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OPENSEQ.org
cIV_B_2_cI_A_4_Pdenitr
Genes: A B A+B
Length: 252 121 346
Sequences: 4628 4975 3048
Seq/Len: 18.37 41.12 8.81
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 0.35
2 0.00 0.00 0.55
5 0.00 0.00 5.38
10 0.01 0.00 5.93
20 0.01 0.00 6.11
100 0.02 0.01 6.35
∞ 0.04 0.02 8.17
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
164_V 53_D 0.93 0.85 0.01
164_V 99_M 0.92 0.85 0.01
92_I 66_V 0.88 0.81 0.01
239_Y 39_P 0.87 0.81 0.01
54_L 119_E 0.84 0.77 0.01
23_A 79_F 0.84 0.77 0.01
76_P 84_A 0.83 0.76 0.01
55_I 85_V 0.80 0.71 0.01
106_M 67_S 0.79 0.70 0.01
31_Q 67_S 0.78 0.69 0.01
139_L 79_F 0.78 0.69 0.01
92_I 82_P 0.78 0.69 0.01
28_A 113_W 0.77 0.68 0.01
160_N 119_E 0.76 0.66 0.01
17_G 68_I 0.75 0.65 0.01
147_A 75_L 0.75 0.65 0.01
169_K 117_A 0.75 0.64 0.01
231_V 37_P 0.74 0.64 0.01
27_L 13_V 0.74 0.63 0.01
51_L 81_F 0.74 0.63 0.01
183_W 78_A 0.73 0.62 0.01
18_M 87_F 0.72 0.61 0.01
46_T 117_A 0.72 0.61 0.01
144_L 75_L 0.72 0.59 0.01
58_V 100_V 0.72 0.59 0.01
170_V 102_L 0.71 0.59 0.01
131_G 95_F 0.71 0.58 0.01
42_I 83_W 0.69 0.56 0.01
228_P 49_F 0.69 0.56 0.01
141_K 117_A 0.69 0.55 0.01
19_N 53_D 0.69 0.54 0.01
54_L 19_S 0.69 0.54 0.01
166_V 18_A 0.68 0.54 0.01
230_V 121_A 0.68 0.54 0.01
52_L 35_R 0.68 0.54 0.01
42_I 62_R 0.67 0.52 0.01
111_D 102_L 0.67 0.52 0.01
237_E 32_I 0.67 0.51 0.01
76_P 11_I 0.67 0.51 0.01
239_Y 44_A 0.66 0.50 0.01
51_L 29_A 0.66 0.50 0.01
83_L 26_I 0.66 0.50 0.01
42_I 117_A 0.66 0.49 0.01
49_V 105_L 0.65 0.49 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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