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OPENSEQ.org
cIV_C_4_cI_K_40_Pdenitr
Genes: A B A+B
Length: 273 101 368
Sequences: 2888 222 199
Seq/Len: 10.58 2.2 0.54
MirrorTree (Pazo et al. 2001) 0.22
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.03
∞ 0.01 0.00 0.53
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
74_E 11_G 1.59 0.65 0.00
236_K 27_K 1.29 0.42 0.00
27_M 31_V 1.28 0.41 0.00
63_F 31_V 1.26 0.40 0.00
210_Y 42_A 1.22 0.37 0.00
82_V 2_I 1.21 0.36 0.00
79_T 2_I 1.15 0.32 0.00
29_T 7_Y 1.14 0.31 0.00
184_C 3_G 1.12 0.30 0.00
137_P 1_M 1.11 0.29 0.00
210_Y 83_V 1.11 0.29 0.00
25_F 3_G 1.09 0.28 0.00
130_E 39_M 1.08 0.28 0.00
127_W 13_I 1.08 0.27 0.00
206_A 17_T 1.07 0.27 0.00
60_Y 17_T 1.07 0.27 0.00
26_V 29_V 1.06 0.26 0.00
113_L 89_G 1.06 0.26 0.00
188_L 83_V 1.05 0.26 0.00
104_W 47_F 1.05 0.25 0.00
179_V 29_V 1.03 0.24 0.00
147_I 47_F 1.03 0.24 0.00
64_G 5_T 1.03 0.24 0.00
197_A 19_I 1.02 0.24 0.00
203_T 47_F 1.02 0.24 0.00
191_Y 61_V 1.02 0.24 0.00
104_W 66_V 1.02 0.24 0.00
188_L 39_M 1.01 0.23 0.00
179_V 9_V 1.00 0.23 0.00
138_W 29_V 0.99 0.22 0.00
175_L 45_I 0.99 0.22 0.00
147_I 27_K 0.98 0.22 0.00
168_R 17_T 0.98 0.21 0.00
234_L 24_V 0.98 0.21 0.00
128_P 22_I 0.97 0.21 0.00
69_V 11_G 0.96 0.21 0.00
140_L 18_G 0.96 0.21 0.00
236_K 61_V 0.96 0.20 0.00
200_L 53_H 0.96 0.20 0.00
28_L 83_V 0.95 0.20 0.00
208_A 64_M 0.95 0.20 0.00
18_F 48_V 0.95 0.20 0.00
52_L 61_V 0.94 0.19 0.00
103_A 72_A 0.93 0.19 0.00
171_T 76_I 0.93 0.19 0.00
140_L 92_A 0.92 0.19 0.00
177_V 98_V 0.92 0.19 0.00
9_Q 18_G 0.92 0.18 0.00
146_L 47_F 0.92 0.18 0.00
92_L 65_F 0.92 0.18 0.00
204_V 90_T 0.91 0.18 0.00
128_P 99_M 0.91 0.18 0.00
15_I 16_V 0.91 0.18 0.00
56_V 27_K 0.91 0.18 0.00
10_I 16_V 0.91 0.18 0.00
6_H 92_A 0.90 0.18 0.00
55_L 74_A 0.90 0.18 0.00
137_P 31_V 0.90 0.18 0.00
109_I 29_V 0.90 0.18 0.00
51_F 31_V 0.90 0.17 0.00
208_A 11_G 0.90 0.17 0.00
172_I 61_V 0.89 0.17 0.00
180_I 31_V 0.88 0.17 0.00
202_D 47_F 0.88 0.17 0.00
24_A 35_S 0.87 0.16 0.00
92_L 96_V 0.87 0.16 0.00
136_D 32_I 0.87 0.16 0.00
98_V 13_I 0.87 0.16 0.00
171_T 24_V 0.87 0.16 0.00
201_A 42_A 0.86 0.16 0.00
241_Q 7_Y 0.86 0.16 0.00
29_T 36_I 0.86 0.16 0.00
10_I 5_T 0.86 0.16 0.00
82_V 58_A 0.86 0.16 0.00
49_W 13_I 0.85 0.16 0.00
91_I 39_M 0.85 0.15 0.00
166_G 81_L 0.85 0.15 0.00
204_V 61_V 0.85 0.15 0.00
115_P 76_I 0.84 0.15 0.00
20_G 55_G 0.84 0.15 0.00
59_L 39_M 0.84 0.15 0.00
240_T 2_I 0.84 0.15 0.00
6_H 32_I 0.84 0.15 0.00
107_A 61_V 0.84 0.15 0.00
70_V 16_V 0.84 0.15 0.00
107_A 66_V 0.84 0.15 0.00
7_D 66_V 0.84 0.15 0.00
58_V 98_V 0.83 0.15 0.00
95_M 16_V 0.83 0.15 0.00
153_V 39_M 0.83 0.14 0.00
221_I 19_I 0.83 0.14 0.00
171_T 27_K 0.82 0.14 0.00
167_D 74_A 0.82 0.14 0.00
53_I 10_V 0.82 0.14 0.00
107_A 83_V 0.82 0.14 0.00
11_L 16_V 0.82 0.14 0.00
180_I 55_G 0.82 0.14 0.00
67_A 31_V 0.82 0.14 0.00
271_W 88_R 0.82 0.14 0.00
203_T 53_H 0.82 0.14 0.00
18_F 97_N 0.82 0.14 0.00
91_I 45_I 0.82 0.14 0.00
80_P 64_M 0.81 0.14 0.00
136_D 84_F 0.81 0.14 0.00
38_I 19_I 0.81 0.14 0.00
176_I 74_A 0.81 0.14 0.00
203_T 64_M 0.81 0.14 0.00
232_I 48_V 0.81 0.14 0.00
57_G 95_D 0.80 0.14 0.00
66_W 10_V 0.80 0.14 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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