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OPENSEQ.org
cIV_B_20_cI_A_10_Pdenitr
Genes: A B A+B
Length: 252 121 346
Sequences: 4606 4764 2994
Seq/Len: 18.28 39.37 8.65
MirrorTree (Pazo et al. 2001) 0.70
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 0.27
2 0.00 0.00 0.45
5 0.00 0.00 5.22
10 0.01 0.00 5.75
20 0.01 0.00 5.97
100 0.02 0.01 6.21
∞ 0.04 0.02 8.03
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
131_G 95_F 1.03 0.92 0.05
76_P 84_A 0.97 0.88 0.04
92_I 66_V 0.96 0.88 0.04
164_V 99_M 0.91 0.84 0.03
17_G 68_I 0.91 0.83 0.03
147_A 75_L 0.91 0.83 0.03
146_D 85_V 0.89 0.82 0.03
58_V 100_V 0.87 0.80 0.03
164_V 53_D 0.85 0.78 0.03
46_T 117_A 0.83 0.75 0.03
54_L 119_E 0.83 0.75 0.03
47_I 26_I 0.82 0.73 0.02
106_M 67_S 0.81 0.72 0.02
239_Y 39_P 0.80 0.71 0.02
169_K 117_A 0.79 0.70 0.02
51_L 81_F 0.79 0.70 0.02
92_I 82_P 0.79 0.70 0.02
237_E 16_G 0.78 0.69 0.02
231_V 37_P 0.77 0.68 0.02
187_A 121_A 0.76 0.66 0.02
180_I 98_L 0.75 0.65 0.02
54_L 23_I 0.75 0.64 0.02
28_A 113_W 0.75 0.64 0.02
142_E 35_R 0.74 0.63 0.02
230_V 121_A 0.74 0.62 0.02
206_V 100_V 0.73 0.61 0.02
47_I 85_V 0.73 0.61 0.02
117_I 11_I 0.73 0.61 0.02
180_I 110_A 0.73 0.60 0.02
160_N 119_E 0.72 0.60 0.02
67_V 14_F 0.72 0.60 0.02
237_E 99_M 0.72 0.60 0.02
137_L 67_S 0.72 0.59 0.02
44_A 84_A 0.72 0.59 0.02
42_I 83_W 0.71 0.58 0.02
92_I 35_R 0.71 0.58 0.02
52_L 83_W 0.71 0.58 0.02
31_Q 67_S 0.71 0.57 0.02
54_L 12_L 0.70 0.57 0.02
139_L 79_F 0.70 0.57 0.02
19_N 53_D 0.70 0.57 0.02
177_T 28_A 0.70 0.56 0.02
42_I 117_A 0.70 0.56 0.02
141_K 117_A 0.70 0.56 0.02
177_T 72_I 0.69 0.55 0.01
239_Y 44_A 0.69 0.54 0.01
74_N 101_F 0.68 0.53 0.01
162_V 68_I 0.68 0.53 0.01
55_I 85_V 0.68 0.53 0.01
44_A 33_A 0.68 0.53 0.01
183_W 78_A 0.68 0.52 0.01
31_Q 29_A 0.68 0.52 0.01
52_L 80_L 0.68 0.52 0.01
23_A 79_F 0.68 0.52 0.01
195_V 90_L 0.67 0.51 0.01
116_A 18_A 0.67 0.51 0.01
243_L 17_M 0.67 0.51 0.01
228_P 49_F 0.67 0.51 0.01
139_L 115_K 0.67 0.51 0.01
240_E 22_A 0.66 0.50 0.01
56_C 77_V 0.66 0.50 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
3230 8.06 cIV_B_4_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3229 8.65 cIV_B_20_cI_A_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3228 8.14 cIV_B_10_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3227 8.15 cIV_B_20_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3226 0.91 cIV_B_40_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3225 8.81 cIV_B_2_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3224 1.06 cIV_B_2_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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