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OPENSEQ.org
cIV_B_6_cI_N_20_1_Pdenitr
Genes: A B A+B
Length: 252 499 704
Sequences: 4627 2180 874
Seq/Len: 18.36 4.37 1.24
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 0.01 0.01
2 0.00 0.01 0.02
5 0.00 0.01 0.05
10 0.01 0.01 0.10
20 0.01 0.02 0.17
100 0.02 0.03 0.27
∞ 0.04 0.05 1.16
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 234_S 1.39 0.74 0.01
80_I 175_A 1.20 0.58 0.01
116_A 120_M 1.16 0.55 0.01
239_Y 433_E 0.95 0.35 0.01
176_A 221_V 0.94 0.34 0.01
25_S 52_M 0.94 0.34 0.01
209_E 374_V 0.93 0.33 0.00
92_I 170_L 0.88 0.28 0.00
68_P 125_D 0.87 0.28 0.00
80_I 341_F 0.85 0.27 0.00
239_Y 435_E 0.84 0.26 0.00
170_V 138_L 0.83 0.24 0.00
237_E 298_M 0.82 0.24 0.00
87_L 50_A 0.81 0.23 0.00
44_A 34_L 0.80 0.23 0.00
25_S 374_V 0.80 0.23 0.00
183_W 234_S 0.80 0.22 0.00
185_I 44_A 0.79 0.22 0.00
194_A 432_G 0.78 0.21 0.00
25_S 246_P 0.78 0.21 0.00
68_P 53_V 0.76 0.20 0.00
58_V 399_V 0.76 0.20 0.00
212_Y 38_L 0.76 0.20 0.00
114_I 318_A 0.76 0.20 0.00
38_V 113_A 0.75 0.20 0.00
212_Y 243_A 0.75 0.20 0.00
114_I 10_L 0.75 0.19 0.00
88_I 111_A 0.75 0.19 0.00
164_V 286_I 0.75 0.19 0.00
104_Q 336_I 0.75 0.19 0.00
114_I 360_R 0.74 0.19 0.00
212_Y 252_A 0.74 0.19 0.00
172_V 390_A 0.74 0.19 0.00
88_I 138_L 0.73 0.18 0.00
239_Y 89_L 0.73 0.18 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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