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OPENSEQ.org
cIp_2_40_cIV_1_40
Genes: A B A+B
Length: 249 513 715
Sequences: 654 3286 196
Seq/Len: 2.63 6.41 0.27
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 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.00 0.02 0.03
∞ 0.00 0.06 0.26
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
148_I 472_I 1.62 0.47 0.00
82_V 37_I 1.48 0.38 0.00
214_P 419_I 1.34 0.29 0.00
130_Y 279_S 1.30 0.28 0.00
94_P 230_L 1.17 0.21 0.00
61_K 205_G 1.12 0.19 0.00
132_I 49_G 1.10 0.18 0.00
93_L 62_A 1.10 0.18 0.00
156_L 121_G 1.09 0.18 0.00
218_P 324_L 1.07 0.17 0.00
56_T 168_I 1.05 0.16 0.00
108_P 467_L 1.03 0.16 0.00
94_P 440_Y 1.03 0.16 0.00
122_Y 162_I 1.03 0.16 0.00
210_A 318_V 1.02 0.15 0.00
108_P 196_I 1.00 0.15 0.00
93_L 363_L 0.99 0.14 0.00
203_E 28_V 0.99 0.14 0.00
101_V 24_A 0.99 0.14 0.00
98_M 306_T 0.98 0.14 0.00
85_L 393_F 0.98 0.14 0.00
203_E 409_Y 0.97 0.14 0.00
204_I 29_L 0.97 0.14 0.00
171_L 121_G 0.97 0.14 0.00
113_Y 469_I 0.96 0.14 0.00
63_I 108_S 0.95 0.13 0.00
125_K 458_S 0.94 0.13 0.00
205_I 150_L 0.94 0.13 0.00
56_T 74_M 0.94 0.13 0.00
155_K 314_I 0.93 0.13 0.00
148_I 294_T 0.93 0.12 0.00
220_S 511_M 0.93 0.12 0.00
188_I 495_L 0.92 0.12 0.00
103_E 462_L 0.92 0.12 0.00
99_N 458_S 0.91 0.12 0.00
125_K 267_P 0.91 0.12 0.00
235_T 267_P 0.91 0.12 0.00
132_I 150_L 0.89 0.12 0.00
218_P 264_K 0.89 0.12 0.00
188_I 153_A 0.89 0.11 0.00
236_E 472_I 0.89 0.11 0.00
199_K 286_I 0.88 0.11 0.00
216_P 59_T 0.88 0.11 0.00
203_E 278_M 0.88 0.11 0.00
121_M 111_L 0.88 0.11 0.00
150_E 21_L 0.87 0.11 0.00
186_V 185_V 0.86 0.11 0.00
72_E 472_I 0.86 0.11 0.00
233_S 112_L 0.86 0.11 0.00
112_V 392_G 0.86 0.11 0.00
108_P 374_V 0.86 0.11 0.00
165_P 391_G 0.86 0.11 0.00
166_D 279_S 0.85 0.10 0.00
214_P 258_V 0.85 0.10 0.00
216_P 346_F 0.85 0.10 0.00
94_P 478_S 0.85 0.10 0.00
228_A 419_I 0.85 0.10 0.00
132_I 324_L 0.85 0.10 0.00
164_T 152_L 0.85 0.10 0.00
52_P 505_F 0.85 0.10 0.00
103_E 231_Y 0.85 0.10 0.00
112_V 149_S 0.84 0.10 0.00
216_P 343_G 0.84 0.10 0.00
181_V 221_D 0.84 0.10 0.00
232_T 426_F 0.84 0.10 0.00
91_G 293_F 0.84 0.10 0.00
52_P 193_V 0.84 0.10 0.00
162_E 463_T 0.83 0.10 0.00
155_K 228_P 0.83 0.10 0.00
45_P 311_I 0.83 0.10 0.00
103_E 32_A 0.82 0.10 0.00
212_K 419_I 0.82 0.10 0.00
94_P 479_K 0.82 0.10 0.00
150_E 222_P 0.82 0.10 0.00
129_K 117_M 0.82 0.10 0.00
120_T 100_M 0.82 0.10 0.00
66_I 116_A 0.82 0.10 0.00
72_E 17_T 0.82 0.10 0.00
198_A 363_L 0.82 0.10 0.00
121_M 278_M 0.81 0.10 0.00
115_V 177_T 0.81 0.10 0.00
174_V 8_F 0.81 0.10 0.00
138_T 209_L 0.81 0.10 0.00
73_G 463_T 0.81 0.10 0.00
141_M 231_Y 0.81 0.09 0.00
74_H 417_M 0.81 0.09 0.00
190_D 393_F 0.81 0.09 0.00
199_K 462_L 0.81 0.09 0.00
215_K 161_A 0.81 0.09 0.00
61_K 473_W 0.80 0.09 0.00
147_S 470_F 0.80 0.09 0.00
216_P 505_F 0.80 0.09 0.00
109_P 367_L 0.80 0.09 0.00
86_A 422_N 0.80 0.09 0.00
211_G 173_P 0.80 0.09 0.00
150_E 32_A 0.80 0.09 0.00
54_D 311_I 0.80 0.09 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
4174 0.27 cIp_2_40_cIV_1_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4173 0.22 cIp_2_4_cIV_1_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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