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OPENSEQ.org
cIV_A_60_cI_J_10_human
Genes: A B A+B
Length: 513 174 679
Sequences: 3040 2877 1178
Seq/Len: 5.93 16.53 1.73
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 0.01
2 0.00 0.00 0.03
5 0.01 0.00 0.15
10 0.01 0.00 1.71
20 0.01 0.00 1.71
100 0.02 0.00 1.71
∞ 0.05 0.00 1.71
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
5_R 73_M 1.63 0.93 0.59
166_T 61_G 1.51 0.89 0.49
5_R 59_Y 1.47 0.87 0.45
21_L 132_S 1.45 0.86 0.43
476_F 63_M 1.40 0.84 0.39
307_S 32_L 1.40 0.83 0.39
286_I 61_G 1.39 0.83 0.39
389_I 66_V 1.32 0.78 0.33
286_I 32_L 1.31 0.78 0.32
489_S 65_V 1.25 0.73 0.27
392_G 61_G 1.23 0.71 0.26
26_A 167_V 1.21 0.70 0.24
479_K 61_G 1.21 0.69 0.24
21_L 164_V 1.18 0.67 0.22
265_K 57_L 1.16 0.65 0.21
286_I 38_V 1.14 0.63 0.20
258_V 167_V 1.13 0.62 0.19
27_G 147_D 1.12 0.60 0.18
193_I 142_A 1.11 0.60 0.18
462_L 49_G 1.11 0.59 0.18
359_A 74_A 1.10 0.58 0.17
337_A 146_Y 1.09 0.58 0.17
26_A 33_I 1.09 0.58 0.17
260_Y 59_Y 1.07 0.56 0.16
405_L 45_N 1.07 0.56 0.16
120_A 164_V 1.07 0.56 0.16
215_L 146_Y 1.07 0.56 0.16
45_G 167_V 1.06 0.55 0.15
139_P 162_V 1.05 0.54 0.15
260_Y 35_S 1.05 0.54 0.14
118_V 152_L 1.04 0.53 0.14
43_Q 153_V 1.04 0.52 0.14
318_V 64_M 1.04 0.52 0.14
434_S 167_V 1.03 0.52 0.14
475_A 40_C 1.03 0.52 0.14
501_P 65_V 1.03 0.51 0.14
152_L 65_V 1.02 0.50 0.13
5_R 78_Y 1.02 0.50 0.13
116_A 52_G 1.01 0.50 0.13
29_L 86_V 1.01 0.49 0.13
180_Q 64_M 1.01 0.49 0.12
265_K 73_M 1.00 0.48 0.12
464_A 171_A 1.00 0.48 0.12
261_Y 35_S 1.00 0.48 0.12
89_A 61_G 1.00 0.48 0.12
145_L 154_V 1.00 0.48 0.12
28_V 24_S 0.99 0.47 0.12
434_S 137_E 0.99 0.47 0.12
22_F 75_I 0.98 0.46 0.11
434_S 59_Y 0.97 0.45 0.11
28_V 58_I 0.97 0.44 0.11
87_I 57_L 0.96 0.44 0.10
390_M 46_F 0.96 0.44 0.10
314_I 31_V 0.96 0.44 0.10
405_L 23_P 0.96 0.44 0.10
87_I 168_I 0.96 0.43 0.10
307_S 73_M 0.94 0.42 0.10
231_Y 36_G 0.94 0.41 0.09
434_S 40_C 0.93 0.41 0.09
468_M 135_I 0.93 0.41 0.09
39_A 32_L 0.93 0.40 0.09
187_S 56_F 0.92 0.40 0.09
43_Q 40_C 0.92 0.40 0.09
57_I 8_L 0.92 0.40 0.09
22_F 61_G 0.91 0.39 0.09
27_G 32_L 0.91 0.39 0.09
32_A 50_Y 0.90 0.38 0.08
137_S 162_V 0.90 0.37 0.08
29_L 58_I 0.89 0.37 0.08
336_A 35_S 0.89 0.36 0.08
136_Y 22_K 0.88 0.36 0.08
190_I 170_I 0.88 0.36 0.08
404_T 152_L 0.88 0.35 0.07
409_Y 49_G 0.88 0.35 0.07
169_I 97_A 0.88 0.35 0.07
113_L 21_S 0.88 0.35 0.07
353_L 65_V 0.88 0.35 0.07
39_A 64_M 0.87 0.35 0.07
320_V 24_S 0.87 0.35 0.07
495_L 156_T 0.87 0.35 0.07
463_T 162_V 0.87 0.35 0.07
468_M 50_Y 0.87 0.35 0.07
135_N 153_V 0.87 0.35 0.07
133_A 137_E 0.87 0.35 0.07
350_V 154_V 0.87 0.34 0.07
135_N 59_Y 0.87 0.34 0.07
500_P 28_G 0.86 0.34 0.07
179_Y 157_G 0.86 0.34 0.07
469_I 43_I 0.86 0.34 0.07
416_I 65_V 0.86 0.34 0.07
100_M 32_L 0.86 0.34 0.07
161_A 74_A 0.85 0.33 0.07
467_L 60_L 0.85 0.33 0.07
511_M 143_G 0.85 0.33 0.07
5_R 58_I 0.85 0.32 0.07
176_M 72_A 0.85 0.32 0.06
87_I 169_E 0.84 0.32 0.06
409_Y 162_V 0.84 0.32 0.06
331_N 79_P 0.84 0.32 0.06
395_H 56_F 0.84 0.32 0.06
404_T 54_M 0.84 0.32 0.06
258_V 145_L 0.84 0.32 0.06
260_Y 157_G 0.84 0.32 0.06
404_T 94_V 0.84 0.31 0.06
359_A 49_G 0.83 0.31 0.06
497_G 28_G 0.83 0.31 0.06
117_M 11_G 0.83 0.31 0.06
175_A 16_F 0.83 0.31 0.06
166_T 56_F 0.83 0.31 0.06
21_L 56_F 0.83 0.31 0.06
122_A 145_L 0.82 0.30 0.06
359_A 161_F 0.82 0.30 0.06
334_W 64_M 0.82 0.30 0.06
139_P 57_L 0.82 0.30 0.06
253_M 73_M 0.82 0.30 0.06
353_L 55_V 0.82 0.30 0.06
314_I 78_Y 0.82 0.30 0.06
35_L 164_V 0.82 0.30 0.06
403_Y 40_C 0.82 0.30 0.06
181_T 145_L 0.82 0.30 0.06
145_L 8_L 0.82 0.30 0.06
389_I 50_Y 0.81 0.29 0.06
469_I 40_C 0.81 0.29 0.06
286_I 31_V 0.81 0.29 0.06
407_Q 154_V 0.81 0.29 0.06
400_F 161_F 0.81 0.29 0.05
492_L 167_V 0.81 0.29 0.05
7_L 43_I 0.81 0.29 0.05
475_A 151_W 0.81 0.29 0.05
259_T 171_A 0.81 0.29 0.05
119_E 162_V 0.80 0.28 0.05
465_V 79_P 0.80 0.28 0.05
335_S 29_G 0.80 0.28 0.05
162_I 30_L 0.80 0.28 0.05
504_T 159_T 0.80 0.28 0.05
408_T 164_V 0.80 0.28 0.05
32_A 44_L 0.80 0.28 0.05
507_E 35_S 0.80 0.28 0.05
286_I 49_G 0.80 0.28 0.05
413_H 169_E 0.80 0.28 0.05
64_V 15_G 0.80 0.28 0.05
223_A 166_I 0.80 0.28 0.05
463_T 94_V 0.80 0.28 0.05
406_D 144_A 0.80 0.28 0.05
57_I 57_L 0.79 0.28 0.05
407_Q 135_I 0.79 0.28 0.05
42_G 64_M 0.79 0.27 0.05
502_Y 66_V 0.79 0.27 0.05
56_V 70_T 0.79 0.27 0.05
476_F 70_T 0.79 0.27 0.05
286_I 58_I 0.79 0.27 0.05
69_M 66_V 0.78 0.27 0.05
181_T 164_V 0.78 0.27 0.05
423_L 152_L 0.78 0.27 0.05
327_L 104_L 0.78 0.27 0.05
47_L 152_L 0.78 0.26 0.05
447_Y 22_K 0.78 0.26 0.05
423_L 10_V 0.78 0.26 0.05
392_G 71_T 0.78 0.26 0.05
70_V 136_R 0.78 0.26 0.05
311_I 52_G 0.78 0.26 0.05
275_W 37_V 0.78 0.26 0.05
505_F 159_T 0.77 0.26 0.05
179_Y 149_G 0.77 0.26 0.05
345_I 82_W 0.77 0.26 0.05
267_P 53_L 0.77 0.26 0.05
97_M 172_R 0.77 0.26 0.05
356_I 166_I 0.77 0.25 0.04
453_L 94_V 0.77 0.25 0.04
162_I 27_Y 0.77 0.25 0.04
135_N 38_V 0.77 0.25 0.04
391_G 159_T 0.77 0.25 0.04
464_A 146_Y 0.77 0.25 0.04
87_I 70_T 0.77 0.25 0.04
345_I 154_V 0.77 0.25 0.04
53_I 32_L 0.76 0.25 0.04
166_T 38_V 0.76 0.25 0.04
168_I 162_V 0.76 0.25 0.04
261_Y 159_T 0.76 0.25 0.04
253_M 54_M 0.76 0.25 0.04
43_Q 71_T 0.76 0.25 0.04
345_I 138_D 0.76 0.25 0.04
8_F 38_V 0.76 0.25 0.04
357_V 61_G 0.76 0.25 0.04
159_L 68_G 0.76 0.25 0.04
4_D 59_Y 0.76 0.25 0.04
278_M 73_M 0.76 0.25 0.04
229_I 94_V 0.76 0.25 0.04
24_A 63_M 0.76 0.25 0.04
189_L 142_A 0.76 0.25 0.04
133_A 19_F 0.75 0.24 0.04
263_G 50_Y 0.75 0.24 0.04
173_P 60_L 0.75 0.24 0.04
419_I 13_V 0.75 0.24 0.04
472_I 164_V 0.75 0.24 0.04
394_I 155_V 0.75 0.24 0.04
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
4528 1.73 cIV_A_60_cI_J_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
4527 0.73 cIV_A_80_cI_J_20_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4526 0.72 cIV_A_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
4525 0.71 cIV_A_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4523 0.09 cIV_A_40_cI_J_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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