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OPENSEQ.org
cI_H_40_cIII_cyt1_2_Pdenitr
Genes: A B A+B
Length: 345 263 580
Sequences: 4228 1022 278
Seq/Len: 12.26 3.89 0.48
MirrorTree (Pazo et al. 2001) 0.57
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.02 0.03
∞ 0.02 0.02 0.46
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
170_I 215_F 1.57 0.60 0.00
201_M 63_G 1.36 0.45 0.00
267_L 249_N 1.34 0.43 0.00
121_F 251_K 1.31 0.40 0.00
174_S 149_G 1.29 0.39 0.00
166_I 196_T 1.25 0.36 0.00
216_P 249_N 1.23 0.35 0.00
39_K 67_V 1.18 0.32 0.00
260_L 240_V 1.16 0.30 0.00
154_M 218_W 1.16 0.30 0.00
313_V 240_V 1.16 0.30 0.00
146_A 18_E 1.16 0.30 0.00
111_A 24_A 1.14 0.29 0.00
252_Y 141_L 1.14 0.29 0.00
267_L 130_R 1.12 0.28 0.00
74_V 216_L 1.08 0.25 0.00
148_L 63_G 1.07 0.25 0.00
325_V 52_Q 1.05 0.24 0.00
164_I 134_H 1.04 0.23 0.00
90_L 177_A 1.02 0.22 0.00
317_L 105_R 1.02 0.22 0.00
84_Y 129_A 1.01 0.22 0.00
66_L 82_E 1.01 0.22 0.00
119_F 131_A 1.01 0.21 0.00
12_A 256_I 1.01 0.21 0.00
206_F 217_M 1.00 0.21 0.00
313_V 107_P 0.99 0.21 0.00
81_K 71_T 0.98 0.20 0.00
42_A 67_V 0.98 0.20 0.00
259_S 95_T 0.97 0.20 0.00
249_I 131_A 0.97 0.19 0.00
35_Y 64_L 0.97 0.19 0.00
144_F 157_V 0.97 0.19 0.00
288_F 136_P 0.96 0.19 0.00
281_V 135_G 0.96 0.19 0.00
77_A 220_A 0.95 0.19 0.00
26_V 175_H 0.95 0.19 0.00
257_L 46_Q 0.95 0.18 0.00
21_A 63_G 0.94 0.18 0.00
199_L 46_Q 0.94 0.18 0.00
134_G 46_Q 0.94 0.18 0.00
121_F 90_A 0.93 0.18 0.00
257_L 256_I 0.93 0.18 0.00
278_W 137_Y 0.93 0.18 0.00
177_L 207_Q 0.93 0.18 0.00
288_F 213_A 0.92 0.17 0.00
178_T 232_F 0.92 0.17 0.00
96_L 240_V 0.91 0.17 0.00
202_V 249_N 0.91 0.17 0.00
131_V 85_V 0.91 0.17 0.00
105_D 246_Y 0.90 0.17 0.00
123_A 66_Y 0.90 0.17 0.00
250_A 128_K 0.90 0.16 0.00
238_T 88_Y 0.90 0.16 0.00
155_I 220_A 0.90 0.16 0.00
199_L 141_L 0.90 0.16 0.00
55_P 240_V 0.90 0.16 0.00
259_S 41_K 0.89 0.16 0.00
22_V 74_D 0.89 0.16 0.00
270_V 240_V 0.89 0.16 0.00
320_G 236_I 0.88 0.16 0.00
167_G 241_L 0.88 0.16 0.00
241_L 242_A 0.88 0.16 0.00
80_D 64_L 0.88 0.16 0.00
35_Y 194_Q 0.88 0.16 0.00
287_W 76_G 0.87 0.15 0.00
73_I 137_Y 0.87 0.15 0.00
216_P 217_M 0.87 0.15 0.00
105_D 131_A 0.87 0.15 0.00
207_V 151_P 0.87 0.15 0.00
13_L 170_G 0.86 0.15 0.00
191_L 83_D 0.86 0.15 0.00
313_V 113_T 0.86 0.15 0.00
199_L 116_G 0.86 0.15 0.00
112_N 135_G 0.85 0.15 0.00
85_F 196_T 0.85 0.14 0.00
112_N 107_P 0.85 0.14 0.00
22_V 226_D 0.85 0.14 0.00
289_Y 246_Y 0.85 0.14 0.00
28_G 60_A 0.84 0.14 0.00
270_V 256_I 0.84 0.14 0.00
39_K 237_F 0.84 0.14 0.00
144_F 125_L 0.84 0.14 0.00
179_A 71_T 0.84 0.14 0.00
120_I 213_A 0.84 0.14 0.00
48_R 213_A 0.84 0.14 0.00
133_M 70_R 0.83 0.14 0.00
11_F 202_P 0.83 0.14 0.00
313_V 119_M 0.83 0.14 0.00
28_G 90_A 0.83 0.14 0.00
236_S 85_V 0.83 0.14 0.00
17_L 203_A 0.83 0.14 0.00
287_W 85_V 0.83 0.14 0.00
201_M 110_H 0.82 0.13 0.00
73_I 105_R 0.82 0.13 0.00
294_V 176_N 0.82 0.13 0.00
127_E 151_P 0.81 0.13 0.00
117_I 242_A 0.81 0.13 0.00
203_V 23_H 0.81 0.13 0.00
197_P 177_A 0.81 0.13 0.00
113_I 14_G 0.81 0.13 0.00
207_V 113_T 0.81 0.13 0.00
113_I 235_V 0.81 0.13 0.00
201_M 176_N 0.81 0.13 0.00
155_I 254_Q 0.81 0.13 0.00
90_L 179_F 0.81 0.13 0.00
143_P 244_L 0.81 0.13 0.00
80_D 178_A 0.81 0.13 0.00
13_L 163_G 0.81 0.13 0.00
199_L 223_K 0.81 0.13 0.00
45_Q 53_V 0.80 0.13 0.00
229_A 165_E 0.80 0.13 0.00
17_L 229_Q 0.80 0.13 0.00
107_G 236_I 0.80 0.13 0.00
120_I 69_L 0.80 0.13 0.00
231_F 202_P 0.80 0.13 0.00
155_I 166_K 0.80 0.13 0.00
102_I 96_D 0.80 0.13 0.00
216_P 246_Y 0.80 0.12 0.00
33_M 157_V 0.80 0.12 0.00
327_I 220_A 0.80 0.12 0.00
45_Q 96_D 0.80 0.12 0.00
329_A 250_K 0.79 0.12 0.00
231_F 146_N 0.79 0.12 0.00
317_L 255_P 0.79 0.12 0.00
56_W 39_F 0.79 0.12 0.00
97_F 148_I 0.79 0.12 0.00
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
3035 0.47 cI_H_40_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3034 0.48 cI_H_40_cIII_cyt1_2_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3033 0.46 cI_H_40_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2726 0.49 cI_H_cIII_cytc1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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