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OPENSEQ.org
cIp_5_4_cIV_1_10
Genes: A B A+B
Length: 264 513 724
Sequences: 309 4400 78
Seq/Len: 1.17 8.58 0.11
MirrorTree (Pazo et al. 2001) 0.11
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 0.00
2 0.00 0.01 0.00
5 0.00 0.02 0.00
10 0.00 0.02 0.00
20 0.00 0.03 0.01
100 0.00 0.04 0.03
∞ 0.00 0.08 0.10
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
86_V 419_I 2.10 0.48 0.01
73_V 460_I 1.85 0.36 0.01
207_Y 419_I 1.52 0.22 0.00
176_V 466_M 1.46 0.20 0.00
156_A 168_I 1.45 0.20 0.00
173_M 481_K 1.42 0.19 0.00
58_L 470_F 1.40 0.18 0.00
171_W 303_A 1.38 0.18 0.00
176_V 511_M 1.37 0.17 0.00
174_F 463_T 1.37 0.17 0.00
204_L 279_S 1.34 0.17 0.00
103_H 216_N 1.30 0.16 0.00
145_T 279_S 1.21 0.13 0.00
220_V 253_M 1.19 0.13 0.00
135_L 336_A 1.18 0.12 0.00
180_N 120_A 1.18 0.12 0.00
170_I 511_M 1.17 0.12 0.00
170_I 470_F 1.16 0.12 0.00
246_R 23_G 1.14 0.12 0.00
207_Y 32_A 1.13 0.11 0.00
214_D 229_I 1.13 0.11 0.00
217_K 414_F 1.12 0.11 0.00
143_V 48_L 1.10 0.11 0.00
73_V 511_M 1.08 0.10 0.00
70_P 110_L 1.07 0.10 0.00
121_T 198_S 1.06 0.10 0.00
220_V 73_I 1.06 0.10 0.00
171_W 267_P 1.05 0.10 0.00
108_F 505_F 1.05 0.10 0.00
180_N 489_S 1.04 0.10 0.00
114_L 456_V 1.04 0.10 0.00
220_V 174_P 1.04 0.10 0.00
171_W 472_I 1.04 0.10 0.00
111_L 419_I 1.04 0.10 0.00
112_V 114_A 1.02 0.09 0.00
110_S 267_P 1.02 0.09 0.00
101_R 257_I 1.02 0.09 0.00
162_A 460_I 1.01 0.09 0.00
229_E 49_G 1.01 0.09 0.00
84_L 389_I 1.01 0.09 0.00
65_V 458_S 1.00 0.09 0.00
154_E 342_L 1.00 0.09 0.00
69_L 230_L 1.00 0.09 0.00
116_A 467_L 0.99 0.09 0.00
170_I 188_V 0.99 0.09 0.00
114_L 168_I 0.99 0.09 0.00
147_T 359_A 0.99 0.09 0.00
86_V 111_L 0.98 0.09 0.00
205_S 137_S 0.97 0.09 0.00
235_L 37_I 0.97 0.09 0.00
171_W 206_I 0.97 0.09 0.00
65_V 340_W 0.97 0.09 0.00
170_I 198_S 0.97 0.08 0.00
216_V 320_V 0.96 0.08 0.00
243_P 469_I 0.96 0.08 0.00
132_L 28_V 0.96 0.08 0.00
187_I 274_V 0.95 0.08 0.00
196_H 450_W 0.95 0.08 0.00
156_A 29_L 0.95 0.08 0.00
114_L 467_L 0.94 0.08 0.00
171_W 231_Y 0.94 0.08 0.00
85_E 286_I 0.94 0.08 0.00
143_V 52_H 0.94 0.08 0.00
132_L 235_F 0.94 0.08 0.00
67_E 21_L 0.94 0.08 0.00
130_Y 6_W 0.93 0.08 0.00
96_V 152_L 0.93 0.08 0.00
164_N 456_V 0.93 0.08 0.00
161_K 314_I 0.93 0.08 0.00
89_H 466_M 0.92 0.08 0.00
147_T 257_I 0.92 0.08 0.00
96_V 472_I 0.92 0.08 0.00
215_E 66_I 0.92 0.08 0.00
159_V 416_I 0.91 0.08 0.00
115_T 311_I 0.91 0.07 0.00
159_V 49_G 0.91 0.07 0.00
194_E 298_D 0.91 0.07 0.00
108_F 350_V 0.90 0.07 0.00
176_V 35_L 0.90 0.07 0.00
96_V 161_A 0.90 0.07 0.00
108_F 511_M 0.90 0.07 0.00
114_L 359_A 0.90 0.07 0.00
187_I 192_A 0.90 0.07 0.00
121_T 391_G 0.90 0.07 0.00
114_L 149_S 0.90 0.07 0.00
174_F 460_I 0.90 0.07 0.00
127_E 122_A 0.90 0.07 0.00
116_A 455_S 0.89 0.07 0.00
174_F 69_M 0.89 0.07 0.00
70_P 152_L 0.89 0.07 0.00
88_I 463_T 0.89 0.07 0.00
214_D 470_F 0.89 0.07 0.00
166_Y 363_L 0.89 0.07 0.00
225_E 395_H 0.89 0.07 0.00
127_E 409_Y 0.89 0.07 0.00
110_S 466_M 0.88 0.07 0.00
97_L 453_L 0.88 0.07 0.00
214_D 161_A 0.88 0.07 0.00
81_F 264_K 0.88 0.07 0.00
221_A 489_S 0.88 0.07 0.00
246_R 467_L 0.88 0.07 0.00
127_E 306_T 0.88 0.07 0.00
216_V 102_F 0.88 0.07 0.00
108_F 339_L 0.87 0.07 0.00
116_A 170_N 0.87 0.07 0.00
115_T 464_A 0.87 0.07 0.00
166_Y 62_A 0.86 0.07 0.00
160_F 466_M 0.86 0.07 0.00
93_V 37_I 0.86 0.07 0.00
214_D 414_F 0.86 0.07 0.00
215_E 324_L 0.85 0.07 0.00
135_L 472_I 0.85 0.07 0.00
145_T 393_F 0.85 0.07 0.00
60_A 456_V 0.85 0.07 0.00
86_V 90_P 0.85 0.07 0.00
252_L 7_L 0.85 0.07 0.00
156_A 481_K 0.85 0.07 0.00
78_V 446_A 0.85 0.07 0.00
98_T 423_L 0.85 0.07 0.00
162_A 257_I 0.85 0.07 0.00
81_F 388_A 0.85 0.07 0.00
155_S 28_V 0.85 0.07 0.00
113_D 130_P 0.85 0.07 0.00
69_L 64_V 0.84 0.07 0.00
207_Y 459_F 0.84 0.07 0.00
157_V 122_A 0.84 0.07 0.00
97_L 197_L 0.84 0.07 0.00
171_W 359_A 0.84 0.07 0.00
161_K 363_L 0.84 0.07 0.00
143_V 453_L 0.84 0.07 0.00
62_G 18_L 0.84 0.07 0.00
106_A 264_K 0.84 0.07 0.00
230_F 195_L 0.84 0.07 0.00
207_Y 357_V 0.83 0.07 0.00
159_V 428_Q 0.83 0.07 0.00
86_V 206_I 0.83 0.07 0.00
127_E 23_G 0.83 0.07 0.00
114_L 23_G 0.83 0.07 0.00
143_V 18_L 0.83 0.07 0.00
79_S 198_S 0.82 0.06 0.00
60_A 36_L 0.82 0.06 0.00
152_P 46_N 0.82 0.06 0.00
229_E 198_S 0.82 0.06 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
4349 0.11 cIp_5_2_cIV_1_20 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4348 0.1 cIp_5_2_cIV_1_40 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4347 0.11 cIp_5_4_cIV_1_10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4340 0.11 cIp_5_2_cIV_1_10 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4339 0.11 cIp_5_2_cIV_1_4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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