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OPENSEQ.org
cIV_C_4_cI_M_60_1_Pdenitr
Genes: A B A+B
Length: 273 513 757
Sequences: 2888 2379 620
Seq/Len: 10.58 4.64 0.82
MirrorTree (Pazo et al. 2001) 0.34
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 0.01 0.03
2 0.00 0.01 0.06
5 0.00 0.01 0.19
10 0.00 0.02 0.30
20 0.00 0.02 0.37
100 0.00 0.03 0.42
∞ 0.01 0.06 0.79
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
121_P 303_A 1.43 0.66 0.00
206_A 393_N 1.28 0.53 0.00
121_P 342_Q 1.25 0.50 0.00
76_G 393_N 1.20 0.46 0.00
222_I 313_I 1.17 0.44 0.00
107_A 248_Q 1.16 0.43 0.00
58_V 473_L 1.14 0.41 0.00
210_Y 17_I 1.14 0.41 0.00
221_I 384_A 1.12 0.40 0.00
210_Y 14_V 1.09 0.37 0.00
98_V 109_K 1.09 0.37 0.00
182_G 161_Y 1.09 0.37 0.00
266_V 182_I 1.09 0.37 0.00
58_V 274_L 1.08 0.36 0.00
121_P 281_S 1.08 0.36 0.00
23_G 226_F 1.08 0.36 0.00
265_F 420_A 1.08 0.36 0.00
210_Y 21_L 1.08 0.36 0.00
187_G 428_I 1.07 0.35 0.00
69_V 296_I 1.06 0.35 0.00
222_I 18_I 1.04 0.33 0.00
251_A 396_L 1.03 0.32 0.00
210_Y 330_A 1.03 0.32 0.00
73_G 279_V 1.03 0.32 0.00
138_W 312_V 1.01 0.30 0.00
142_L 365_H 1.00 0.30 0.00
182_G 447_I 0.99 0.29 0.00
137_P 270_L 0.99 0.29 0.00
21_A 411_G 0.99 0.29 0.00
168_R 125_I 0.99 0.29 0.00
155_V 119_V 0.99 0.29 0.00
228_F 421_L 0.98 0.28 0.00
175_L 429_L 0.98 0.28 0.00
167_D 427_V 0.97 0.28 0.00
95_M 421_L 0.97 0.28 0.00
123_K 312_V 0.97 0.28 0.00
27_M 332_N 0.96 0.27 0.00
229_V 382_Y 0.96 0.27 0.00
98_V 392_A 0.96 0.27 0.00
69_V 423_A 0.96 0.27 0.00
140_L 96_M 0.95 0.27 0.00
90_F 435_L 0.95 0.26 0.00
154_A 124_M 0.95 0.26 0.00
250_A 160_I 0.95 0.26 0.00
187_G 44_A 0.94 0.26 0.00
195_H 318_V 0.94 0.26 0.00
218_A 52_V 0.94 0.26 0.00
18_F 299_T 0.94 0.25 0.00
179_V 50_L 0.94 0.25 0.00
48_P 348_F 0.93 0.25 0.00
58_V 89_V 0.93 0.25 0.00
238_Q 322_G 0.92 0.24 0.00
22_I 182_I 0.92 0.24 0.00
182_G 343_M 0.91 0.24 0.00
15_I 148_F 0.91 0.24 0.00
157_W 291_L 0.91 0.24 0.00
154_A 248_Q 0.91 0.23 0.00
201_A 236_W 0.91 0.23 0.00
140_L 125_I 0.91 0.23 0.00
116_M 113_Y 0.90 0.23 0.00
99_M 251_T 0.90 0.23 0.00
204_V 47_V 0.90 0.23 0.00
52_L 200_D 0.90 0.23 0.00
204_V 412_V 0.90 0.23 0.00
224_T 349_I 0.90 0.23 0.00
18_F 383_A 0.89 0.22 0.00
53_I 466_I 0.89 0.22 0.00
10_I 260_V 0.88 0.22 0.00
28_L 175_V 0.88 0.22 0.00
21_A 428_I 0.88 0.22 0.00
153_V 416_D 0.88 0.22 0.00
172_I 441_V 0.88 0.22 0.00
182_G 247_V 0.88 0.22 0.00
203_T 229_F 0.88 0.22 0.00
188_L 17_I 0.88 0.22 0.00
66_W 95_M 0.87 0.21 0.00
114_Y 427_V 0.87 0.21 0.00
147_I 349_I 0.87 0.21 0.00
18_F 37_L 0.86 0.21 0.00
222_I 384_A 0.86 0.21 0.00
200_L 291_L 0.86 0.21 0.00
200_L 97_P 0.86 0.21 0.00
221_I 332_N 0.86 0.20 0.00
18_F 322_G 0.85 0.20 0.00
73_G 88_F 0.85 0.20 0.00
90_F 126_G 0.85 0.20 0.00
203_T 188_A 0.85 0.20 0.00
204_V 318_V 0.85 0.20 0.00
224_T 220_L 0.85 0.20 0.00
239_M 469_I 0.85 0.20 0.00
28_L 220_L 0.85 0.20 0.00
180_I 422_V 0.84 0.20 0.00
262_L 113_Y 0.84 0.20 0.00
53_I 480_R 0.84 0.19 0.00
177_V 472_T 0.84 0.19 0.00
267_V 304_L 0.84 0.19 0.00
267_V 159_R 0.84 0.19 0.00
266_V 326_M 0.83 0.19 0.00
18_F 338_G 0.83 0.19 0.00
56_V 61_T 0.83 0.19 0.00
58_V 287_Y 0.83 0.19 0.00
191_Y 421_L 0.83 0.19 0.00
161_A 348_F 0.83 0.19 0.00
66_W 265_G 0.83 0.19 0.00
195_H 473_L 0.83 0.19 0.00
116_M 391_M 0.82 0.19 0.00
104_W 265_G 0.82 0.18 0.00
23_G 344_L 0.82 0.18 0.00
32_V 260_V 0.82 0.18 0.00
250_A 159_R 0.82 0.18 0.00
238_Q 430_S 0.81 0.18 0.00
218_A 163_S 0.81 0.18 0.00
166_G 58_P 0.81 0.18 0.00
215_F 113_Y 0.81 0.18 0.00
139_H 125_I 0.81 0.18 0.00
90_F 142_A 0.81 0.18 0.00
187_G 477_V 0.81 0.18 0.00
133_V 176_L 0.81 0.18 0.00
24_A 233_M 0.81 0.18 0.00
245_V 256_L 0.81 0.18 0.00
205_Y 145_I 0.81 0.18 0.00
24_A 318_V 0.81 0.18 0.00
35_M 72_I 0.81 0.18 0.00
91_I 81_V 0.81 0.18 0.00
98_V 388_F 0.81 0.18 0.00
21_A 431_A 0.80 0.17 0.00
23_G 369_I 0.80 0.17 0.00
38_I 79_M 0.80 0.17 0.00
174_G 472_T 0.80 0.17 0.00
171_T 14_V 0.80 0.17 0.00
15_I 267_Y 0.80 0.17 0.00
64_G 418_W 0.80 0.17 0.00
228_F 459_P 0.79 0.17 0.00
8_Y 201_F 0.79 0.17 0.00
180_I 318_V 0.79 0.17 0.00
22_I 351_G 0.79 0.17 0.00
50_M 466_I 0.79 0.17 0.00
203_T 186_R 0.78 0.17 0.00
174_G 15_A 0.78 0.16 0.00
212_A 312_V 0.78 0.16 0.00
52_L 108_D 0.78 0.16 0.00
166_G 28_E 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
4052 3.95 cIV_C_6_cI_M_80_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
3192 2.03 cIV_C_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3191 1.88 cIV_C_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3190 0.82 cIV_C_4_cI_M_60_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3189 3.94 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
3188 4.24 cIV_C_4_cI_M_60_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3187 4.42 cIV_C_4_cI_M_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
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