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OPENSEQ.org
cIV_C_2_cI_K_4_Pdenitr
Genes: A B A+B
Length: 273 101 354
Sequences: 2897 4825 2251
Seq/Len: 10.61 47.77 6.36
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 0.10
2 0.00 0.00 1.85
5 0.00 0.01 4.16
10 0.00 0.01 4.61
20 0.00 0.02 4.80
100 0.00 0.03 5.01
∞ 0.01 0.07 6.02
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 1.04 0.88 0.05
81_V 80_I 1.04 0.88 0.05
135_F 74_A 0.98 0.83 0.04
61_V 34_M 0.97 0.82 0.04
98_V 42_A 0.96 0.81 0.04
48_P 64_M 0.92 0.78 0.04
169_K 74_A 0.91 0.76 0.04
135_F 66_V 0.90 0.75 0.04
38_I 39_M 0.86 0.71 0.03
183_V 13_I 0.82 0.65 0.03
186_T 79_A 0.82 0.65 0.03
6_H 74_A 0.81 0.64 0.03
150_L 31_V 0.81 0.64 0.03
208_A 47_F 0.80 0.63 0.03
108_F 85_F 0.80 0.62 0.03
208_A 23_F 0.80 0.61 0.02
180_I 80_I 0.79 0.61 0.02
36_K 99_M 0.79 0.61 0.02
135_F 38_L 0.79 0.60 0.02
8_Y 70_A 0.78 0.60 0.02
237_G 44_N 0.78 0.60 0.02
135_F 71_A 0.78 0.59 0.02
134_T 25_N 0.78 0.59 0.02
103_A 38_L 0.78 0.59 0.02
147_I 74_A 0.78 0.58 0.02
23_G 80_I 0.77 0.58 0.02
238_Q 99_M 0.77 0.58 0.02
132_I 19_I 0.77 0.57 0.02
87_Q 93_V 0.76 0.56 0.02
268_I 68_T 0.76 0.56 0.02
158_A 18_G 0.76 0.56 0.02
99_M 62_F 0.76 0.56 0.02
25_F 80_I 0.76 0.56 0.02
125_G 32_I 0.76 0.56 0.02
182_G 55_G 0.75 0.55 0.02
80_P 62_F 0.75 0.55 0.02
162_F 92_A 0.75 0.55 0.02
180_I 13_I 0.75 0.54 0.02
113_L 89_G 0.75 0.54 0.02
24_A 64_M 0.74 0.53 0.02
5_N 25_N 0.73 0.52 0.02
237_G 55_G 0.73 0.52 0.02
196_A 31_V 0.73 0.51 0.02
49_W 14_L 0.73 0.51 0.02
221_I 46_N 0.73 0.51 0.02
168_R 25_N 0.73 0.51 0.02
164_L 80_I 0.72 0.51 0.02
111_N 81_L 0.72 0.50 0.02
170_T 74_A 0.72 0.50 0.02
98_V 87_N 0.72 0.50 0.02
54_G 68_T 0.72 0.49 0.02
265_F 96_V 0.71 0.49 0.02
229_V 65_F 0.71 0.49 0.02
87_Q 64_M 0.71 0.48 0.02
121_P 12_A 0.71 0.48 0.02
103_A 63_T 0.71 0.48 0.02
146_L 69_V 0.70 0.48 0.02
77_E 99_M 0.70 0.47 0.02
58_V 12_A 0.69 0.46 0.02
147_I 53_H 0.69 0.46 0.02
83_R 39_M 0.69 0.45 0.02
61_V 43_V 0.69 0.45 0.02
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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