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OPENSEQ.org
cIV_B_40_cI_K_40_Pdenitr
Genes: A B A+B
Length: 252 101 344
Sequences: 4089 222 215
Seq/Len: 16.23 2.2 0.62
MirrorTree (Pazo et al. 2001) 0.23
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 0.01 0.00 0.00
100 0.01 0.00 0.04
∞ 0.03 0.00 0.61
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
239_Y 64_M 1.35 0.51 0.00
90_V 5_T 1.23 0.41 0.00
55_I 36_I 1.17 0.36 0.00
39_L 17_T 1.13 0.34 0.00
182_A 11_G 1.12 0.33 0.00
167_G 19_I 1.11 0.32 0.00
109_D 47_F 1.10 0.32 0.00
238_K 42_A 1.09 0.31 0.00
160_N 17_T 1.09 0.31 0.00
83_L 61_V 1.07 0.30 0.00
43_T 61_V 1.05 0.28 0.00
164_V 61_V 1.04 0.28 0.00
167_G 42_A 1.04 0.28 0.00
59_R 36_I 1.02 0.26 0.00
47_I 74_A 0.97 0.23 0.00
205_S 31_V 0.96 0.23 0.00
84_V 99_M 0.96 0.23 0.00
114_I 42_A 0.95 0.22 0.00
134_F 31_V 0.95 0.22 0.00
243_L 31_V 0.95 0.22 0.00
59_R 66_V 0.94 0.22 0.00
169_K 13_I 0.94 0.21 0.00
75_T 54_L 0.94 0.21 0.00
61_N 65_F 0.94 0.21 0.00
104_Q 55_G 0.93 0.21 0.00
34_L 65_F 0.93 0.21 0.00
226_Y 47_F 0.93 0.20 0.00
135_D 35_S 0.92 0.20 0.00
230_V 64_M 0.92 0.20 0.00
169_K 99_M 0.92 0.20 0.00
114_I 10_V 0.92 0.20 0.00
133_A 29_V 0.92 0.20 0.00
77_I 42_A 0.92 0.20 0.00
97_L 16_V 0.91 0.20 0.00
225_A 94_E 0.91 0.20 0.00
38_V 85_F 0.91 0.20 0.00
44_A 27_K 0.91 0.20 0.00
60_F 31_V 0.90 0.19 0.00
83_L 36_I 0.90 0.19 0.00
130_D 13_I 0.90 0.19 0.00
124_S 31_V 0.90 0.19 0.00
248_E 99_M 0.90 0.19 0.00
132_V 54_L 0.89 0.19 0.00
97_L 63_T 0.89 0.19 0.00
170_V 11_G 0.89 0.18 0.00
225_A 74_A 0.88 0.18 0.00
174_V 35_S 0.88 0.18 0.00
168_K 7_Y 0.88 0.18 0.00
25_S 42_A 0.86 0.17 0.00
183_W 95_D 0.85 0.17 0.00
230_V 42_A 0.85 0.17 0.00
95_F 76_I 0.84 0.17 0.00
244_A 36_I 0.84 0.17 0.00
79_V 53_H 0.84 0.17 0.00
110_P 29_V 0.84 0.16 0.00
60_F 64_M 0.84 0.16 0.00
154_Y 1_M 0.84 0.16 0.00
200_A 16_V 0.83 0.16 0.00
114_I 55_G 0.83 0.16 0.00
205_S 39_M 0.83 0.16 0.00
250_F 32_I 0.82 0.16 0.00
240_E 11_G 0.82 0.16 0.00
203_W 72_A 0.82 0.15 0.00
217_S 94_E 0.82 0.15 0.00
34_L 16_V 0.82 0.15 0.00
199_I 12_A 0.82 0.15 0.00
97_L 83_V 0.82 0.15 0.00
110_P 95_D 0.81 0.15 0.00
105_E 29_V 0.81 0.15 0.00
29_H 52_T 0.81 0.15 0.00
64_A 57_L 0.80 0.15 0.00
236_Q 39_M 0.80 0.15 0.00
173_Q 5_T 0.80 0.15 0.00
58_V 47_F 0.80 0.15 0.00
201_Q 74_A 0.80 0.15 0.00
50_C 84_F 0.80 0.14 0.00
130_D 17_T 0.80 0.14 0.00
245_G 29_V 0.79 0.14 0.00
43_T 55_G 0.79 0.14 0.00
177_T 19_I 0.78 0.14 0.00
153_E 63_T 0.78 0.14 0.00
177_T 47_F 0.78 0.14 0.00
208_Q 9_V 0.77 0.14 0.00
217_S 42_A 0.77 0.14 0.00
249_E 39_M 0.77 0.13 0.00
209_E 9_V 0.76 0.13 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
3301 8.31 cIV_B_10_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
3300 8.28 cIV_B_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
3299 2.61 cIV_B_6_cI_K_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3297 7.24 cIV_B_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3296 7.26 cIV_B_4_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3295 8.33 cIV_B_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3294 8.64 cIV_B_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3239 0.62 cIV_B_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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