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OPENSEQ.org
cIV_C_4_cI_K_20_Pdenitr
Genes: A B A+B
Length: 273 101 367
Sequences: 2888 1319 483
Seq/Len: 10.58 13.06 1.32
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 0.00 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 0.56
∞ 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 1.37 0.75 0.02
210_Y 83_V 1.25 0.65 0.01
13_P 38_L 1.23 0.63 0.01
19_F 99_M 1.22 0.62 0.01
31_A 84_F 1.19 0.59 0.01
99_M 44_N 1.19 0.59 0.01
104_W 47_F 1.11 0.51 0.01
271_W 76_I 1.09 0.50 0.01
168_R 75_A 1.08 0.49 0.01
183_V 9_V 1.06 0.47 0.01
113_L 89_G 1.06 0.47 0.01
9_Q 18_G 1.03 0.44 0.01
176_I 35_S 1.02 0.43 0.01
210_Y 42_A 1.02 0.42 0.01
125_G 32_I 1.01 0.42 0.01
174_G 31_V 1.01 0.42 0.01
259_V 79_A 1.01 0.42 0.01
21_A 29_V 1.00 0.40 0.01
231_L 85_F 0.99 0.39 0.01
183_V 26_R 0.99 0.39 0.01
202_D 55_G 0.98 0.39 0.01
104_W 67_L 0.97 0.38 0.01
90_F 34_M 0.97 0.38 0.01
5_N 36_I 0.97 0.37 0.01
29_T 7_Y 0.96 0.37 0.01
10_I 16_V 0.94 0.35 0.01
71_N 10_V 0.93 0.34 0.01
205_Y 39_M 0.93 0.34 0.01
88_Y 10_V 0.92 0.34 0.01
91_I 99_M 0.92 0.33 0.01
173_N 42_A 0.92 0.33 0.01
69_V 43_V 0.91 0.32 0.01
179_V 80_I 0.90 0.32 0.01
232_I 81_L 0.90 0.32 0.01
92_L 84_F 0.90 0.32 0.01
164_L 80_I 0.90 0.32 0.01
30_G 47_F 0.90 0.32 0.01
31_A 7_Y 0.89 0.30 0.01
177_V 20_F 0.89 0.30 0.01
149_L 78_L 0.89 0.30 0.01
221_I 19_I 0.89 0.30 0.01
104_W 79_A 0.88 0.29 0.01
91_I 88_R 0.88 0.29 0.01
140_L 18_G 0.88 0.29 0.01
4_K 2_I 0.88 0.29 0.01
251_A 50_F 0.87 0.29 0.00
143_I 87_N 0.86 0.28 0.00
22_I 9_V 0.86 0.28 0.00
58_V 93_V 0.85 0.28 0.00
218_A 34_M 0.85 0.28 0.00
256_F 33_L 0.84 0.27 0.00
116_M 18_G 0.84 0.27 0.00
138_W 19_I 0.84 0.27 0.00
58_V 30_I 0.84 0.26 0.00
66_W 79_A 0.84 0.26 0.00
140_L 80_I 0.83 0.26 0.00
184_C 16_V 0.83 0.26 0.00
271_W 88_R 0.83 0.26 0.00
222_I 85_F 0.83 0.26 0.00
204_V 99_M 0.83 0.26 0.00
259_V 68_T 0.82 0.25 0.00
8_Y 35_S 0.82 0.25 0.00
134_T 90_T 0.82 0.25 0.00
140_L 90_T 0.82 0.25 0.00
242_K 13_I 0.82 0.25 0.00
27_M 31_V 0.82 0.25 0.00
87_Q 71_A 0.82 0.25 0.00
98_V 13_I 0.82 0.25 0.00
107_A 66_V 0.82 0.25 0.00
150_L 14_L 0.81 0.25 0.00
136_D 19_I 0.81 0.24 0.00
134_T 42_A 0.81 0.24 0.00
88_Y 93_V 0.80 0.24 0.00
28_L 16_V 0.80 0.23 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
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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