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OPENSEQ.org
cI_NDUA_6_cIII_QCR2_6_mouse
Genes: A B A+B
Length: 377 453 729
Sequences: 13654 11788 185
Seq/Len: 36.22 26.02 0.25
MirrorTree (Pazo et al. 2001) 0.25
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 0.06 0.17 0.01
2 0.08 0.17 0.02
5 0.09 0.18 0.05
10 0.11 0.19 0.10
20 0.14 0.20 0.22
100 0.17 0.21 0.90
∞ 0.22 0.26 3.45
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
163_R 427_A 1.31 0.26 0.00
195_F 288_V 1.27 0.24 0.00
74_G 110_L 1.24 0.23 0.00
128_N 201_T 1.20 0.21 0.00
160_G 336_F 1.19 0.21 0.00
58_V 366_L 1.19 0.21 0.00
58_V 222_G 1.18 0.20 0.00
146_V 139_N 1.16 0.20 0.00
155_A 80_S 1.16 0.20 0.00
191_V 322_D 1.13 0.18 0.00
349_S 382_Y 1.12 0.18 0.00
350_I 313_V 1.08 0.17 0.00
278_K 323_V 1.07 0.17 0.00
272_L 207_Y 1.07 0.16 0.00
163_R 210_Q 1.06 0.16 0.00
155_A 205_L 1.06 0.16 0.00
261_K 139_N 1.05 0.16 0.00
339_G 205_L 1.05 0.16 0.00
285_H 182_Y 1.04 0.15 0.00
188_E 238_L 1.03 0.15 0.00
58_V 207_Y 1.02 0.15 0.00
58_V 210_Q 1.00 0.14 0.00
169_H 359_K 0.99 0.14 0.00
354_R 197_M 0.99 0.14 0.00
148_I 211_N 0.99 0.14 0.00
58_V 379_K 0.98 0.14 0.00
280_I 263_G 0.97 0.13 0.00
163_R 80_S 0.97 0.13 0.00
128_N 232_Q 0.96 0.13 0.00
112_D 72_E 0.96 0.13 0.00
242_V 128_S 0.94 0.12 0.00
178_S 367_S 0.94 0.12 0.00
126_V 413_L 0.94 0.12 0.00
57_T 443_N 0.94 0.12 0.00
334_G 367_S 0.94 0.12 0.00
166_H 226_S 0.93 0.12 0.00
95_R 421_D 0.93 0.12 0.00
126_V 345_A 0.93 0.12 0.00
252_A 136_F 0.91 0.11 0.00
119_A 115_T 0.89 0.11 0.00
263_F 177_L 0.89 0.11 0.00
339_G 160_I 0.89 0.11 0.00
108_W 234_A 0.89 0.11 0.00
95_R 106_V 0.89 0.11 0.00
120_V 369_A 0.88 0.11 0.00
293_L 420_A 0.88 0.11 0.00
74_G 80_S 0.88 0.11 0.00
332_L 426_K 0.88 0.11 0.00
280_I 419_V 0.87 0.11 0.00
165_I 440_A 0.87 0.10 0.00
199_I 169_S 0.87 0.10 0.00
248_G 146_F 0.87 0.10 0.00
260_G 338_I 0.86 0.10 0.00
81_I 252_K 0.86 0.10 0.00
339_G 282_E 0.86 0.10 0.00
276_L 296_G 0.86 0.10 0.00
149_P 144_P 0.86 0.10 0.00
346_E 368_S 0.86 0.10 0.00
75_R 247_A 0.85 0.10 0.00
83_P 431_F 0.85 0.10 0.00
60_G 224_G 0.85 0.10 0.00
63_G 224_G 0.85 0.10 0.00
242_V 90_T 0.84 0.10 0.00
335_L 414_Q 0.84 0.10 0.00
96_L 130_I 0.84 0.10 0.00
209_R 240_M 0.83 0.10 0.00
335_L 205_L 0.83 0.10 0.00
280_I 355_Y 0.83 0.10 0.00
279_Y 354_A 0.83 0.10 0.00
346_E 370_D 0.83 0.10 0.00
131_G 72_E 0.83 0.10 0.00
64_F 121_Y 0.82 0.09 0.00
304_L 181_A 0.82 0.09 0.00
67_R 195_Y 0.82 0.09 0.00
263_F 222_G 0.82 0.09 0.00
73_L 407_M 0.82 0.09 0.00
106_L 289_L 0.82 0.09 0.00
263_F 205_L 0.81 0.09 0.00
158_E 42_K 0.81 0.09 0.00
160_G 396_I 0.81 0.09 0.00
155_A 215_S 0.81 0.09 0.00
292_P 323_V 0.81 0.09 0.00
69_V 367_S 0.81 0.09 0.00
146_V 249_A 0.81 0.09 0.00
188_E 224_G 0.80 0.09 0.00
65_L 420_A 0.80 0.09 0.00
60_G 78_G 0.80 0.09 0.00
63_G 78_G 0.80 0.09 0.00
109_D 68_G 0.80 0.09 0.00
83_P 146_F 0.80 0.09 0.00
276_L 184_N 0.80 0.09 0.00
126_V 118_N 0.79 0.09 0.00
354_R 225_V 0.79 0.09 0.00
124_N 108_G 0.79 0.09 0.00
112_D 44_P 0.79 0.09 0.00
263_F 268_H 0.79 0.09 0.00
97_M 46_G 0.79 0.09 0.00
109_D 79_T 0.79 0.09 0.00
58_V 435_K 0.79 0.09 0.00
217_F 288_V 0.78 0.09 0.00
61_A 395_E 0.78 0.09 0.00
167_V 352_N 0.78 0.09 0.00
341_Q 48_V 0.78 0.09 0.00
119_A 418_S 0.78 0.09 0.00
143_D 306_T 0.78 0.08 0.00
76_M 373_A 0.77 0.08 0.00
314_T 203_E 0.77 0.08 0.00
163_R 307_S 0.77 0.08 0.00
57_T 234_A 0.77 0.08 0.00
316_K 223_L 0.77 0.08 0.00
183_S 131_E 0.77 0.08 0.00
104_T 367_S 0.76 0.08 0.00
114_D 230_L 0.76 0.08 0.00
58_V 89_L 0.76 0.08 0.00
154_Q 351_I 0.76 0.08 0.00
248_G 400_A 0.76 0.08 0.00
183_S 352_N 0.76 0.08 0.00
339_G 211_N 0.75 0.08 0.00
221_R 91_T 0.75 0.08 0.00
108_W 49_I 0.75 0.08 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
3513 0.24 cI_NDUA_40_cIII_QCR2_40_mouse Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3512 0 cI_NDUA_40_1_cIII_QCR2_40_1_mouse Δgene:(1, 20) A:(1E-40, 1) B:(1E-40, 1) msa: Jackhmmer (2015_06) Killed - Shared
3511 0.34 cI_NDUA_20_cIII_QCR2_20_mouse Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3510 0.25 cI_NDUA_6_cIII_QCR2_6_mouse Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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