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OPENSEQ.org
cIV_C_40_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 273 440 637
Sequences: 2504 3285 2304
Seq/Len: 9.17 7.47 3.62
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 0.17
2 0.00 0.00 0.31
5 0.00 0.00 0.77
10 0.00 0.00 2.77
20 0.00 0.00 2.80
100 0.00 0.00 2.91
∞ 0.00 0.01 3.23
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
35_M 89_G 1.16 0.84 0.10
8_Y 137_L 1.09 0.79 0.08
262_L 339_A 1.09 0.79 0.08
204_V 211_V 1.08 0.78 0.08
103_A 293_V 1.02 0.72 0.07
237_G 121_Y 0.97 0.67 0.06
138_W 350_D 0.96 0.65 0.05
186_T 328_A 0.95 0.65 0.05
56_V 89_G 0.95 0.65 0.05
155_V 63_I 0.91 0.60 0.05
191_Y 278_D 0.89 0.57 0.04
73_G 349_L 0.89 0.56 0.04
115_P 274_L 0.87 0.55 0.04
22_I 348_W 0.86 0.53 0.04
199_G 387_G 0.84 0.51 0.04
157_W 361_P 0.83 0.49 0.04
147_I 135_I 0.83 0.49 0.04
162_F 298_F 0.83 0.49 0.04
87_Q 107_A 0.82 0.48 0.03
83_R 360_R 0.82 0.47 0.03
108_F 343_M 0.82 0.47 0.03
12_P 72_H 0.81 0.47 0.03
240_T 360_R 0.81 0.47 0.03
18_F 208_L 0.81 0.47 0.03
226_F 99_N 0.80 0.45 0.03
19_F 176_I 0.80 0.45 0.03
26_V 345_L 0.79 0.44 0.03
142_L 284_N 0.79 0.44 0.03
262_L 51_L 0.79 0.43 0.03
58_V 406_I 0.78 0.43 0.03
252_W 150_P 0.78 0.43 0.03
73_G 134_L 0.78 0.42 0.03
164_L 135_I 0.77 0.41 0.03
147_I 358_Q 0.76 0.41 0.03
267_V 93_L 0.76 0.41 0.03
12_P 75_L 0.76 0.40 0.03
4_K 364_K 0.76 0.40 0.03
55_L 258_V 0.76 0.40 0.03
221_I 361_P 0.75 0.39 0.03
113_L 61_T 0.75 0.39 0.03
190_A 138_M 0.75 0.39 0.03
266_V 248_F 0.75 0.39 0.03
228_F 375_V 0.74 0.38 0.03
166_G 364_K 0.74 0.38 0.03
86_L 60_A 0.74 0.38 0.03
103_A 404_F 0.74 0.38 0.03
218_A 131_V 0.74 0.38 0.03
146_L 374_F 0.74 0.37 0.02
262_L 336_M 0.74 0.37 0.02
260_V 104_F 0.74 0.37 0.02
52_L 395_A 0.73 0.37 0.02
158_A 195_F 0.73 0.37 0.02
231_L 285_P 0.73 0.36 0.02
210_Y 65_L 0.73 0.36 0.02
266_V 360_R 0.73 0.36 0.02
199_G 254_F 0.72 0.36 0.02
162_F 263_F 0.72 0.35 0.02
18_F 350_D 0.72 0.35 0.02
207_G 342_V 0.72 0.35 0.02
206_A 58_Q 0.72 0.35 0.02
236_K 263_F 0.72 0.35 0.02
103_A 354_V 0.72 0.35 0.02
267_V 205_I 0.71 0.34 0.02
201_A 254_F 0.71 0.34 0.02
166_G 370_L 0.71 0.34 0.02
18_F 343_M 0.71 0.34 0.02
240_T 103_L 0.70 0.34 0.02
23_G 365_W 0.70 0.34 0.02
239_M 100_G 0.70 0.33 0.02
154_A 131_V 0.70 0.33 0.02
98_V 290_A 0.70 0.33 0.02
98_V 86_D 0.70 0.33 0.02
272_G 85_R 0.70 0.33 0.02
211_M 32_T 0.70 0.33 0.02
56_V 375_V 0.70 0.33 0.02
108_F 66_V 0.70 0.33 0.02
180_I 398_A 0.70 0.33 0.02
225_I 261_V 0.70 0.33 0.02
265_F 113_F 0.70 0.33 0.02
28_L 205_I 0.70 0.33 0.02
262_L 300_P 0.69 0.32 0.02
228_F 29_V 0.69 0.32 0.02
252_W 151_W 0.69 0.32 0.02
270_I 64_V 0.69 0.32 0.02
25_F 394_L 0.69 0.32 0.02
232_I 60_A 0.69 0.32 0.02
237_G 22_R 0.69 0.32 0.02
265_F 200_L 0.69 0.32 0.02
52_L 406_I 0.69 0.31 0.02
26_V 31_D 0.69 0.31 0.02
94_I 291_H 0.69 0.31 0.02
87_Q 91_Y 0.68 0.31 0.02
179_V 374_F 0.68 0.31 0.02
122_I 27_S 0.68 0.31 0.02
138_W 44_W 0.68 0.31 0.02
79_T 98_A 0.68 0.31 0.02
21_A 254_F 0.68 0.30 0.02
7_D 172_V 0.67 0.30 0.02
150_L 175_A 0.67 0.30 0.02
79_T 54_C 0.67 0.30 0.02
18_F 188_N 0.67 0.30 0.02
38_I 278_D 0.67 0.30 0.02
55_L 413_I 0.67 0.29 0.02
171_T 273_Y 0.67 0.29 0.02
182_G 378_M 0.67 0.29 0.02
135_F 403_Y 0.67 0.29 0.02
32_V 335_A 0.66 0.29 0.02
21_A 119_G 0.66 0.29 0.02
171_T 207_A 0.66 0.29 0.02
95_M 227_V 0.66 0.29 0.02
31_A 127_V 0.66 0.28 0.02
23_G 143_A 0.66 0.28 0.02
29_T 334_I 0.66 0.28 0.02
252_W 179_W 0.66 0.28 0.02
174_G 275_G 0.66 0.28 0.02
158_A 40_N 0.65 0.28 0.02
10_I 80_V 0.65 0.28 0.02
7_D 142_T 0.65 0.28 0.02
149_L 186_V 0.65 0.28 0.02
208_A 180_L 0.65 0.28 0.02
117_G 138_M 0.65 0.27 0.02
116_M 140_M 0.65 0.27 0.02
176_I 138_M 0.65 0.27 0.02
218_A 61_T 0.65 0.27 0.02
59_L 395_A 0.65 0.27 0.02
87_Q 166_F 0.65 0.27 0.02
90_F 248_F 0.65 0.27 0.02
111_N 49_I 0.65 0.27 0.02
207_G 80_V 0.65 0.27 0.02
87_Q 343_M 0.64 0.27 0.02
94_I 150_P 0.64 0.27 0.02
11_L 185_A 0.64 0.27 0.02
149_L 195_F 0.64 0.27 0.02
183_V 406_I 0.64 0.27 0.02
60_Y 366_W 0.64 0.27 0.02
235_L 341_L 0.64 0.27 0.02
76_G 51_L 0.64 0.27 0.02
73_G 209_V 0.64 0.26 0.02
153_V 340_I 0.64 0.26 0.02
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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