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OPENSEQ.org
cIV_C_2_cI_K_20_Pdenitr
Genes: A B A+B
Length: 273 101 366
Sequences: 2897 1319 483
Seq/Len: 10.61 13.06 1.32
MirrorTree (Pazo et al. 2001) 0.29
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 0.02
2 0.00 0.00 0.07
5 0.00 0.00 0.21
10 0.00 0.01 0.31
20 0.00 0.01 0.43
100 0.00 0.02 0.55
∞ 0.01 0.03 1.29
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
179_V 13_I 1.45 0.81 0.05
210_Y 83_V 1.24 0.64 0.03
164_L 80_I 1.21 0.61 0.03
99_M 44_N 1.20 0.60 0.03
13_P 38_L 1.15 0.56 0.02
104_W 47_F 1.12 0.53 0.02
183_V 9_V 1.10 0.51 0.02
271_W 76_I 1.09 0.49 0.02
31_A 84_F 1.07 0.48 0.02
168_R 75_A 1.05 0.46 0.02
113_L 89_G 1.05 0.45 0.02
125_G 32_I 1.05 0.45 0.02
19_F 99_M 1.05 0.45 0.02
183_V 26_R 1.03 0.43 0.01
134_T 42_A 1.01 0.41 0.01
9_Q 18_G 1.00 0.41 0.01
164_L 20_F 0.99 0.40 0.01
176_I 35_S 0.99 0.40 0.01
5_N 36_I 0.97 0.38 0.01
90_F 34_M 0.97 0.38 0.01
231_L 85_F 0.95 0.36 0.01
179_V 80_I 0.95 0.36 0.01
58_V 93_V 0.95 0.36 0.01
259_V 79_A 0.93 0.34 0.01
140_L 90_T 0.92 0.34 0.01
21_A 29_V 0.92 0.33 0.01
104_W 67_L 0.92 0.33 0.01
196_A 90_T 0.91 0.33 0.01
92_L 84_F 0.91 0.32 0.01
4_K 2_I 0.90 0.32 0.01
138_W 19_I 0.90 0.32 0.01
58_V 30_I 0.89 0.30 0.01
186_T 17_T 0.88 0.30 0.01
251_A 50_F 0.88 0.29 0.01
29_T 7_Y 0.87 0.29 0.01
91_I 99_M 0.87 0.29 0.01
88_Y 10_V 0.87 0.29 0.01
104_W 79_A 0.87 0.29 0.01
8_Y 35_S 0.86 0.28 0.01
222_I 85_F 0.86 0.28 0.01
256_F 33_L 0.86 0.28 0.01
174_G 31_V 0.86 0.28 0.01
184_C 16_V 0.85 0.27 0.01
173_N 42_A 0.85 0.27 0.01
107_A 66_V 0.85 0.27 0.01
205_Y 39_M 0.85 0.27 0.01
218_A 34_M 0.84 0.27 0.01
140_L 80_I 0.84 0.27 0.01
10_I 16_V 0.84 0.27 0.01
161_A 24_V 0.84 0.26 0.01
91_I 88_R 0.83 0.26 0.01
202_D 55_G 0.83 0.26 0.01
87_Q 71_A 0.83 0.26 0.01
142_L 94_E 0.83 0.26 0.01
69_V 43_V 0.82 0.25 0.01
239_M 36_I 0.82 0.25 0.01
236_K 30_I 0.82 0.25 0.01
71_N 47_F 0.82 0.25 0.01
30_G 67_L 0.82 0.25 0.01
242_K 13_I 0.81 0.25 0.01
56_V 93_V 0.81 0.24 0.01
221_I 19_I 0.81 0.24 0.01
222_I 22_I 0.81 0.24 0.01
205_Y 58_A 0.80 0.24 0.01
146_L 11_G 0.80 0.24 0.01
232_I 14_L 0.80 0.23 0.01
116_M 18_G 0.80 0.23 0.01
138_W 61_V 0.80 0.23 0.01
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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