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OPENSEQ.org
cIV_B_6_cI_N_60_1_Pdenitr
Genes: A B A+B
Length: 252 499 705
Sequences: 4627 1133 588
Seq/Len: 18.36 2.27 0.83
MirrorTree (Pazo et al. 2001) 0.35
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.04
10 0.01 0.00 0.07
20 0.01 0.02 0.13
100 0.02 0.03 0.20
∞ 0.04 0.03 0.78
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
212_Y 243_A 1.33 0.58 0.00
212_Y 234_S 1.21 0.48 0.00
239_Y 435_E 1.21 0.48 0.00
168_K 221_V 1.18 0.44 0.00
233_A 355_L 1.14 0.41 0.00
53_L 232_E 1.05 0.34 0.00
94_A 175_A 1.01 0.31 0.00
92_I 297_L 1.01 0.31 0.00
104_Q 336_I 0.98 0.29 0.00
204_F 379_L 0.98 0.28 0.00
94_A 63_A 0.96 0.27 0.00
68_P 125_D 0.95 0.26 0.00
176_A 221_V 0.93 0.25 0.00
86_V 92_S 0.92 0.25 0.00
31_Q 238_V 0.92 0.24 0.00
96_S 232_E 0.91 0.24 0.00
80_I 175_A 0.90 0.23 0.00
94_A 273_V 0.90 0.23 0.00
170_V 415_V 0.89 0.22 0.00
170_V 35_A 0.87 0.21 0.00
194_A 432_G 0.86 0.21 0.00
116_A 21_A 0.86 0.21 0.00
167_G 113_A 0.86 0.21 0.00
202_L 417_G 0.85 0.20 0.00
92_I 170_L 0.85 0.20 0.00
83_L 403_M 0.84 0.20 0.00
112_L 419_F 0.84 0.20 0.00
88_I 416_I 0.84 0.20 0.00
60_F 221_V 0.84 0.20 0.00
241_A 106_F 0.84 0.20 0.00
186_P 172_L 0.84 0.20 0.00
172_V 390_A 0.84 0.19 0.00
116_A 20_L 0.83 0.19 0.00
103_S 234_S 0.81 0.18 0.00
239_Y 433_E 0.81 0.18 0.00
185_I 359_N 0.81 0.18 0.00
195_V 285_S 0.81 0.18 0.00
206_V 132_G 0.81 0.18 0.00
233_A 342_I 0.81 0.18 0.00
212_Y 13_V 0.80 0.18 0.00
225_A 237_P 0.80 0.18 0.00
47_I 390_A 0.80 0.18 0.00
117_I 297_L 0.80 0.17 0.00
184_T 136_Q 0.79 0.17 0.00
128_P 252_A 0.79 0.17 0.00
209_E 374_V 0.78 0.17 0.00
36_H 132_G 0.78 0.16 0.00
94_A 241_F 0.78 0.16 0.00
50_C 162_V 0.77 0.16 0.00
228_P 128_T 0.77 0.16 0.00
84_V 326_L 0.77 0.16 0.00
164_V 362_A 0.77 0.16 0.00
231_V 15_L 0.76 0.16 0.00
176_A 416_I 0.76 0.16 0.00
176_A 317_T 0.76 0.15 0.00
90_V 85_A 0.75 0.15 0.00
80_I 294_I 0.75 0.15 0.00
208_Q 451_V 0.75 0.15 0.00
167_G 46_F 0.75 0.15 0.00
219_L 211_L 0.75 0.15 0.00
58_V 308_F 0.74 0.15 0.00
27_L 214_L 0.74 0.15 0.00
49_V 123_A 0.74 0.15 0.00
158_T 322_Q 0.74 0.15 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
3315 1.12 cIV_B_2_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.26 Done - Shared
3314 1.11 cIV_B_4_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.27 Done - Shared
3313 0.83 cIV_B_6_cI_N_60_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3312 1.12 cIV_B_6_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3311 1.65 cIV_B_6_cI_N_10_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3308 1.24 cIV_B_6_cI_N_20_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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