 0.00
108_F 242_F 0.89 0.16 0.00
195_H 145_A 0.89 0.16 0.00
180_I 364_T 0.89 0.16 0.00
26_V 252_A 0.89 0.16 0.00
7_D 379_L 0.89 0.16 0.00
18_F 19_A 0.88 0.16 0.00
73_G 336_I 0.88 0.15 0.00
59_L 294_I 0.88 0.15 0.00
158_A 249_A 0.88 0.15 0.00
22_I 41_V 0.88 0.15 0.00
61_V 308_F 0.88 0.15 0.00
121_P 243_A 0.87 0.15 0.00
106_W 26_G 0.87 0.15 0.00
236_K 189_G 0.87 0.15 0.00
161_A 281_M 0.87 0.15 0.00
210_Y 261_A 0.87 0.15 0.00
143_I 131_M 0.87 0.15 0.00
146_L 73_F 0.87 0.15 0.00
238_Q 417_G 0.86 0.15 0.00
200_L 337_G 0.86 0.15 0.00
138_W 210_M 0.86 0.15 0.00
179_V 38_L 0.86 0.15 0.00
140_L 409_L 0.86 0.15 0.00
122_I 131_M 0.86 0.15 0.00
177_V 294_I 0.86 0.15 0.00
182_G 166_L 0.86 0.15 0.00
239_M 169_G 0.86 0.15 0.00
85_G 18_Y 0.86 0.15 0.00
52_L 408_V 0.86 0.15 0.00
179_V 74_S 0.86 0.15 0.00
58_V 306_M 0.85 0.15 0.00
79_T 242_F 0.85 0.14 0.00
211_M 312_G 0.85 0.14 0.00
20_G 221_V 0.85 0.14 0.00
12_P 305_H 0.85 0.14 0.00
104_W 290_G 0.85 0.14 0.00
184_C 409_L 0.85 0.14 0.00
221_I 367_V 0.85 0.14 0.00
140_L 14_V 0.85 0.14 0.00
218_A 209_F 0.85 0.14 0.00
243_Q 382_V 0.84 0.14 0.00
70_V 9_I 0.84 0.14 0.00
265_F 117_M 0.84 0.14 0.00
147_I 238_V 0.84 0.14 0.00
126_V 63_A 0.84 0.14 0.00
166_G 207_L 0.84 0.14 0.00
32_V 304_A 0.84 0.14 0.00
63_F 416_I 0.84 0.14 0.00
210_Y 194_I 0.83 0.14 0.00
242_K 221_V 0.83 0.14 0.00
20_G 334_M 0.83 0.14 0.00
29_T 112_L 0.83 0.14 0.00
23_G 128_T 0.83 0.14 0.00
50_M 368_K 0.83 0.14 0.00
83_R 364_T 0.83 0.14 0.00
51_F 218_V 0.83 0.14 0.00
179_V 340_A 0.82 0.13 0.00
138_W 370_L 0.82 0.13 0.00
190_A 313_L 0.82 0.13 0.00
182_G 215_S 0.82 0.13 0.00
89_G 187_F 0.82 0.13 0.00
67_A 435_E 0.82 0.13 0.00
22_I 203_V 0.82 0.13 0.00
52_L 188_E 0.82 0.13 0.00
197_A 273_V 0.82 0.13 0.00
143_I 182_A 0.82 0.13 0.00
23_G 390_A 0.82 0.13 0.00
180_I 321_V 0.81 0.13 0.00
63_F 392_F 0.81 0.13 0.00
150_L 73_F 0.81 0.13 0.00
23_G 19_A 0.81 0.13 0.00
98_V 167_S 0.81 0.13 0.00
23_G 101_M 0.81 0.13 0.00
22_I 190_I 0.81 0.13 0.00
2_H 277_A 0.81 0.13 0.00
137_P 334_M 0.81 0.13 0.00
138_W 393_G 0.81 0.13 0.00
170_T 379_L 0.81 0.13 0.00
228_F 313_L 0.80 0.13 0.00
146_L 429_Y 0.80 0.13 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
3195 0.48 cIV_C_4_cI_N_60_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3194 0.61 cIV_C_4_cI_N_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3193 0.58 cIV_C_4_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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