May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_A_20_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 147 440 497
Sequences: 3799 3303 2211
Seq/Len: 25.84 7.51 4.45
MirrorTree (Pazo et al. 2001) 0.75
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 0.19
5 0.00 0.00 2.70
10 0.00 0.00 2.95
20 0.00 0.00 3.00
100 0.01 0.00 3.09
∞ 0.02 0.01 3.77
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
50_F 261_V 1.17 0.89 0.17
25_G 19_L 1.12 0.86 0.14
83_L 145_M 1.08 0.83 0.13
106_F 281_I 1.06 0.82 0.12
80_V 360_R 1.06 0.82 0.12
40_R 41_L 1.04 0.80 0.12
106_F 76_A 0.98 0.74 0.09
77_I 403_Y 0.97 0.73 0.09
112_A 108_V 0.95 0.71 0.09
77_I 397_S 0.94 0.69 0.08
84_Y 44_W 0.94 0.69 0.08
71_V 80_V 0.93 0.68 0.08
92_I 169_I 0.93 0.68 0.08
31_L 243_P 0.91 0.66 0.07
26_L 355_R 0.90 0.64 0.07
69_Y 95_Y 0.90 0.64 0.07
85_L 351_T 0.88 0.61 0.07
124_D 364_K 0.87 0.61 0.06
50_F 415_E 0.87 0.61 0.06
69_Y 20_H 0.86 0.59 0.06
120_I 66_V 0.85 0.58 0.06
105_I 402_A 0.85 0.58 0.06
28_C 211_V 0.85 0.58 0.06
72_A 76_A 0.84 0.57 0.06
74_F 256_L 0.84 0.56 0.06
34_G 145_M 0.83 0.56 0.06
44_R 107_A 0.82 0.54 0.05
74_F 71_P 0.81 0.53 0.05
19_F 41_L 0.80 0.52 0.05
107_I 290_A 0.80 0.52 0.05
88_W 268_G 0.80 0.51 0.05
94_E 176_I 0.80 0.51 0.05
34_G 196_S 0.79 0.50 0.05
47_N 180_L 0.79 0.50 0.05
66_A 57_L 0.79 0.49 0.05
124_D 255_A 0.79 0.49 0.05
34_G 272_N 0.79 0.49 0.05
100_F 349_L 0.78 0.49 0.05
29_L 61_T 0.78 0.48 0.04
105_I 25_I 0.78 0.48 0.04
84_Y 343_M 0.77 0.47 0.04
91_S 135_I 0.77 0.47 0.04
34_G 404_F 0.77 0.47 0.04
29_L 362_L 0.77 0.47 0.04
85_L 178_T 0.77 0.47 0.04
67_K 94_R 0.77 0.46 0.04
27_C 127_V 0.76 0.46 0.04
115_V 44_W 0.76 0.46 0.04
40_R 390_P 0.76 0.46 0.04
45_S 275_G 0.76 0.45 0.04
111_L 40_N 0.76 0.45 0.04
74_F 95_Y 0.76 0.45 0.04
16_F 168_A 0.75 0.45 0.04
24_I 258_V 0.75 0.45 0.04
94_E 261_V 0.75 0.44 0.04
92_I 346_V 0.75 0.44 0.04
80_V 415_E 0.75 0.44 0.04
34_G 169_I 0.75 0.44 0.04
31_L 253_L 0.74 0.43 0.04
113_G 121_Y 0.74 0.43 0.04
66_A 56_V 0.74 0.43 0.04
98_V 398_A 0.74 0.43 0.04
116_Y 415_E 0.74 0.43 0.04
72_A 37_T 0.74 0.43 0.04
74_F 396_G 0.74 0.43 0.04
67_K 364_K 0.74 0.43 0.04
112_A 371_A 0.74 0.42 0.04
25_G 60_A 0.73 0.42 0.04
112_A 174_E 0.73 0.42 0.04
125_W 291_H 0.73 0.42 0.04
115_V 392_I 0.73 0.42 0.04
120_I 145_M 0.73 0.42 0.04
50_F 185_A 0.73 0.42 0.04
74_F 415_E 0.73 0.42 0.04
57_V 61_T 0.73 0.42 0.04
105_I 138_M 0.72 0.41 0.04
95_S 200_L 0.72 0.41 0.04
72_A 128_T 0.72 0.41 0.04
84_Y 81_E 0.72 0.40 0.04
98_V 106_L 0.72 0.40 0.04
23_A 141_G 0.72 0.40 0.04
43_A 106_L 0.72 0.40 0.04
76_V 99_N 0.72 0.40 0.04
35_W 63_I 0.72 0.40 0.04
26_L 33_L 0.72 0.40 0.04
48_V 379_W 0.71 0.39 0.04
67_K 255_A 0.71 0.39 0.04
107_I 178_T 0.71 0.39 0.04
16_F 19_L 0.71 0.39 0.03
28_C 227_V 0.71 0.39 0.03
64_L 381_G 0.71 0.39 0.03
101_V 398_A 0.71 0.39 0.03
104_A 89_G 0.71 0.39 0.03
100_F 22_R 0.70 0.38 0.03
120_I 240_D 0.70 0.38 0.03
112_A 145_M 0.70 0.38 0.03
68_F 163_T 0.70 0.38 0.03
28_C 410_L 0.70 0.38 0.03
39_G 360_R 0.70 0.37 0.03
67_K 350_D 0.69 0.37 0.03
34_G 172_V 0.69 0.37 0.03
84_Y 336_M 0.69 0.37 0.03
71_V 390_P 0.69 0.37 0.03
66_A 237_A 0.69 0.36 0.03
84_Y 178_T 0.69 0.36 0.03
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
2967 4.45 cI_A_20_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
2965 4.54 cI_A_6_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
2964 3.88 cI_A_10_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.43 Done - Shared
2963 3.87 cI_A_10_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.50 Done - Shared
2961 3.86 cI_A_10_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.46 Done - Shared
2265 4.36 cI_E_cIII_cytb Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.09 Done - Shared
2264 0.07 cI_E_cIII_cytb Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
Page generated in 0.441 seconds.