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OPENSEQ.org
cIV_C_60_cIII_cytb_60_Pdenitr
Genes: A B A+B
Length: 273 440 635
Sequences: 2410 3220 2243
Seq/Len: 8.83 7.32 3.53
MirrorTree (Pazo et al. 2001) 0.90
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 0.15
2 0.00 0.00 0.29
5 0.00 0.00 0.73
10 0.00 0.00 2.72
20 0.00 0.00 2.77
100 0.00 0.00 2.83
∞ 0.00 0.00 3.15
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
204_V 211_V 1.28 0.91 0.33
35_M 89_G 1.28 0.91 0.33
262_L 339_A 1.14 0.82 0.23
8_Y 137_L 1.01 0.70 0.15
155_V 63_I 1.00 0.69 0.15
103_A 293_V 0.99 0.69 0.14
186_T 328_A 0.99 0.68 0.14
162_F 298_F 0.92 0.60 0.11
73_G 349_L 0.91 0.59 0.11
191_Y 278_D 0.91 0.58 0.11
147_I 135_I 0.90 0.58 0.10
98_V 86_D 0.89 0.57 0.10
221_I 361_P 0.88 0.55 0.10
237_G 121_Y 0.88 0.55 0.10
108_F 343_M 0.88 0.55 0.10
265_F 113_F 0.87 0.53 0.09
252_W 150_P 0.87 0.53 0.09
138_W 350_D 0.86 0.53 0.09
12_P 72_H 0.86 0.52 0.09
56_V 89_G 0.86 0.52 0.09
73_G 134_L 0.85 0.51 0.09
138_W 44_W 0.84 0.50 0.08
262_L 336_M 0.84 0.49 0.08
58_V 406_I 0.83 0.48 0.08
265_F 200_L 0.83 0.48 0.08
265_F 301_F 0.82 0.47 0.07
262_L 51_L 0.81 0.46 0.07
164_L 135_I 0.79 0.44 0.07
22_I 348_W 0.79 0.43 0.07
267_V 93_L 0.79 0.43 0.07
10_I 80_V 0.78 0.43 0.07
266_V 248_F 0.78 0.42 0.07
87_Q 107_A 0.78 0.42 0.07
83_R 360_R 0.78 0.42 0.06
206_A 58_Q 0.78 0.42 0.06
25_F 394_L 0.77 0.41 0.06
262_L 300_P 0.77 0.40 0.06
225_I 261_V 0.76 0.40 0.06
240_T 360_R 0.76 0.40 0.06
23_G 365_W 0.76 0.39 0.06
210_Y 65_L 0.76 0.39 0.06
236_K 263_F 0.76 0.39 0.06
154_A 131_V 0.75 0.39 0.06
4_K 364_K 0.75 0.39 0.06
272_G 85_R 0.75 0.39 0.06
103_A 404_F 0.75 0.39 0.06
86_L 60_A 0.75 0.38 0.06
31_A 127_V 0.75 0.38 0.06
34_W 32_T 0.75 0.38 0.06
252_W 179_W 0.74 0.38 0.06
55_L 108_V 0.74 0.38 0.06
158_A 195_F 0.74 0.38 0.06
140_L 286_L 0.74 0.38 0.06
73_G 174_E 0.74 0.37 0.06
26_V 31_D 0.74 0.37 0.05
166_G 364_K 0.74 0.37 0.05
231_L 285_P 0.74 0.37 0.05
146_L 286_L 0.74 0.37 0.05
79_T 54_C 0.73 0.36 0.05
52_L 356_S 0.73 0.35 0.05
270_I 64_V 0.73 0.35 0.05
73_G 257_A 0.72 0.35 0.05
211_M 32_T 0.72 0.35 0.05
266_V 360_R 0.72 0.35 0.05
103_A 354_V 0.72 0.35 0.05
226_F 99_N 0.72 0.35 0.05
115_P 274_L 0.72 0.35 0.05
218_A 197_L 0.72 0.35 0.05
240_T 103_L 0.72 0.34 0.05
95_M 227_V 0.72 0.34 0.05
267_V 205_I 0.71 0.34 0.05
179_V 40_N 0.71 0.33 0.05
25_F 174_E 0.71 0.33 0.05
8_Y 416_K 0.71 0.33 0.05
52_L 395_A 0.70 0.33 0.05
199_G 254_F 0.70 0.32 0.05
215_F 291_H 0.70 0.32 0.05
251_A 331_F 0.70 0.32 0.04
79_T 98_A 0.70 0.32 0.04
23_G 143_A 0.70 0.32 0.04
94_I 291_H 0.70 0.32 0.04
199_G 387_G 0.70 0.32 0.04
18_F 208_L 0.70 0.32 0.04
73_G 209_V 0.70 0.32 0.04
182_G 245_W 0.69 0.32 0.04
114_Y 261_V 0.69 0.32 0.04
150_L 355_R 0.69 0.32 0.04
99_M 108_V 0.69 0.32 0.04
239_M 100_G 0.69 0.32 0.04
149_L 186_V 0.69 0.32 0.04
18_F 350_D 0.69 0.32 0.04
157_W 361_P 0.69 0.31 0.04
38_I 278_D 0.69 0.31 0.04
113_L 61_T 0.69 0.31 0.04
153_V 340_I 0.69 0.31 0.04
234_L 116_L 0.69 0.31 0.04
98_V 290_A 0.69 0.31 0.04
55_L 413_I 0.69 0.31 0.04
208_A 257_A 0.69 0.31 0.04
79_T 40_N 0.69 0.31 0.04
260_V 104_F 0.68 0.31 0.04
229_V 98_A 0.68 0.30 0.04
180_I 398_A 0.68 0.30 0.04
21_A 119_G 0.68 0.30 0.04
76_G 51_L 0.68 0.30 0.04
87_Q 91_Y 0.68 0.30 0.04
26_V 135_I 0.68 0.30 0.04
18_F 188_N 0.68 0.30 0.04
158_A 40_N 0.68 0.30 0.04
19_F 176_I 0.68 0.30 0.04
174_G 275_G 0.68 0.30 0.04
262_L 382_A 0.68 0.30 0.04
196_A 75_L 0.68 0.30 0.04
188_L 42_N 0.68 0.30 0.04
218_A 201_L 0.67 0.29 0.04
11_L 185_A 0.67 0.29 0.04
161_A 389_Y 0.67 0.29 0.04
140_L 42_N 0.67 0.29 0.04
146_L 374_F 0.67 0.29 0.04
37_G 145_M 0.67 0.29 0.04
56_V 375_V 0.67 0.29 0.04
7_D 142_T 0.67 0.29 0.04
116_M 140_M 0.67 0.29 0.04
30_G 268_G 0.67 0.29 0.04
26_V 345_L 0.67 0.29 0.04
32_V 335_A 0.67 0.28 0.04
135_F 403_Y 0.66 0.28 0.04
262_L 165_L 0.66 0.28 0.04
7_D 172_V 0.66 0.28 0.04
239_M 53_F 0.66 0.28 0.04
111_N 49_I 0.66 0.28 0.04
177_V 137_L 0.66 0.28 0.04
203_T 308_F 0.66 0.28 0.04
29_T 334_I 0.66 0.28 0.04
134_T 269_F 0.65 0.27 0.04
108_F 66_V 0.65 0.27 0.04
8_Y 262_V 0.65 0.27 0.04
235_L 341_L 0.65 0.27 0.04
252_W 151_W 0.65 0.27 0.04
158_A 76_A 0.65 0.27 0.04
208_A 180_L 0.65 0.27 0.04
21_A 156_F 0.65 0.27 0.04
250_A 116_L 0.65 0.27 0.04
201_A 254_F 0.65 0.27 0.04
228_F 375_V 0.65 0.27 0.04
124_D 160_T 0.65 0.27 0.04
155_V 371_A 0.65 0.27 0.04
5_N 185_A 0.64 0.26 0.04
139_H 373_D 0.64 0.26 0.04
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
3132 3.41 cIV_C_80_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.29 Done - Shared
3130 3.53 cIV_C_60_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
3129 3.59 cIV_C_40_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3128 3.65 cIV_C_20_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3127 3.6 cIV_C_40_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3126 3.62 cIV_C_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
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