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OPENSEQ.org
cIV_A_40_cI_K_20_human
Genes: A B A+B
Length: 513 98 610
Sequences: 3245 1088 202
Seq/Len: 6.33 11.1 0.33
MirrorTree (Pazo et al. 2001) 0.55
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 0.02
5 0.01 0.00 0.04
10 0.01 0.00 0.33
20 0.01 0.00 0.33
100 0.02 0.00 0.33
∞ 0.06 0.00 0.33
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
272_G 33_L 1.61 0.52 0.00
258_V 63_M 1.60 0.51 0.00
168_I 33_L 1.53 0.47 0.00
204_A 38_L 1.38 0.36 0.00
275_W 36_M 1.33 0.33 0.00
58_V 63_M 1.32 0.33 0.00
36_L 78_L 1.29 0.31 0.00
8_F 73_V 1.28 0.30 0.00
359_A 87_L 1.26 0.29 0.00
185_V 17_L 1.26 0.29 0.00
28_V 33_L 1.26 0.29 0.00
188_V 8_I 1.24 0.28 0.00
307_S 22_Y 1.24 0.28 0.00
330_S 38_L 1.23 0.27 0.00
508_P 60_P 1.22 0.27 0.00
63_F 19_M 1.22 0.27 0.00
179_Y 35_G 1.20 0.26 0.00
281_G 33_L 1.19 0.25 0.00
231_Y 72_A 1.18 0.25 0.00
128_V 19_M 1.18 0.25 0.00
116_A 23_R 1.18 0.24 0.00
109_L 97_Q 1.18 0.24 0.00
189_L 35_G 1.17 0.24 0.00
338_V 36_M 1.17 0.24 0.00
223_A 23_R 1.16 0.23 0.00
215_L 98_C 1.15 0.23 0.00
443_Y 64_L 1.15 0.23 0.00
257_I 61_I 1.15 0.23 0.00
198_S 97_Q 1.15 0.23 0.00
188_V 66_F 1.14 0.23 0.00
307_S 72_A 1.14 0.23 0.00
172_K 38_L 1.14 0.23 0.00
413_H 33_L 1.14 0.22 0.00
390_M 38_L 1.13 0.22 0.00
403_Y 97_Q 1.09 0.20 0.00
63_F 22_Y 1.09 0.20 0.00
390_M 35_G 1.09 0.20 0.00
430_F 83_N 1.09 0.20 0.00
57_I 85_Y 1.09 0.20 0.00
306_T 83_N 1.08 0.20 0.00
172_K 60_P 1.07 0.20 0.00
262_S 90_V 1.07 0.19 0.00
197_L 26_L 1.06 0.19 0.00
35_L 98_C 1.05 0.19 0.00
423_L 33_L 1.05 0.19 0.00
314_I 72_A 1.05 0.19 0.00
128_V 22_Y 1.05 0.18 0.00
479_K 38_L 1.05 0.18 0.00
64_V 45_T 1.03 0.18 0.00
63_F 82_S 1.03 0.18 0.00
262_S 41_F 1.03 0.18 0.00
20_L 78_L 1.03 0.18 0.00
87_I 67_A 1.03 0.18 0.00
403_Y 59_V 1.02 0.18 0.00
314_I 82_S 1.02 0.17 0.00
415_T 58_I 1.02 0.17 0.00
218_T 66_F 1.02 0.17 0.00
139_P 58_I 1.02 0.17 0.00
430_F 67_A 1.02 0.17 0.00
505_F 21_V 1.02 0.17 0.00
465_V 86_G 1.02 0.17 0.00
306_T 67_A 1.02 0.17 0.00
141_A 36_M 1.01 0.17 0.00
135_N 30_L 1.01 0.17 0.00
394_I 46_F 1.01 0.17 0.00
415_T 62_A 1.00 0.17 0.00
128_V 86_G 1.00 0.17 0.00
40_E 83_N 1.00 0.17 0.00
168_I 27_M 1.00 0.17 0.00
58_V 87_L 0.99 0.16 0.00
262_S 2_P 0.99 0.16 0.00
28_V 8_I 0.99 0.16 0.00
275_W 35_G 0.99 0.16 0.00
350_V 19_M 0.99 0.16 0.00
406_D 87_L 0.98 0.16 0.00
170_N 26_L 0.98 0.16 0.00
117_M 15_S 0.98 0.16 0.00
346_F 83_N 0.98 0.16 0.00
64_V 78_L 0.98 0.16 0.00
336_A 72_A 0.97 0.16 0.00
3_A 90_V 0.97 0.16 0.00
136_Y 89_Y 0.97 0.15 0.00
472_I 78_L 0.97 0.15 0.00
179_Y 38_L 0.97 0.15 0.00
63_F 15_S 0.96 0.15 0.00
318_V 22_Y 0.95 0.15 0.00
359_A 37_M 0.95 0.15 0.00
265_K 93_L 0.95 0.15 0.00
452_T 66_F 0.95 0.15 0.00
466_M 16_L 0.94 0.15 0.00
413_H 92_N 0.94 0.14 0.00
58_V 86_G 0.94 0.14 0.00
307_S 82_S 0.94 0.14 0.00
189_L 60_P 0.94 0.14 0.00
110_L 79_V 0.92 0.14 0.00
259_T 36_M 0.92 0.14 0.00
318_V 72_A 0.92 0.14 0.00
477_A 51_T 0.92 0.14 0.00
406_D 27_M 0.91 0.14 0.00
120_A 90_V 0.91 0.14 0.00
507_E 63_M 0.91 0.14 0.00
188_V 9_M 0.91 0.14 0.00
509_V 60_P 0.91 0.13 0.00
415_T 93_L 0.91 0.13 0.00
363_L 93_L 0.91 0.13 0.00
31_T 33_L 0.90 0.13 0.00
449_T 80_S 0.90 0.13 0.00
342_L 97_Q 0.90 0.13 0.00
189_L 14_I 0.90 0.13 0.00
198_S 78_L 0.90 0.13 0.00
205_G 88_D 0.90 0.13 0.00
275_W 38_L 0.89 0.13 0.00
143_V 86_G 0.89 0.13 0.00
229_I 90_V 0.89 0.13 0.00
185_V 39_S 0.88 0.13 0.00
259_T 35_G 0.88 0.13 0.00
410_A 66_F 0.88 0.13 0.00
174_P 64_L 0.88 0.12 0.00
318_V 40_L 0.88 0.12 0.00
26_A 18_G 0.88 0.12 0.00
172_K 35_G 0.88 0.12 0.00
204_A 35_G 0.88 0.12 0.00
188_V 92_N 0.87 0.12 0.00
350_V 22_Y 0.87 0.12 0.00
395_H 67_A 0.87 0.12 0.00
25_W 19_M 0.87 0.12 0.00
160_G 38_L 0.87 0.12 0.00
160_G 27_M 0.86 0.12 0.00
258_V 85_Y 0.86 0.12 0.00
471_M 19_M 0.86 0.12 0.00
507_E 87_L 0.86 0.12 0.00
174_P 15_S 0.86 0.12 0.00
327_L 44_G 0.86 0.12 0.00
83_V 14_I 0.86 0.12 0.00
192_A 49_L 0.85 0.12 0.00
419_I 55_L 0.85 0.12 0.00
257_I 48_T 0.85 0.12 0.00
50_N 85_Y 0.85 0.12 0.00
365_I 27_M 0.84 0.12 0.00
56_V 63_M 0.84 0.11 0.00
204_A 60_P 0.84 0.11 0.00
417_M 88_D 0.84 0.11 0.00
253_M 23_R 0.84 0.11 0.00
452_T 92_N 0.84 0.11 0.00
350_V 82_S 0.84 0.11 0.00
134_G 23_R 0.84 0.11 0.00
391_G 21_V 0.84 0.11 0.00
272_G 8_I 0.84 0.11 0.00
272_G 61_I 0.83 0.11 0.00
401_S 13_T 0.83 0.11 0.00
35_L 78_L 0.83 0.11 0.00
253_M 88_D 0.83 0.11 0.00
40_E 67_A 0.83 0.11 0.00
137_S 78_L 0.83 0.11 0.00
110_L 13_T 0.83 0.11 0.00
430_F 87_L 0.83 0.11 0.00
143_V 83_N 0.82 0.11 0.00
49_G 78_L 0.82 0.11 0.00
306_T 87_L 0.82 0.11 0.00
299_V 67_A 0.82 0.11 0.00
83_V 63_M 0.82 0.11 0.00
168_I 61_I 0.82 0.11 0.00
390_M 36_M 0.82 0.11 0.00
231_Y 65_V 0.82 0.11 0.00
218_T 9_M 0.82 0.11 0.00
270_Y 65_V 0.81 0.11 0.00
406_D 48_T 0.81 0.11 0.00
136_Y 23_R 0.81 0.11 0.00
419_I 6_M 0.81 0.11 0.00
314_I 33_L 0.81 0.10 0.00
53_I 48_T 0.81 0.10 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
4519 2.81 cIV_A_20_cI_K_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4518 2.49 cIV_A_60_cI_K_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4517 2.53 cIV_A_40_cI_K_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4516 0.33 cIV_A_40_cI_K_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4515 0.03 cIV_A_40_cI_K_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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