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OPENSEQ.org
cIV_C_2_cI_K_10_Pdenitr
Genes: A B A+B
Length: 273 101 356
Sequences: 2897 4172 1792
Seq/Len: 10.61 41.31 5.03
MirrorTree (Pazo et al. 2001) 0.59
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 0.06
2 0.00 0.00 1.71
5 0.00 0.01 3.25
10 0.00 0.01 3.48
20 0.00 0.01 3.61
100 0.00 0.03 3.84
∞ 0.01 0.07 4.79
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
23_G 80_I 1.08 0.86 0.07
60_Y 75_A 1.08 0.86 0.07
196_A 31_V 1.07 0.85 0.07
125_G 32_I 1.05 0.84 0.07
21_A 29_V 1.05 0.84 0.07
164_L 80_I 1.05 0.84 0.07
107_A 65_F 1.04 0.83 0.07
139_H 93_V 0.98 0.78 0.05
167_D 27_K 0.95 0.74 0.05
87_Q 64_M 0.94 0.73 0.05
208_A 23_F 0.93 0.72 0.05
179_V 17_T 0.93 0.71 0.04
266_V 48_V 0.91 0.70 0.04
61_V 34_M 0.91 0.70 0.04
87_Q 93_V 0.91 0.69 0.04
211_M 68_T 0.91 0.69 0.04
125_G 35_S 0.89 0.67 0.04
155_V 30_I 0.86 0.64 0.04
33_A 25_N 0.86 0.63 0.04
98_V 42_A 0.85 0.62 0.04
161_A 43_V 0.85 0.62 0.04
48_P 64_M 0.84 0.61 0.03
225_I 50_F 0.83 0.60 0.03
168_R 25_N 0.83 0.59 0.03
150_L 31_V 0.82 0.57 0.03
150_L 32_I 0.82 0.57 0.03
114_Y 12_A 0.81 0.57 0.03
113_L 89_G 0.81 0.56 0.03
265_F 96_V 0.81 0.56 0.03
168_R 75_A 0.81 0.56 0.03
53_I 97_N 0.81 0.56 0.03
237_G 55_G 0.80 0.54 0.03
242_K 70_A 0.80 0.54 0.03
215_F 34_M 0.79 0.54 0.03
135_F 74_A 0.79 0.53 0.03
191_Y 64_M 0.79 0.53 0.03
242_K 14_L 0.78 0.53 0.03
32_V 51_S 0.78 0.53 0.03
13_P 21_G 0.78 0.52 0.03
235_L 43_V 0.78 0.52 0.03
25_F 80_I 0.78 0.52 0.03
161_A 30_I 0.78 0.51 0.03
184_C 28_N 0.77 0.51 0.03
132_I 47_F 0.77 0.50 0.03
58_V 13_I 0.77 0.50 0.03
28_L 64_M 0.76 0.50 0.03
86_L 66_V 0.76 0.49 0.03
140_L 90_T 0.76 0.49 0.03
109_I 29_V 0.75 0.47 0.02
183_V 13_I 0.74 0.47 0.02
150_L 69_V 0.74 0.47 0.02
95_M 70_A 0.74 0.46 0.02
158_A 29_V 0.74 0.46 0.02
150_L 26_R 0.73 0.46 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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