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OPENSEQ.org
cIp_6_40_cIV_1_40
Genes: A B A+B
Length: 213 513 685
Sequences: 401 3286 150
Seq/Len: 1.88 6.41 0.22
MirrorTree (Pazo et al. 2001) 0.48
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.01 0.02 0.04
∞ 0.01 0.06 0.21
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
103_M 500_P 1.24 0.21 0.00
135_R 153_A 1.22 0.20 0.00
201_I 124_T 1.18 0.19 0.00
191_L 472_I 1.16 0.18 0.00
139_D 395_H 1.12 0.17 0.00
101_Y 357_V 1.08 0.15 0.00
66_K 108_S 1.07 0.15 0.00
91_V 455_S 1.06 0.15 0.00
139_D 496_H 1.06 0.15 0.00
143_E 510_Y 1.05 0.15 0.00
147_V 62_A 1.03 0.14 0.00
191_L 48_L 1.02 0.14 0.00
194_I 408_T 1.02 0.14 0.00
145_R 404_T 1.01 0.13 0.00
120_M 206_I 1.01 0.13 0.00
98_A 314_I 1.01 0.13 0.00
176_V 305_F 1.01 0.13 0.00
91_V 276_A 0.99 0.13 0.00
104_D 107_P 0.99 0.13 0.00
148_V 410_A 0.98 0.12 0.00
199_R 259_T 0.97 0.12 0.00
63_V 54_Y 0.97 0.12 0.00
152_S 264_K 0.97 0.12 0.00
110_F 62_A 0.96 0.12 0.00
98_A 37_I 0.96 0.12 0.00
109_V 161_A 0.96 0.12 0.00
101_Y 79_G 0.96 0.12 0.00
152_S 362_S 0.95 0.12 0.00
99_P 417_M 0.95 0.12 0.00
204_E 411_K 0.94 0.12 0.00
120_M 385_A 0.94 0.12 0.00
152_S 262_S 0.94 0.11 0.00
117_S 153_A 0.93 0.11 0.00
178_I 266_E 0.93 0.11 0.00
112_A 318_V 0.93 0.11 0.00
119_V 58_V 0.92 0.11 0.00
119_V 373_V 0.92 0.11 0.00
152_S 336_A 0.92 0.11 0.00
180_I 327_L 0.92 0.11 0.00
62_Y 354_T 0.92 0.11 0.00
152_S 162_I 0.92 0.11 0.00
199_R 204_A 0.92 0.11 0.00
198_Q 238_F 0.92 0.11 0.00
191_L 345_I 0.92 0.11 0.00
131_A 89_A 0.91 0.11 0.00
199_R 423_L 0.90 0.10 0.00
122_V 82_L 0.90 0.10 0.00
121_I 322_S 0.90 0.10 0.00
79_L 180_Q 0.89 0.10 0.00
50_R 497_G 0.89 0.10 0.00
94_M 462_L 0.89 0.10 0.00
180_I 444_P 0.89 0.10 0.00
98_A 54_Y 0.88 0.10 0.00
131_A 458_S 0.88 0.10 0.00
194_I 409_Y 0.88 0.10 0.00
91_V 382_S 0.88 0.10 0.00
186_T 471_M 0.87 0.10 0.00
72_N 54_Y 0.87 0.10 0.00
191_L 458_S 0.86 0.10 0.00
145_R 336_A 0.86 0.10 0.00
104_D 293_F 0.86 0.10 0.00
106_F 397_F 0.86 0.10 0.00
119_V 34_S 0.86 0.10 0.00
122_V 416_I 0.86 0.10 0.00
160_Y 259_T 0.85 0.09 0.00
180_I 195_L 0.85 0.09 0.00
99_P 201_V 0.85 0.09 0.00
103_M 359_A 0.85 0.09 0.00
139_D 349_T 0.85 0.09 0.00
193_G 389_I 0.85 0.09 0.00
205_R 350_V 0.85 0.09 0.00
160_Y 207_T 0.85 0.09 0.00
194_I 141_A 0.85 0.09 0.00
201_I 281_G 0.84 0.09 0.00
160_Y 503_H 0.84 0.09 0.00
79_L 181_T 0.84 0.09 0.00
101_Y 157_S 0.84 0.09 0.00
119_V 329_G 0.84 0.09 0.00
130_M 270_Y 0.84 0.09 0.00
163_S 317_G 0.84 0.09 0.00
160_Y 192_A 0.83 0.09 0.00
173_I 452_I 0.83 0.09 0.00
69_D 262_S 0.83 0.09 0.00
63_V 502_Y 0.83 0.09 0.00
180_I 45_G 0.83 0.09 0.00
63_V 37_I 0.83 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
4328 0.29 cIp_6_4_cIV_1_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4327 0.22 cIp_6_40_cIV_1_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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