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OPENSEQ.org
cI_Bcterm_cIII_cytb
Genes: A B A+B
Length: 128 440 522
Sequences: 3196 3168 1080
Seq/Len: 24.97 7.2 2.07
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 0.08
2 0.00 0.00 0.77
5 0.00 0.00 0.86
10 0.00 0.00 1.00
20 0.00 0.00 1.07
100 0.01 0.00 1.15
∞ 0.01 0.01 1.90
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
112_S 172_V 1.43 0.89 0.30
106_L 364_K 1.35 0.85 0.25
57_D 124_P 1.22 0.75 0.17
57_D 276_H 1.13 0.67 0.13
22_L 342_V 1.12 0.66 0.13
106_L 166_F 1.11 0.65 0.12
118_V 180_L 1.10 0.64 0.12
67_P 348_W 1.09 0.64 0.12
117_A 186_V 1.08 0.63 0.11
110_V 126_E 1.08 0.62 0.11
103_N 106_L 1.06 0.60 0.10
62_K 205_I 1.05 0.59 0.10
24_A 395_A 1.04 0.58 0.10
59_L 375_V 1.04 0.57 0.10
11_T 286_L 1.03 0.57 0.09
102_E 291_H 1.03 0.56 0.09
80_L 135_I 1.02 0.56 0.09
57_D 125_R 1.02 0.56 0.09
6_L 71_P 1.02 0.56 0.09
22_L 138_M 1.01 0.55 0.09
18_V 334_I 0.99 0.52 0.08
63_V 398_A 0.98 0.51 0.08
107_R 156_F 0.96 0.49 0.07
78_D 196_S 0.95 0.48 0.07
57_D 280_Y 0.94 0.47 0.07
102_E 384_P 0.94 0.47 0.07
113_M 127_V 0.94 0.47 0.07
72_A 156_F 0.94 0.46 0.07
113_M 366_W 0.93 0.46 0.07
46_L 257_A 0.93 0.46 0.07
54_W 254_F 0.93 0.45 0.06
60_Y 259_V 0.93 0.45 0.06
46_L 19_L 0.91 0.44 0.06
12_S 192_N 0.90 0.43 0.06
41_A 269_F 0.90 0.42 0.06
80_L 363_F 0.90 0.42 0.06
103_N 189_P 0.90 0.42 0.06
80_L 164_G 0.90 0.42 0.06
103_N 344_A 0.89 0.41 0.06
52_N 51_L 0.88 0.40 0.05
46_L 209_V 0.88 0.40 0.05
60_Y 124_P 0.88 0.39 0.05
60_Y 71_P 0.87 0.39 0.05
99_L 35_I 0.87 0.39 0.05
8_L 196_S 0.87 0.39 0.05
78_D 77_F 0.87 0.39 0.05
55_G 361_P 0.86 0.38 0.05
18_V 57_L 0.86 0.38 0.05
48_T 371_A 0.86 0.38 0.05
60_Y 43_W 0.85 0.37 0.05
92_R 345_L 0.85 0.37 0.05
117_A 341_L 0.85 0.37 0.05
38_A 204_V 0.85 0.37 0.05
26_L 237_A 0.85 0.37 0.05
56_F 100_G 0.84 0.36 0.05
17_V 338_G 0.84 0.36 0.05
64_F 169_I 0.84 0.36 0.05
40_S 338_G 0.84 0.36 0.05
109_Y 59_I 0.84 0.36 0.04
125_M 343_M 0.84 0.35 0.04
74_L 25_I 0.83 0.35 0.04
23_A 196_S 0.83 0.35 0.04
124_L 344_A 0.83 0.35 0.04
43_G 250_I 0.83 0.35 0.04
46_L 75_L 0.83 0.35 0.04
64_F 71_P 0.83 0.35 0.04
19_G 100_G 0.83 0.34 0.04
53_A 300_P 0.83 0.34 0.04
22_L 395_A 0.82 0.34 0.04
60_Y 122_K 0.82 0.34 0.04
67_P 29_V 0.82 0.34 0.04
65_V 51_L 0.82 0.33 0.04
106_L 128_T 0.81 0.33 0.04
60_Y 301_F 0.81 0.33 0.04
102_E 179_W 0.81 0.33 0.04
125_M 379_W 0.81 0.33 0.04
118_V 169_I 0.81 0.33 0.04
121_L 345_L 0.81 0.32 0.04
56_F 156_F 0.81 0.32 0.04
116_G 22_R 0.81 0.32 0.04
57_D 81_E 0.81 0.32 0.04
119_V 248_F 0.81 0.32 0.04
55_G 282_E 0.81 0.32 0.04
6_L 208_L 0.81 0.32 0.04
54_W 142_T 0.80 0.32 0.04
112_S 242_L 0.80 0.32 0.04
59_L 372_V 0.80 0.32 0.04
102_E 35_I 0.80 0.31 0.04
90_L 411_L 0.80 0.31 0.04
18_V 369_L 0.79 0.31 0.04
55_G 339_A 0.79 0.31 0.04
47_S 373_D 0.79 0.31 0.04
54_W 291_H 0.79 0.31 0.04
119_V 204_V 0.79 0.31 0.04
109_Y 47_W 0.79 0.31 0.04
64_F 405_L 0.79 0.31 0.04
117_A 138_M 0.79 0.31 0.04
93_F 121_Y 0.79 0.30 0.04
36_S 172_V 0.79 0.30 0.04
95_G 171_G 0.79 0.30 0.04
87_P 374_F 0.79 0.30 0.04
37_I 74_D 0.79 0.30 0.04
75_L 393_A 0.78 0.30 0.04
24_A 26_V 0.78 0.30 0.04
27_W 284_N 0.78 0.30 0.04
53_A 141_G 0.78 0.30 0.04
68_F 263_F 0.78 0.29 0.04
57_D 293_V 0.78 0.29 0.04
4_S 29_V 0.77 0.29 0.03
59_L 103_L 0.77 0.29 0.03
112_S 25_I 0.77 0.29 0.03
18_V 180_L 0.77 0.29 0.03
98_L 137_L 0.77 0.29 0.03
110_V 270_M 0.77 0.29 0.03
122_A 398_A 0.77 0.28 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
2278 2.07 cI_Bcterm_cIII_cytb Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.30 Done - Shared
2277 0 cI_Bcterm_cIII_cytb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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