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OPENSEQ.org
cI_H_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 345 440 698
Sequences: 4768 3282 2817
Seq/Len: 13.82 7.46 4.04
MirrorTree (Pazo et al. 2001) 0.77
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 1.13
2 0.00 0.00 1.38
5 0.00 0.00 1.72
10 0.01 0.00 1.92
20 0.01 0.00 2.96
100 0.02 0.00 3.03
∞ 0.05 0.01 3.59
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
120_I 37_T 1.06 0.79 0.04
204_L 96_L 1.05 0.78 0.04
58_L 390_P 1.01 0.75 0.03
252_Y 256_L 0.98 0.71 0.03
263_F 25_I 0.95 0.67 0.03
257_L 56_V 0.94 0.66 0.03
242_L 336_M 0.92 0.64 0.02
16_L 362_L 0.89 0.61 0.02
144_F 135_I 0.89 0.60 0.02
178_T 60_A 0.89 0.60 0.02
205_F 192_N 0.87 0.58 0.02
59_L 365_W 0.86 0.56 0.02
237_S 192_N 0.85 0.55 0.02
83_V 116_L 0.85 0.55 0.02
267_L 352_S 0.85 0.55 0.02
170_I 112_I 0.84 0.54 0.02
43_A 20_H 0.83 0.53 0.02
225_S 51_L 0.83 0.53 0.02
259_S 61_T 0.83 0.52 0.02
213_C 286_L 0.82 0.52 0.02
310_G 286_L 0.82 0.51 0.02
131_V 206_A 0.82 0.51 0.02
284_M 19_L 0.81 0.50 0.02
225_S 35_I 0.81 0.50 0.02
131_V 66_V 0.81 0.50 0.02
124_S 281_I 0.81 0.49 0.02
133_M 197_L 0.80 0.49 0.02
17_L 136_Y 0.80 0.49 0.02
177_L 139_M 0.79 0.47 0.02
314_F 81_E 0.79 0.46 0.02
90_L 180_L 0.78 0.46 0.02
258_L 141_G 0.78 0.46 0.02
163_L 33_L 0.78 0.45 0.01
16_L 242_L 0.77 0.45 0.01
121_F 204_V 0.77 0.45 0.01
223_A 300_P 0.77 0.44 0.01
223_A 35_I 0.77 0.44 0.01
323_V 121_Y 0.77 0.44 0.01
102_I 103_L 0.76 0.44 0.01
323_V 403_Y 0.76 0.43 0.01
90_L 75_L 0.76 0.43 0.01
297_I 50_V 0.76 0.43 0.01
120_I 175_A 0.76 0.42 0.01
181_V 56_V 0.75 0.42 0.01
216_P 197_L 0.75 0.42 0.01
263_F 337_F 0.75 0.42 0.01
176_N 261_V 0.75 0.41 0.01
280_M 272_N 0.74 0.41 0.01
328_L 366_W 0.74 0.41 0.01
54_G 141_G 0.74 0.41 0.01
112_N 106_L 0.74 0.41 0.01
287_W 206_A 0.74 0.41 0.01
104_F 402_A 0.74 0.41 0.01
29_S 136_Y 0.74 0.41 0.01
176_N 344_A 0.74 0.40 0.01
291_F 23_L 0.74 0.40 0.01
142_Y 76_A 0.74 0.40 0.01
301_Y 66_V 0.73 0.39 0.01
202_V 256_L 0.73 0.39 0.01
133_M 334_I 0.73 0.39 0.01
111_A 209_V 0.73 0.39 0.01
206_F 61_T 0.73 0.39 0.01
223_A 301_F 0.72 0.39 0.01
294_V 201_L 0.72 0.38 0.01
216_P 263_F 0.72 0.38 0.01
150_S 180_L 0.72 0.38 0.01
74_V 121_Y 0.72 0.38 0.01
314_F 44_W 0.72 0.38 0.01
59_L 248_F 0.72 0.38 0.01
83_V 72_H 0.72 0.38 0.01
204_L 110_I 0.72 0.38 0.01
287_W 249_V 0.72 0.37 0.01
263_F 172_V 0.71 0.37 0.01
31_I 46_I 0.71 0.37 0.01
251_M 189_P 0.71 0.37 0.01
17_L 344_A 0.71 0.37 0.01
268_S 73_V 0.71 0.37 0.01
284_M 341_L 0.71 0.37 0.01
203_V 213_I 0.71 0.37 0.01
290_M 56_V 0.71 0.36 0.01
33_M 239_K 0.71 0.36 0.01
147_S 135_I 0.71 0.36 0.01
237_S 93_L 0.71 0.36 0.01
170_I 138_M 0.70 0.36 0.01
221_V 197_L 0.70 0.36 0.01
185_R 103_L 0.70 0.36 0.01
36_G 215_A 0.70 0.36 0.01
86_L 264_F 0.70 0.36 0.01
203_V 116_L 0.70 0.35 0.01
90_L 269_F 0.70 0.35 0.01
94_L 92_M 0.70 0.35 0.01
43_A 245_W 0.70 0.35 0.01
231_F 51_L 0.70 0.35 0.01
285_W 262_V 0.70 0.35 0.01
125_S 108_V 0.69 0.35 0.01
233_T 345_L 0.69 0.35 0.01
82_F 59_I 0.69 0.35 0.01
141_K 172_V 0.69 0.34 0.01
236_S 360_R 0.69 0.34 0.01
17_L 257_A 0.69 0.34 0.01
102_I 122_K 0.69 0.34 0.01
105_D 261_V 0.69 0.34 0.01
323_V 204_V 0.69 0.34 0.01
164_I 331_F 0.69 0.34 0.01
328_L 110_I 0.69 0.34 0.01
194_Y 348_W 0.69 0.34 0.01
313_V 25_I 0.69 0.34 0.01
35_Y 241_T 0.68 0.33 0.01
137_A 286_L 0.68 0.33 0.01
218_F 61_T 0.68 0.33 0.01
30_L 300_P 0.68 0.33 0.01
96_L 189_P 0.68 0.33 0.01
29_S 135_I 0.68 0.33 0.01
102_I 369_L 0.68 0.33 0.01
237_S 266_I 0.68 0.33 0.01
102_I 411_L 0.68 0.33 0.01
52_V 280_Y 0.68 0.33 0.01
186_G 402_A 0.68 0.33 0.01
126_L 205_I 0.68 0.33 0.01
180_I 95_Y 0.68 0.32 0.01
205_F 85_R 0.68 0.32 0.01
116_G 197_L 0.67 0.32 0.01
90_L 139_M 0.67 0.32 0.01
86_L 338_G 0.67 0.32 0.01
137_A 42_N 0.67 0.32 0.01
267_L 93_L 0.67 0.32 0.01
170_I 33_L 0.67 0.32 0.01
246_G 351_T 0.67 0.32 0.01
318_S 213_I 0.67 0.31 0.01
24_A 362_L 0.67 0.31 0.01
92_M 395_A 0.67 0.31 0.01
42_A 240_D 0.67 0.31 0.01
68_Y 49_I 0.67 0.31 0.01
183_A 222_N 0.67 0.31 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
3032 4 cI_H_20_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3031 3.98 cI_H_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3029 4.02 cI_H_4_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
3028 4 cI_H_4_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3027 4.02 cI_H_4_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
2727 4.04 cI_H_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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