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cI_A_20_cIII_cytb_20_Pdenitr_corr

Genes: A B A+B
Length: 121 440 492
Sequences: 4481 3290 2616
Seq/Len: 37.03 7.48 5.32
MirrorTree (Pazo et al. 2001) 0.74
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 0.07
2 0.00 0.00 0.21
5 0.00 0.00 3.43
10 0.00 0.00 3.77
20 0.00 0.00 3.84
100 0.01 0.00 3.92
0.02 0.01 4.66
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
79_F 343_M 1.44 0.98 0.78
19_S 242_L 1.18 0.92 0.56
75_L 360_R 1.11 0.89 0.49
35_R 41_L 1.06 0.86 0.44
101_F 281_I 1.02 0.82 0.39
91_S 29_V 0.95 0.76 0.33
93_V 261_V 0.93 0.74 0.30
55_A 197_L 0.92 0.72 0.29
20_A 19_L 0.91 0.71 0.28
93_V 398_A 0.90 0.70 0.28
72_I 403_Y 0.89 0.69 0.26
45_Y 261_V 0.88 0.67 0.25
27_L 405_L 0.84 0.62 0.22
34_V 360_R 0.83 0.61 0.21
100_V 138_M 0.82 0.60 0.21
106_T 40_N 0.82 0.59 0.20
21_L 33_L 0.82 0.59 0.20
83_W 360_R 0.81 0.58 0.20
72_I 411_L 0.81 0.58 0.20
60_D 276_H 0.80 0.56 0.19
78_A 145_M 0.80 0.56 0.19
67_S 128_T 0.80 0.56 0.19
71_I 99_N 0.80 0.56 0.19
66_V 390_P 0.79 0.55 0.18
115_K 43_W 0.78 0.54 0.17
64_Y 20_H 0.78 0.53 0.17
93_V 369_L 0.77 0.53 0.17
16_G 57_L 0.77 0.53 0.17
80_L 394_L 0.76 0.51 0.16
50_N 115_G 0.76 0.50 0.16
101_F 243_P 0.76 0.50 0.16
26_I 208_L 0.75 0.49 0.15
26_I 328_A 0.75 0.49 0.15
93_V 260_L 0.74 0.48 0.15
115_K 66_V 0.74 0.48 0.15
78_A 171_G 0.74 0.48 0.15
30_A 63_I 0.74 0.48 0.15
19_S 249_V 0.74 0.48 0.15
40_E 275_G 0.73 0.47 0.14
29_A 145_M 0.72 0.45 0.14
59_F 381_G 0.72 0.45 0.14
84_A 158_G 0.72 0.45 0.13
107_V 108_V 0.72 0.45 0.13
23_I 211_V 0.71 0.44 0.13
16_G 134_L 0.71 0.44 0.13
66_V 80_V 0.71 0.44 0.13
111_Y 78_A 0.71 0.44 0.13
67_S 139_M 0.71 0.44 0.13
98_L 176_I 0.71 0.43 0.13
28_A 57_L 0.70 0.43 0.13
72_I 397_S 0.70 0.43 0.13
101_F 76_A 0.70 0.43 0.12
91_S 180_L 0.70 0.42 0.12
45_Y 386_E 0.70 0.42 0.12
39_P 185_A 0.70 0.42 0.12
21_L 123_A 0.70 0.42 0.12
119_E 255_A 0.70 0.42 0.12
20_A 60_A 0.69 0.41 0.12
96_W 338_G 0.69 0.41 0.12
117_A 374_F 0.69 0.41 0.12
25_L 74_D 0.69 0.40 0.11
11_I 19_L 0.68 0.40 0.11
11_I 371_A 0.68 0.40 0.11
53_D 350_D 0.68 0.39 0.11
114_K 348_W 0.68 0.39 0.11
39_P 107_A 0.68 0.39 0.11
85_V 263_F 0.68 0.39 0.11
98_L 257_A 0.67 0.38 0.11
72_I 127_V 0.67 0.38 0.11
121_A 262_V 0.67 0.38 0.10
67_S 116_L 0.67 0.38 0.10
116_G 92_M 0.67 0.38 0.10
83_W 269_F 0.67 0.38 0.10
26_I 243_P 0.66 0.37 0.10
77_V 46_I 0.66 0.37 0.10
19_S 408_L 0.66 0.36 0.10
87_F 264_F 0.66 0.36 0.10
14_F 108_V 0.66 0.36 0.10
62_R 94_R 0.65 0.36 0.10
115_K 240_D 0.65 0.35 0.10
95_F 81_E 0.65 0.35 0.10
20_A 410_L 0.65 0.35 0.10
38_D 106_L 0.65 0.35 0.10
12_L 410_L 0.65 0.35 0.10
110_A 392_I 0.65 0.35 0.10
23_I 63_I 0.65 0.35 0.09
53_D 260_L 0.64 0.34 0.09
67_S 76_A 0.64 0.34 0.09
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
2988 5.32 cI_A_20_cIII_cytb_40_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
2987 5.29 cI_A_20_cIII_cytb_40_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.82 Done - Shared
2986 0.61 cI_A_40_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2985 5.32 cI_A_20_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.78 Done - Shared
2984 5.68 cI_A_10_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.66 Done - Shared
2983 5.68 cI_A_10_cIII_cytb_10_Pdenitr_corr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.61 Done - Shared

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