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OPENSEQ.org
cI_H_cIII_cytc1_Pdenitr
Genes: A B A+B
Length: 345 263 576
Sequences: 4768 973 282
Seq/Len: 13.82 3.7 0.49
MirrorTree (Pazo et al. 2001) 0.26
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 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.04
∞ 0.05 0.01 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
313_V 240_V 1.37 0.46 0.00
201_M 63_G 1.33 0.42 0.00
216_P 249_N 1.23 0.35 0.00
267_L 130_R 1.23 0.35 0.00
174_S 149_G 1.21 0.34 0.00
21_A 63_G 1.20 0.33 0.00
267_L 249_N 1.18 0.32 0.00
241_L 221_E 1.14 0.29 0.00
123_A 66_Y 1.07 0.25 0.00
261_L 215_F 1.07 0.25 0.00
66_L 82_E 1.06 0.25 0.00
121_F 90_A 1.06 0.24 0.00
154_M 218_W 1.00 0.21 0.00
90_L 84_Q 1.00 0.21 0.00
147_S 241_L 0.99 0.21 0.00
320_G 236_I 0.99 0.21 0.00
26_V 220_A 0.99 0.21 0.00
80_D 64_L 0.99 0.21 0.00
231_F 146_N 0.98 0.20 0.00
238_T 88_Y 0.98 0.20 0.00
143_P 107_P 0.98 0.20 0.00
242_L 95_T 0.98 0.20 0.00
270_V 125_L 0.97 0.20 0.00
26_V 246_Y 0.97 0.20 0.00
120_I 213_A 0.97 0.20 0.00
287_W 76_G 0.96 0.20 0.00
143_P 244_L 0.96 0.19 0.00
42_A 43_D 0.96 0.19 0.00
74_V 216_L 0.96 0.19 0.00
231_F 156_A 0.96 0.19 0.00
155_I 201_T 0.96 0.19 0.00
46_M 69_L 0.95 0.19 0.00
252_Y 141_L 0.95 0.19 0.00
197_P 177_A 0.95 0.19 0.00
35_Y 64_L 0.95 0.19 0.00
240_Y 78_P 0.95 0.19 0.00
177_L 207_Q 0.94 0.19 0.00
155_I 220_A 0.94 0.18 0.00
90_L 177_A 0.94 0.18 0.00
199_L 223_K 0.94 0.18 0.00
195_W 108_T 0.94 0.18 0.00
120_I 237_F 0.94 0.18 0.00
101_V 221_E 0.93 0.18 0.00
146_A 18_E 0.93 0.18 0.00
80_D 251_K 0.92 0.18 0.00
164_I 134_H 0.92 0.17 0.00
199_L 46_Q 0.92 0.17 0.00
39_K 67_V 0.92 0.17 0.00
241_L 242_A 0.92 0.17 0.00
113_I 221_E 0.91 0.17 0.00
179_A 196_T 0.91 0.17 0.00
93_M 151_P 0.91 0.17 0.00
28_G 60_A 0.91 0.17 0.00
13_L 170_G 0.90 0.17 0.00
48_R 213_A 0.90 0.17 0.00
281_V 135_G 0.90 0.17 0.00
22_V 74_D 0.89 0.16 0.00
12_A 256_I 0.89 0.16 0.00
18_Q 235_V 0.89 0.16 0.00
236_S 227_R 0.89 0.16 0.00
117_I 213_A 0.89 0.16 0.00
121_F 251_K 0.88 0.16 0.00
237_S 248_T 0.88 0.16 0.00
319_L 201_T 0.88 0.16 0.00
13_L 163_G 0.88 0.16 0.00
201_M 176_N 0.88 0.16 0.00
203_V 169_A 0.88 0.16 0.00
20_L 86_R 0.88 0.16 0.00
207_V 101_E 0.87 0.15 0.00
9_Y 250_K 0.87 0.15 0.00
167_G 241_L 0.87 0.15 0.00
170_I 73_A 0.86 0.15 0.00
178_T 250_K 0.86 0.15 0.00
207_V 256_I 0.85 0.15 0.00
48_R 214_A 0.85 0.15 0.00
22_V 208_M 0.85 0.15 0.00
227_L 190_L 0.85 0.15 0.00
16_L 83_D 0.85 0.15 0.00
121_F 163_G 0.85 0.14 0.00
33_M 105_R 0.85 0.14 0.00
178_T 106_V 0.84 0.14 0.00
182_E 63_G 0.84 0.14 0.00
121_F 162_D 0.84 0.14 0.00
320_G 229_Q 0.83 0.14 0.00
126_L 59_S 0.83 0.14 0.00
34_V 249_N 0.83 0.14 0.00
66_L 129_A 0.83 0.14 0.00
121_F 127_A 0.82 0.14 0.00
206_F 217_M 0.82 0.13 0.00
42_A 67_V 0.82 0.13 0.00
250_A 128_K 0.82 0.13 0.00
253_L 131_A 0.81 0.13 0.00
270_V 110_H 0.81 0.13 0.00
250_A 122_D 0.81 0.13 0.00
112_N 235_V 0.81 0.13 0.00
79_A 255_P 0.81 0.13 0.00
121_F 244_L 0.81 0.13 0.00
127_E 249_N 0.81 0.13 0.00
29_S 52_Q 0.81 0.13 0.00
267_L 64_L 0.81 0.13 0.00
26_V 67_V 0.81 0.13 0.00
105_D 246_Y 0.81 0.13 0.00
216_P 246_Y 0.81 0.13 0.00
290_M 256_I 0.80 0.13 0.00
74_V 256_I 0.80 0.13 0.00
207_V 151_P 0.80 0.13 0.00
327_I 124_S 0.80 0.13 0.00
282_I 32_S 0.80 0.13 0.00
83_V 105_R 0.79 0.13 0.00
70_V 216_L 0.79 0.13 0.00
256_A 228_K 0.79 0.13 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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