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OPENSEQ.org
cIV_C_4_cI_N_40_1_Pdenitr
Genes: A B A+B
Length: 273 499 730
Sequences: 2888 1784 422
Seq/Len: 10.58 3.58 0.58
MirrorTree (Pazo et al. 2001) 0.30
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 0.03
5 0.00 0.00 0.05
10 0.00 0.00 0.10
20 0.00 0.02 0.13
100 0.00 0.02 0.17
∞ 0.01 0.04 0.55
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_L 110_V 1.68 0.74 0.01
143_I 42_T 1.41 0.54 0.01
243_Q 382_V 1.24 0.40 0.00
125_G 425_V 1.23 0.39 0.00
22_I 190_I 1.20 0.37 0.00
211_M 342_I 1.18 0.36 0.00
25_F 67_M 1.18 0.36 0.00
161_A 281_M 1.17 0.35 0.00
26_V 252_A 1.14 0.33 0.00
188_L 150_S 1.12 0.32 0.00
222_I 416_I 1.12 0.31 0.00
121_P 243_A 1.10 0.30 0.00
154_A 300_Y 1.10 0.30 0.00
31_A 358_L 1.10 0.30 0.00
50_M 79_V 1.07 0.28 0.00
204_V 374_V 1.07 0.28 0.00
190_A 110_V 1.07 0.28 0.00
51_F 43_V 1.06 0.28 0.00
98_V 38_L 1.05 0.27 0.00
153_V 83_V 1.04 0.26 0.00
207_G 412_I 1.04 0.26 0.00
89_G 187_F 1.03 0.26 0.00
187_G 126_L 1.01 0.24 0.00
95_M 124_G 1.01 0.24 0.00
8_Y 417_G 1.00 0.24 0.00
61_V 308_F 1.00 0.24 0.00
207_G 355_L 1.00 0.23 0.00
195_H 336_I 0.99 0.23 0.00
52_L 84_A 0.99 0.23 0.00
166_G 370_L 0.99 0.23 0.00
166_G 89_L 0.98 0.23 0.00
218_A 425_V 0.98 0.23 0.00
179_V 203_V 0.98 0.23 0.00
56_V 424_I 0.98 0.23 0.00
234_L 234_S 0.97 0.22 0.00
149_L 374_V 0.97 0.22 0.00
18_F 241_F 0.97 0.22 0.00
23_G 19_A 0.96 0.22 0.00
204_V 401_A 0.95 0.21 0.00
204_V 248_V 0.94 0.20 0.00
177_V 294_I 0.94 0.20 0.00
135_F 389_F 0.93 0.20 0.00
210_Y 170_L 0.93 0.20 0.00
211_M 312_G 0.93 0.20 0.00
63_F 79_V 0.93 0.20 0.00
91_I 422_L 0.93 0.20 0.00
172_I 82_L 0.92 0.20 0.00
133_V 83_V 0.92 0.19 0.00
23_G 115_L 0.92 0.19 0.00
73_G 211_L 0.92 0.19 0.00
26_V 287_A 0.92 0.19 0.00
22_I 412_I 0.92 0.19 0.00
136_D 329_T 0.91 0.19 0.00
218_A 175_A 0.91 0.19 0.00
235_L 360_R 0.91 0.19 0.00
177_V 221_V 0.91 0.19 0.00
178_A 426_Y 0.91 0.19 0.00
48_P 306_M 0.90 0.18 0.00
183_V 205_F 0.90 0.18 0.00
18_F 119_F 0.90 0.18 0.00
7_D 205_F 0.89 0.18 0.00
120_S 292_T 0.89 0.18 0.00
24_A 69_I 0.89 0.18 0.00
135_F 131_M 0.89 0.18 0.00
73_G 336_I 0.89 0.18 0.00
155_V 424_I 0.89 0.18 0.00
19_F 277_A 0.89 0.18 0.00
13_P 212_V 0.88 0.17 0.00
20_G 221_V 0.88 0.17 0.00
20_G 377_F 0.88 0.17 0.00
59_L 294_I 0.88 0.17 0.00
242_K 221_V 0.88 0.17 0.00
204_V 393_G 0.88 0.17 0.00
238_Q 417_G 0.88 0.17 0.00
55_L 207_L 0.87 0.17 0.00
186_T 260_D 0.87 0.17 0.00
79_T 242_F 0.87 0.17 0.00
155_V 370_L 0.87 0.17 0.00
268_I 119_F 0.87 0.17 0.00
239_M 113_A 0.87 0.17 0.00
191_Y 213_G 0.87 0.17 0.00
241_Q 245_A 0.86 0.17 0.00
222_I 90_A 0.86 0.17 0.00
179_V 359_N 0.86 0.17 0.00
138_W 238_V 0.86 0.17 0.00
5_N 417_G 0.86 0.17 0.00
207_G 303_I 0.86 0.17 0.00
146_L 234_S 0.86 0.17 0.00
63_F 463_M 0.86 0.16 0.00
179_V 88_V 0.85 0.16 0.00
221_I 201_L 0.84 0.16 0.00
204_V 127_L 0.84 0.16 0.00
221_I 367_V 0.84 0.16 0.00
58_V 382_V 0.84 0.16 0.00
175_L 398_A 0.84 0.16 0.00
265_F 241_F 0.84 0.16 0.00
179_V 366_P 0.84 0.15 0.00
195_H 145_A 0.84 0.15 0.00
83_R 164_G 0.84 0.15 0.00
51_F 218_V 0.83 0.15 0.00
137_P 15_L 0.83 0.15 0.00
211_M 85_A 0.83 0.15 0.00
263_F 177_L 0.83 0.15 0.00
112_A 351_P 0.83 0.15 0.00
172_I 87_G 0.83 0.15 0.00
239_M 345_M 0.83 0.15 0.00
222_I 242_F 0.82 0.15 0.00
108_F 242_F 0.82 0.15 0.00
63_F 309_A 0.82 0.15 0.00
51_F 139_A 0.82 0.15 0.00
268_I 304_A 0.82 0.15 0.00
23_G 390_A 0.81 0.14 0.00
190_A 57_N 0.81 0.14 0.00
207_G 18_Y 0.81 0.14 0.00
113_L 385_T 0.81 0.14 0.00
270_I 433_E 0.81 0.14 0.00
179_V 126_L 0.81 0.14 0.00
154_A 245_A 0.81 0.14 0.00
146_L 73_F 0.81 0.14 0.00
236_K 379_L 0.81 0.14 0.00
58_V 306_M 0.80 0.14 0.00
23_G 135_L 0.80 0.14 0.00
166_G 189_G 0.80 0.14 0.00
180_I 153_S 0.80 0.14 0.00
172_I 252_A 0.80 0.14 0.00
107_A 127_L 0.80 0.14 0.00
143_I 131_M 0.80 0.14 0.00
127_W 414_S 0.79 0.14 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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