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OPENSEQ.org
cI_A_6_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 147 440 498
Sequences: 3938 3303 2259
Seq/Len: 26.79 7.51 4.54
MirrorTree (Pazo et al. 2001) 0.76
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 0.20
5 0.00 0.00 2.74
10 0.00 0.00 3.00
20 0.01 0.00 3.10
100 0.01 0.00 3.18
∞ 0.02 0.01 3.85
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 1.16 0.89 0.16
80_V 360_R 1.14 0.88 0.15
83_L 145_M 1.11 0.86 0.14
71_V 80_V 1.04 0.81 0.11
40_R 41_L 0.98 0.75 0.09
107_I 290_A 0.98 0.74 0.09
84_Y 343_M 0.97 0.74 0.09
34_G 145_M 0.96 0.73 0.09
77_I 403_Y 0.96 0.73 0.09
25_G 19_L 0.95 0.71 0.08
106_F 281_I 0.92 0.68 0.08
26_L 355_R 0.92 0.67 0.07
77_I 397_S 0.91 0.67 0.07
113_G 121_Y 0.87 0.62 0.06
29_L 362_L 0.86 0.60 0.06
50_F 415_E 0.85 0.59 0.06
44_R 107_A 0.85 0.59 0.06
40_R 390_P 0.85 0.58 0.06
85_L 351_T 0.84 0.58 0.06
69_Y 20_H 0.84 0.57 0.06
115_V 44_W 0.83 0.56 0.06
107_I 260_L 0.83 0.56 0.05
124_D 364_K 0.82 0.55 0.05
67_K 141_G 0.81 0.53 0.05
125_W 291_H 0.81 0.53 0.05
29_L 61_T 0.80 0.51 0.05
67_K 94_R 0.79 0.51 0.05
84_Y 263_F 0.79 0.51 0.05
24_I 402_A 0.79 0.50 0.05
67_K 255_A 0.79 0.50 0.05
76_V 99_N 0.79 0.50 0.05
92_I 71_P 0.78 0.49 0.04
92_I 346_V 0.78 0.49 0.04
90_T 166_F 0.78 0.48 0.04
66_A 57_L 0.77 0.48 0.04
20_L 265_A 0.77 0.48 0.04
92_I 169_I 0.77 0.48 0.04
72_A 128_T 0.77 0.48 0.04
42_R 360_R 0.77 0.48 0.04
34_G 196_S 0.77 0.48 0.04
67_K 350_D 0.77 0.47 0.04
103_A 41_L 0.77 0.47 0.04
124_D 255_A 0.77 0.47 0.04
74_F 396_G 0.77 0.47 0.04
69_Y 95_Y 0.77 0.47 0.04
21_I 265_A 0.76 0.47 0.04
88_W 268_G 0.76 0.46 0.04
93_R 60_A 0.76 0.46 0.04
100_F 349_L 0.76 0.46 0.04
24_I 365_W 0.75 0.46 0.04
28_C 211_V 0.75 0.45 0.04
98_V 398_A 0.75 0.45 0.04
69_Y 39_K 0.75 0.45 0.04
47_N 397_S 0.75 0.45 0.04
34_G 272_N 0.75 0.44 0.04
45_S 275_G 0.75 0.44 0.04
121_G 374_F 0.74 0.44 0.04
94_E 261_V 0.74 0.44 0.04
84_Y 336_M 0.74 0.44 0.04
36_F 206_A 0.74 0.43 0.04
74_F 415_E 0.74 0.43 0.04
47_N 180_L 0.74 0.43 0.04
74_F 156_F 0.73 0.43 0.04
24_I 345_L 0.73 0.42 0.04
97_W 258_V 0.73 0.42 0.04
42_R 267_V 0.73 0.42 0.04
29_L 184_P 0.73 0.42 0.04
105_I 25_I 0.73 0.42 0.04
71_V 390_P 0.73 0.42 0.04
30_M 353_R 0.72 0.41 0.04
84_Y 178_T 0.72 0.41 0.04
80_V 256_L 0.72 0.41 0.04
106_F 287_V 0.72 0.41 0.04
84_Y 44_W 0.72 0.41 0.04
24_I 249_V 0.72 0.41 0.04
25_G 204_V 0.72 0.41 0.04
88_W 72_H 0.72 0.41 0.04
25_G 60_A 0.72 0.40 0.04
80_V 415_E 0.72 0.40 0.04
101_V 398_A 0.71 0.40 0.04
120_I 66_V 0.71 0.40 0.04
92_I 402_A 0.71 0.40 0.03
72_A 76_A 0.71 0.40 0.03
35_W 392_I 0.71 0.39 0.03
39_G 360_R 0.71 0.39 0.03
26_L 373_D 0.70 0.39 0.03
24_I 242_L 0.70 0.39 0.03
112_A 108_V 0.70 0.39 0.03
36_F 116_L 0.70 0.39 0.03
112_A 145_M 0.70 0.39 0.03
120_I 43_W 0.70 0.38 0.03
31_L 253_L 0.70 0.38 0.03
83_L 171_G 0.70 0.38 0.03
126_T 119_G 0.70 0.38 0.03
29_L 188_N 0.70 0.38 0.03
19_F 392_I 0.70 0.38 0.03
94_E 211_V 0.70 0.38 0.03
41_A 366_W 0.70 0.38 0.03
94_E 59_I 0.69 0.37 0.03
100_F 22_R 0.69 0.37 0.03
22_V 369_L 0.69 0.37 0.03
76_V 50_V 0.69 0.37 0.03
43_A 106_L 0.69 0.37 0.03
94_E 176_I 0.69 0.37 0.03
22_V 354_V 0.69 0.37 0.03
34_G 172_V 0.69 0.37 0.03
31_L 243_P 0.69 0.36 0.03
103_A 257_A 0.69 0.36 0.03
35_W 63_I 0.68 0.36 0.03
105_I 402_A 0.68 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
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