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OPENSEQ.org
cIV_C_20_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 273 440 636
Sequences: 2634 3285 2319
Seq/Len: 9.65 7.47 3.65
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 0.18
2 0.00 0.00 0.32
5 0.00 0.00 0.79
10 0.00 0.00 2.78
20 0.00 0.00 2.81
100 0.00 0.00 2.92
∞ 0.00 0.01 3.25
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 1.10 0.80 0.05
204_V 211_V 1.08 0.78 0.05
237_G 121_Y 0.98 0.69 0.04
262_L 339_A 0.97 0.68 0.03
138_W 350_D 0.95 0.65 0.03
103_A 293_V 0.94 0.63 0.03
56_V 89_G 0.92 0.62 0.03
228_F 375_V 0.90 0.58 0.03
22_I 348_W 0.89 0.57 0.03
115_P 274_L 0.88 0.56 0.03
199_G 387_G 0.87 0.55 0.03
8_Y 137_L 0.87 0.54 0.02
73_G 349_L 0.86 0.54 0.02
221_I 361_P 0.86 0.54 0.02
155_V 63_I 0.85 0.53 0.02
12_P 72_H 0.82 0.49 0.02
18_F 208_L 0.81 0.47 0.02
147_I 135_I 0.81 0.47 0.02
206_A 58_Q 0.81 0.47 0.02
186_T 328_A 0.81 0.46 0.02
225_I 261_V 0.81 0.46 0.02
252_W 150_P 0.80 0.45 0.02
191_Y 278_D 0.79 0.45 0.02
157_W 361_P 0.79 0.45 0.02
240_T 103_L 0.79 0.45 0.02
39_T 267_V 0.79 0.44 0.02
235_L 341_L 0.78 0.43 0.02
262_L 51_L 0.77 0.42 0.02
87_Q 107_A 0.77 0.42 0.02
58_V 406_I 0.77 0.41 0.02
108_F 343_M 0.77 0.41 0.02
267_V 93_L 0.77 0.41 0.02
83_R 360_R 0.77 0.41 0.02
26_V 345_L 0.76 0.41 0.02
252_W 151_W 0.76 0.41 0.02
21_A 254_F 0.76 0.41 0.02
12_P 75_L 0.76 0.40 0.02
55_L 258_V 0.76 0.40 0.02
199_G 254_F 0.75 0.40 0.02
52_L 406_I 0.75 0.40 0.02
260_V 104_F 0.75 0.39 0.02
55_L 413_I 0.74 0.39 0.02
4_K 364_K 0.74 0.39 0.02
266_V 360_R 0.74 0.38 0.02
18_F 188_N 0.74 0.38 0.02
158_A 195_F 0.74 0.38 0.02
232_I 60_A 0.74 0.38 0.02
103_A 354_V 0.74 0.38 0.01
164_L 135_I 0.74 0.37 0.01
267_V 205_I 0.74 0.37 0.01
146_L 374_F 0.73 0.37 0.01
172_I 242_L 0.73 0.37 0.01
19_F 176_I 0.73 0.37 0.01
183_V 406_I 0.73 0.37 0.01
226_F 99_N 0.73 0.37 0.01
266_V 248_F 0.73 0.36 0.01
215_F 291_H 0.72 0.36 0.01
240_T 360_R 0.72 0.36 0.01
31_A 127_V 0.72 0.35 0.01
210_Y 339_A 0.72 0.35 0.01
122_I 27_S 0.72 0.35 0.01
103_A 404_F 0.72 0.35 0.01
265_F 113_F 0.71 0.34 0.01
70_V 169_I 0.71 0.34 0.01
272_G 85_R 0.71 0.34 0.01
25_F 394_L 0.71 0.34 0.01
18_F 350_D 0.70 0.34 0.01
155_V 371_A 0.70 0.34 0.01
150_L 41_L 0.70 0.33 0.01
208_A 257_A 0.70 0.33 0.01
23_G 365_W 0.70 0.33 0.01
108_F 66_V 0.70 0.33 0.01
29_T 334_I 0.70 0.33 0.01
237_G 22_R 0.70 0.33 0.01
147_I 358_Q 0.70 0.33 0.01
86_L 60_A 0.69 0.32 0.01
28_L 205_I 0.69 0.32 0.01
25_F 174_E 0.69 0.32 0.01
162_F 298_F 0.69 0.32 0.01
113_L 61_T 0.69 0.32 0.01
138_W 44_W 0.69 0.32 0.01
179_V 374_F 0.69 0.32 0.01
154_A 131_V 0.69 0.32 0.01
166_G 258_V 0.69 0.31 0.01
236_K 263_F 0.68 0.31 0.01
73_G 134_L 0.68 0.31 0.01
190_A 138_M 0.68 0.31 0.01
180_I 398_A 0.68 0.31 0.01
218_A 131_V 0.68 0.30 0.01
228_F 345_L 0.68 0.30 0.01
262_L 336_M 0.68 0.30 0.01
38_I 278_D 0.68 0.30 0.01
62_M 134_L 0.67 0.30 0.01
234_L 374_F 0.67 0.30 0.01
26_V 31_D 0.67 0.30 0.01
23_G 405_L 0.67 0.29 0.01
52_L 395_A 0.67 0.29 0.01
140_L 286_L 0.67 0.29 0.01
59_L 172_V 0.67 0.29 0.01
73_G 209_V 0.66 0.29 0.01
239_M 100_G 0.66 0.29 0.01
236_K 134_L 0.66 0.28 0.01
252_W 298_F 0.66 0.28 0.01
182_G 378_M 0.66 0.28 0.01
162_F 263_F 0.66 0.28 0.01
150_L 175_A 0.65 0.28 0.01
262_L 300_P 0.65 0.28 0.01
79_T 54_C 0.65 0.28 0.01
98_V 290_A 0.65 0.28 0.01
79_T 98_A 0.65 0.28 0.01
158_A 40_N 0.65 0.28 0.01
174_G 275_G 0.65 0.28 0.01
91_I 33_L 0.65 0.27 0.01
121_P 138_M 0.65 0.27 0.01
218_A 201_L 0.65 0.27 0.01
211_M 32_T 0.65 0.27 0.01
265_F 158_G 0.65 0.27 0.01
52_L 392_I 0.65 0.27 0.01
270_I 64_V 0.65 0.27 0.01
166_G 370_L 0.64 0.27 0.01
134_T 269_F 0.64 0.27 0.01
228_F 29_V 0.64 0.27 0.01
182_G 245_W 0.64 0.27 0.01
99_M 337_F 0.64 0.27 0.01
87_Q 166_F 0.64 0.27 0.01
155_V 122_K 0.64 0.27 0.01
236_K 341_L 0.64 0.27 0.01
180_I 265_A 0.64 0.27 0.01
199_G 69_Y 0.64 0.26 0.01
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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