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OPENSEQ.org
cIV_C_2_cI_K_6_Pdenitr
Genes: A B A+B
Length: 273 101 356
Sequences: 2897 4661 2129
Seq/Len: 10.61 46.15 5.98
MirrorTree (Pazo et al. 2001) 0.60
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 0.09
2 0.00 0.00 1.85
5 0.00 0.01 3.99
10 0.00 0.01 4.37
20 0.00 0.01 4.55
100 0.00 0.03 4.82
∞ 0.01 0.07 5.69
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
32_V 51_S 1.15 0.92 0.17
81_V 80_I 1.12 0.91 0.16
48_P 64_M 1.04 0.86 0.12
125_G 32_I 1.03 0.86 0.12
183_V 13_I 0.98 0.81 0.10
164_L 80_I 0.95 0.79 0.09
162_F 92_A 0.92 0.75 0.08
169_K 74_A 0.91 0.74 0.08
135_F 74_A 0.91 0.74 0.08
61_V 34_M 0.90 0.73 0.08
150_L 31_V 0.89 0.72 0.08
208_A 23_F 0.88 0.71 0.07
237_G 44_N 0.87 0.70 0.07
158_A 18_G 0.87 0.70 0.07
135_F 38_L 0.86 0.69 0.07
238_Q 99_M 0.85 0.67 0.07
196_A 31_V 0.85 0.67 0.07
186_T 79_A 0.84 0.66 0.06
98_V 42_A 0.84 0.66 0.06
21_A 93_V 0.84 0.65 0.06
103_A 38_L 0.83 0.65 0.06
147_I 74_A 0.82 0.63 0.06
139_H 93_V 0.81 0.61 0.06
208_A 47_F 0.80 0.61 0.06
135_F 66_V 0.80 0.60 0.05
237_G 55_G 0.79 0.59 0.05
36_K 99_M 0.79 0.59 0.05
37_G 93_V 0.79 0.59 0.05
113_L 89_G 0.79 0.58 0.05
146_L 69_V 0.78 0.58 0.05
21_A 29_V 0.78 0.57 0.05
170_T 74_A 0.78 0.57 0.05
84_I 45_I 0.77 0.56 0.05
134_T 42_A 0.77 0.55 0.05
8_Y 70_A 0.76 0.55 0.05
6_H 74_A 0.76 0.54 0.05
98_V 87_N 0.76 0.54 0.05
5_N 25_N 0.76 0.54 0.05
70_V 98_V 0.75 0.53 0.04
168_R 25_N 0.74 0.52 0.04
103_A 66_V 0.74 0.52 0.04
10_I 59_G 0.74 0.52 0.04
167_D 27_K 0.74 0.51 0.04
229_V 65_F 0.74 0.51 0.04
25_F 80_I 0.74 0.51 0.04
87_Q 64_M 0.73 0.50 0.04
103_A 63_T 0.73 0.49 0.04
70_V 46_N 0.73 0.49 0.04
90_F 34_M 0.72 0.49 0.04
18_F 92_A 0.72 0.48 0.04
38_I 39_M 0.72 0.48 0.04
132_I 19_I 0.71 0.47 0.04
79_T 34_M 0.71 0.47 0.04
22_I 80_I 0.71 0.47 0.04
180_I 13_I 0.71 0.47 0.04
62_M 89_G 0.71 0.47 0.04
134_T 25_N 0.71 0.46 0.04
225_I 50_F 0.70 0.46 0.04
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
3171 6.36 cIV_C_2_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3170 5.98 cIV_C_2_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
3169 5.03 cIV_C_2_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3168 1.32 cIV_C_2_cI_K_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3167 0.54 cIV_C_4_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3166 1.32 cIV_C_4_cI_K_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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