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OPENSEQ.org
cIV_C_4_cI_J_20_Pdenitr
Genes: A B A+B
Length: 273 200 432
Sequences: 2897 6534 2876
Seq/Len: 10.61 32.67 6.66
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 0.13
2 0.00 0.00 0.27
5 0.00 0.01 4.52
10 0.00 0.01 4.99
20 0.00 0.01 5.13
100 0.00 0.03 5.24
∞ 0.01 0.06 6.08
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
13_P 59_V 1.17 0.94 0.23
167_D 164_L 1.14 0.94 0.21
238_Q 157_A 1.05 0.89 0.16
136_D 29_S 0.99 0.85 0.14
55_L 145_L 0.97 0.83 0.12
61_V 147_F 0.97 0.83 0.12
21_A 62_G 0.96 0.82 0.12
108_F 165_T 0.94 0.81 0.11
138_W 74_M 0.94 0.81 0.11
131_G 66_V 0.93 0.79 0.11
8_Y 55_L 0.90 0.77 0.10
52_L 97_G 0.89 0.75 0.10
21_A 151_G 0.89 0.75 0.09
203_T 155_L 0.89 0.75 0.09
23_G 72_V 0.87 0.73 0.09
125_G 49_A 0.87 0.73 0.09
34_W 64_V 0.86 0.72 0.09
234_L 61_V 0.86 0.72 0.09
69_V 92_L 0.86 0.72 0.09
205_Y 150_A 0.85 0.71 0.08
210_Y 100_L 0.84 0.69 0.08
169_K 8_L 0.84 0.69 0.08
187_G 15_V 0.82 0.67 0.07
110_K 9_F 0.82 0.66 0.07
4_K 147_F 0.82 0.66 0.07
37_G 147_F 0.82 0.66 0.07
229_V 93_A 0.81 0.66 0.07
31_A 42_G 0.81 0.66 0.07
225_I 12_S 0.81 0.65 0.07
225_I 43_L 0.81 0.65 0.07
175_L 53_A 0.80 0.64 0.07
138_W 72_V 0.80 0.64 0.07
92_L 65_A 0.80 0.64 0.07
265_F 26_P 0.80 0.63 0.07
8_Y 32_W 0.79 0.62 0.06
201_A 122_A 0.76 0.58 0.06
147_I 159_I 0.76 0.58 0.06
63_F 10_A 0.76 0.58 0.06
183_V 105_G 0.76 0.58 0.06
211_M 158_M 0.76 0.57 0.06
196_A 29_S 0.75 0.57 0.06
187_G 19_M 0.75 0.56 0.06
54_G 139_L 0.75 0.56 0.06
86_L 160_G 0.75 0.56 0.06
191_Y 150_A 0.75 0.56 0.06
236_K 38_L 0.75 0.56 0.06
158_A 15_V 0.75 0.56 0.05
150_L 58_V 0.74 0.55 0.05
177_V 105_G 0.74 0.55 0.05
187_G 47_Q 0.74 0.55 0.05
201_A 76_D 0.73 0.54 0.05
22_I 39_S 0.73 0.53 0.05
70_V 33_L 0.73 0.53 0.05
79_T 30_V 0.73 0.53 0.05
241_Q 156_V 0.72 0.52 0.05
203_T 153_V 0.72 0.52 0.05
150_L 144_V 0.72 0.51 0.05
229_V 40_A 0.71 0.51 0.05
182_G 56_L 0.71 0.51 0.05
51_F 59_V 0.71 0.50 0.05
210_Y 77_V 0.71 0.50 0.05
146_L 60_Y 0.71 0.50 0.05
154_A 140_Y 0.71 0.49 0.05
23_G 133_L 0.70 0.48 0.04
4_K 156_V 0.69 0.48 0.04
168_R 147_F 0.69 0.47 0.04
21_A 16_A 0.69 0.47 0.04
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
3179 5.65 cIV_C_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
3178 5.68 cIV_C_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3177 5.65 cIV_C_2_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
3176 5.68 cIV_C_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3175 1.26 cIV_C_4_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3174 1.24 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3173 6.66 cIV_C_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
3172 6.66 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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