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OPENSEQ.org
cI_H_40_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 345 440 697
Sequences: 4228 3285 2773
Seq/Len: 12.26 7.47 3.98
MirrorTree (Pazo et al. 2001) 0.79
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 0.00 0.00 1.92
20 0.01 0.00 2.94
100 0.01 0.00 3.00
∞ 0.02 0.01 3.53
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 1.10 0.83 0.07
58_L 390_P 1.06 0.79 0.06
204_L 96_L 1.03 0.76 0.05
83_V 116_L 0.99 0.72 0.05
252_Y 256_L 0.94 0.66 0.04
225_S 35_I 0.94 0.66 0.04
242_L 336_M 0.92 0.64 0.04
90_L 180_L 0.91 0.62 0.04
17_L 136_Y 0.91 0.62 0.04
121_F 204_V 0.88 0.59 0.03
144_F 135_I 0.86 0.56 0.03
284_M 19_L 0.85 0.55 0.03
131_V 206_A 0.85 0.55 0.03
163_L 33_L 0.85 0.54 0.03
137_A 286_L 0.84 0.53 0.03
102_I 103_L 0.84 0.53 0.03
133_M 197_L 0.84 0.53 0.03
59_L 365_W 0.84 0.53 0.03
225_S 51_L 0.84 0.53 0.03
257_L 56_V 0.84 0.53 0.03
124_S 281_I 0.83 0.52 0.03
203_V 116_L 0.82 0.51 0.03
205_F 192_N 0.82 0.50 0.03
133_M 334_I 0.82 0.50 0.03
178_T 60_A 0.81 0.49 0.03
177_L 139_M 0.81 0.49 0.03
237_S 192_N 0.81 0.49 0.03
291_F 23_L 0.80 0.48 0.03
206_F 61_T 0.80 0.48 0.03
36_G 215_A 0.80 0.48 0.03
310_G 286_L 0.80 0.48 0.03
243_F 360_R 0.80 0.48 0.03
141_K 172_V 0.79 0.47 0.02
112_N 106_L 0.79 0.47 0.02
90_L 269_F 0.79 0.47 0.02
221_V 285_P 0.79 0.47 0.02
204_L 110_I 0.79 0.46 0.02
258_L 141_G 0.78 0.46 0.02
142_Y 76_A 0.78 0.45 0.02
202_V 256_L 0.78 0.45 0.02
131_V 66_V 0.78 0.45 0.02
218_F 61_T 0.77 0.45 0.02
242_L 348_W 0.77 0.44 0.02
263_F 25_I 0.77 0.44 0.02
43_A 20_H 0.77 0.43 0.02
164_I 331_F 0.76 0.43 0.02
170_I 33_L 0.76 0.43 0.02
223_A 301_F 0.76 0.43 0.02
116_G 197_L 0.76 0.43 0.02
314_F 81_E 0.76 0.42 0.02
180_I 357_G 0.76 0.42 0.02
54_G 141_G 0.76 0.42 0.02
223_A 300_P 0.75 0.41 0.02
82_F 59_I 0.75 0.41 0.02
223_A 35_I 0.75 0.41 0.02
120_I 175_A 0.75 0.41 0.02
154_M 277_P 0.74 0.40 0.02
237_S 266_I 0.74 0.40 0.02
93_M 257_A 0.74 0.40 0.02
259_S 61_T 0.74 0.40 0.02
213_C 286_L 0.73 0.39 0.02
221_V 276_H 0.73 0.39 0.02
12_A 371_A 0.73 0.39 0.02
111_A 209_V 0.73 0.39 0.02
305_Q 360_R 0.72 0.38 0.02
236_S 360_R 0.72 0.38 0.02
17_L 257_A 0.72 0.38 0.02
233_T 345_L 0.72 0.37 0.02
42_A 240_D 0.72 0.37 0.02
297_I 50_V 0.72 0.37 0.02
96_L 189_P 0.72 0.37 0.02
16_L 242_L 0.71 0.37 0.02
41_W 245_W 0.71 0.36 0.02
253_L 339_A 0.71 0.36 0.02
105_D 108_V 0.71 0.36 0.02
170_I 112_I 0.71 0.36 0.02
323_V 403_Y 0.71 0.36 0.02
332_E 406_I 0.71 0.36 0.02
216_P 209_V 0.71 0.36 0.02
33_M 239_K 0.71 0.36 0.02
35_Y 241_T 0.71 0.36 0.02
74_V 121_Y 0.70 0.35 0.02
264_G 67_M 0.70 0.35 0.02
52_V 280_Y 0.70 0.35 0.02
175_M 392_I 0.70 0.35 0.02
110_M 399_Y 0.70 0.35 0.02
61_T 150_P 0.70 0.35 0.02
102_I 369_L 0.70 0.35 0.02
144_F 108_V 0.70 0.35 0.02
90_L 75_L 0.70 0.35 0.02
287_W 206_A 0.70 0.35 0.02
184_Q 76_A 0.70 0.35 0.02
72_E 274_L 0.70 0.35 0.02
31_I 46_I 0.70 0.35 0.02
314_F 44_W 0.70 0.35 0.02
137_A 42_N 0.69 0.34 0.02
318_S 213_I 0.69 0.34 0.02
263_F 399_Y 0.69 0.34 0.02
43_A 245_W 0.69 0.34 0.02
216_P 263_F 0.69 0.34 0.02
29_S 135_I 0.69 0.34 0.02
68_Y 49_I 0.69 0.33 0.02
97_F 174_E 0.69 0.33 0.02
180_I 95_Y 0.68 0.33 0.02
195_W 376_V 0.68 0.33 0.02
294_V 201_L 0.68 0.33 0.02
92_M 51_L 0.68 0.33 0.02
236_S 397_S 0.68 0.32 0.02
252_Y 245_W 0.68 0.32 0.02
301_Y 66_V 0.68 0.32 0.02
90_L 139_M 0.68 0.32 0.02
270_V 208_L 0.68 0.32 0.02
181_V 266_I 0.68 0.32 0.02
306_L 99_N 0.68 0.32 0.02
161_L 282_E 0.67 0.32 0.02
96_L 208_L 0.67 0.32 0.01
323_V 73_V 0.67 0.32 0.01
104_F 402_A 0.67 0.32 0.01
170_I 346_V 0.67 0.31 0.01
263_F 337_F 0.67 0.31 0.01
159_V 237_A 0.67 0.31 0.01
152_A 226_G 0.67 0.31 0.01
166_I 394_L 0.67 0.31 0.01
75_I 375_V 0.67 0.31 0.01
315_L 99_N 0.66 0.31 0.01
323_V 204_V 0.66 0.31 0.01
165_I 242_L 0.66 0.31 0.01
86_L 264_F 0.66 0.31 0.01
218_F 85_R 0.66 0.31 0.01
118_L 407_I 0.66 0.31 0.01
216_P 197_L 0.66 0.31 0.01
147_S 135_I 0.66 0.31 0.01
132_I 371_A 0.66 0.30 0.01
43_A 64_V 0.66 0.30 0.01
94_L 92_M 0.66 0.30 0.01
88_P 76_A 0.66 0.30 0.01
81_K 272_N 0.66 0.30 0.01
290_M 56_V 0.66 0.30 0.01
251_M 189_P 0.66 0.30 0.01
133_M 21_R 0.66 0.30 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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