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OPENSEQ.org
cIV_A_20_cI_A_40_human
Genes: A B A+B
Length: 513 115 627
Sequences: 4396 1332 215
Seq/Len: 8.57 11.58 0.34
MirrorTree (Pazo et al. 2001) 0.45
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.02 0.00 0.31
10 0.02 0.00 0.34
20 0.03 0.00 0.34
100 0.04 0.00 0.34
∞ 0.08 0.00 0.34
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
410_A 95_I 2.11 0.82 0.18
143_V 110_G 1.82 0.67 0.09
443_Y 58_V 1.68 0.57 0.06
272_G 54_K 1.67 0.57 0.06
122_A 110_G 1.55 0.49 0.04
8_F 110_G 1.53 0.47 0.04
401_S 16_L 1.51 0.46 0.04
430_F 61_T 1.45 0.41 0.03
306_T 61_T 1.45 0.41 0.03
413_H 54_K 1.44 0.41 0.03
447_Y 49_V 1.42 0.39 0.03
447_Y 32_E 1.40 0.38 0.03
448_T 7_L 1.37 0.36 0.02
58_V 114_A 1.36 0.35 0.02
58_V 110_G 1.34 0.34 0.02
198_S 24_L 1.33 0.34 0.02
37_I 16_L 1.30 0.32 0.02
307_S 22_F 1.30 0.32 0.02
472_I 100_L 1.29 0.32 0.02
136_Y 108_Q 1.25 0.29 0.02
119_E 95_I 1.24 0.28 0.01
134_G 58_V 1.24 0.28 0.01
346_F 61_T 1.23 0.28 0.01
481_K 13_L 1.23 0.28 0.01
395_H 61_T 1.21 0.27 0.01
36_L 53_M 1.21 0.27 0.01
274_V 63_L 1.19 0.26 0.01
97_M 86_L 1.19 0.26 0.01
409_Y 103_A 1.18 0.25 0.01
401_S 9_I 1.18 0.25 0.01
259_T 114_A 1.16 0.24 0.01
8_F 114_A 1.15 0.24 0.01
229_I 5_L 1.15 0.23 0.01
229_I 10_N 1.13 0.23 0.01
407_Q 13_L 1.12 0.22 0.01
391_G 75_L 1.11 0.22 0.01
40_E 61_T 1.11 0.22 0.01
311_I 61_T 1.11 0.21 0.01
511_M 20_I 1.10 0.21 0.01
205_G 54_K 1.10 0.21 0.01
459_F 30_Y 1.09 0.21 0.01
279_S 22_F 1.09 0.21 0.01
143_V 61_T 1.09 0.21 0.01
26_A 32_E 1.09 0.20 0.01
297_M 61_T 1.09 0.20 0.01
467_L 19_I 1.08 0.20 0.01
83_V 114_A 1.08 0.20 0.01
198_S 51_F 1.08 0.20 0.01
471_M 95_I 1.08 0.20 0.01
128_V 61_T 1.07 0.20 0.01
108_S 32_E 1.07 0.20 0.01
330_S 77_W 1.06 0.20 0.01
281_G 54_K 1.06 0.19 0.01
39_A 2_N 1.06 0.19 0.01
393_F 54_K 1.06 0.19 0.01
430_F 110_G 1.06 0.19 0.01
28_V 87_M 1.05 0.19 0.01
306_T 110_G 1.05 0.19 0.01
141_A 114_A 1.05 0.19 0.01
176_M 112_D 1.04 0.19 0.01
136_Y 9_I 1.04 0.19 0.01
390_M 77_W 1.04 0.19 0.01
286_I 82_T 1.04 0.18 0.01
278_M 110_G 1.04 0.18 0.01
204_A 77_W 1.04 0.18 0.01
359_A 13_L 1.03 0.18 0.01
28_V 54_K 1.03 0.18 0.01
198_S 100_L 1.03 0.18 0.01
391_G 9_I 1.03 0.18 0.01
161_A 16_L 1.03 0.18 0.01
176_M 42_D 1.02 0.18 0.01
353_L 78_A 1.02 0.18 0.01
110_L 12_L 1.02 0.18 0.01
194_L 78_A 1.02 0.18 0.01
301_T 78_A 1.02 0.18 0.01
419_I 93_L 1.02 0.18 0.01
477_A 100_L 1.02 0.18 0.01
488_P 58_V 1.01 0.17 0.01
401_S 75_L 1.01 0.17 0.01
58_V 88_V 1.01 0.17 0.01
447_Y 51_F 1.01 0.17 0.01
477_A 75_L 1.00 0.17 0.01
409_Y 54_K 0.99 0.17 0.01
25_W 61_T 0.99 0.17 0.01
189_L 92_L 0.99 0.17 0.01
430_F 14_A 0.99 0.17 0.01
391_G 7_L 0.99 0.17 0.01
193_V 114_A 0.99 0.17 0.01
306_T 14_A 0.99 0.16 0.01
198_S 21_T 0.99 0.16 0.01
490_M 45_S 0.99 0.16 0.01
363_L 104_Y 0.99 0.16 0.01
484_M 100_L 0.98 0.16 0.01
146_T 85_P 0.98 0.16 0.01
266_E 78_A 0.98 0.16 0.01
496_H 3_F 0.98 0.16 0.01
35_L 97_I 0.98 0.16 0.01
448_T 96_I 0.98 0.16 0.01
511_M 5_L 0.98 0.16 0.01
37_I 93_L 0.97 0.16 0.01
57_I 93_L 0.97 0.16 0.01
350_V 24_L 0.97 0.16 0.01
496_H 94_L 0.96 0.15 0.01
478_S 58_V 0.96 0.15 0.01
146_T 2_N 0.96 0.15 0.01
363_L 21_T 0.96 0.15 0.01
495_L 58_V 0.96 0.15 0.01
400_F 61_T 0.96 0.15 0.01
281_G 32_E 0.96 0.15 0.01
322_S 78_A 0.96 0.15 0.01
327_L 115_E 0.95 0.15 0.01
56_V 93_L 0.95 0.15 0.01
133_A 11_T 0.95 0.15 0.01
443_Y 30_Y 0.95 0.15 0.01
419_I 91_S 0.95 0.15 0.01
198_S 53_M 0.95 0.15 0.01
330_S 29_G 0.94 0.15 0.01
478_S 30_Y 0.94 0.15 0.01
281_G 61_T 0.94 0.15 0.01
114_A 90_S 0.94 0.15 0.01
443_Y 46_P 0.94 0.15 0.01
260_Y 97_I 0.94 0.15 0.01
47_L 58_V 0.94 0.15 0.01
155_V 53_M 0.94 0.15 0.01
314_I 22_F 0.94 0.15 0.01
412_I 108_Q 0.94 0.14 0.01
275_W 77_W 0.93 0.14 0.01
405_L 84_L 0.93 0.14 0.01
403_Y 75_L 0.93 0.14 0.01
390_M 29_G 0.93 0.14 0.01
257_I 3_F 0.93 0.14 0.01
229_I 45_S 0.92 0.14 0.01
359_A 14_A 0.92 0.14 0.01
48_L 5_L 0.92 0.14 0.01
35_L 73_L 0.92 0.14 0.01
400_F 110_G 0.92 0.14 0.01
496_H 6_I 0.92 0.14 0.01
8_F 14_A 0.92 0.14 0.01
52_H 61_T 0.92 0.14 0.01
400_F 103_A 0.92 0.14 0.01
366_V 61_T 0.92 0.14 0.01
467_L 100_L 0.92 0.14 0.01
146_T 84_L 0.92 0.14 0.01
391_G 103_A 0.92 0.14 0.01
350_V 45_S 0.92 0.14 0.01
391_G 81_T 0.92 0.14 0.01
257_I 46_P 0.91 0.14 0.01
338_V 115_E 0.91 0.14 0.01
160_G 108_Q 0.91 0.14 0.00
423_L 46_P 0.91 0.14 0.00
137_S 63_L 0.90 0.14 0.00
469_I 115_E 0.90 0.13 0.00
272_G 115_E 0.90 0.13 0.00
394_I 16_L 0.90 0.13 0.00
204_A 29_G 0.90 0.13 0.00
231_Y 54_K 0.90 0.13 0.00
443_Y 10_N 0.90 0.13 0.00
479_K 29_G 0.89 0.13 0.00
180_Q 54_K 0.89 0.13 0.00
404_T 26_Q 0.89 0.13 0.00
109_L 49_V 0.89 0.13 0.00
406_D 13_L 0.88 0.13 0.00
60_A 60_I 0.88 0.13 0.00
229_I 2_N 0.88 0.13 0.00
505_F 94_L 0.88 0.13 0.00
192_A 92_L 0.88 0.13 0.00
64_V 21_T 0.88 0.13 0.00
215_L 26_Q 0.88 0.13 0.00
332_M 45_S 0.88 0.13 0.00
327_L 95_I 0.88 0.13 0.00
189_L 16_L 0.88 0.13 0.00
198_S 49_V 0.88 0.13 0.00
413_H 115_E 0.88 0.13 0.00
297_M 46_P 0.88 0.13 0.00
416_I 15_L 0.87 0.12 0.00
509_V 17_L 0.87 0.12 0.00
57_I 91_S 0.87 0.12 0.00
109_L 70_A 0.87 0.12 0.00
21_L 110_G 0.87 0.12 0.00
505_F 95_I 0.87 0.12 0.00
63_F 51_F 0.87 0.12 0.00
401_S 95_I 0.87 0.12 0.00
332_M 112_D 0.86 0.12 0.00
146_T 10_N 0.86 0.12 0.00
26_A 49_V 0.86 0.12 0.00
139_P 54_K 0.86 0.12 0.00
31_T 45_S 0.86 0.12 0.00
8_F 61_T 0.86 0.12 0.00
155_V 94_L 0.86 0.12 0.00
218_T 1_M 0.86 0.12 0.00
198_S 7_L 0.86 0.12 0.00
479_K 77_W 0.85 0.12 0.00
345_I 77_W 0.85 0.12 0.00
205_G 13_L 0.85 0.12 0.00
161_A 9_I 0.85 0.12 0.00
401_S 85_P 0.85 0.12 0.00
417_M 50_P 0.85 0.12 0.00
409_Y 19_I 0.85 0.12 0.00
205_G 80_Q 0.85 0.12 0.00
443_Y 94_L 0.84 0.12 0.00
357_V 103_A 0.84 0.12 0.00
339_L 114_A 0.84 0.12 0.00
467_L 31_M 0.84 0.12 0.00
469_I 54_K 0.84 0.12 0.00
177_T 28_N 0.84 0.12 0.00
336_A 7_L 0.84 0.12 0.00
83_V 89_M 0.84 0.12 0.00
449_T 30_Y 0.84 0.12 0.00
177_T 32_E 0.84 0.11 0.00
31_T 5_L 0.83 0.11 0.00
338_V 54_K 0.83 0.11 0.00
483_L 2_N 0.83 0.11 0.00
87_I 3_F 0.83 0.11 0.00
231_Y 46_P 0.83 0.11 0.00
176_M 15_L 0.83 0.11 0.00
338_V 13_L 0.83 0.11 0.00
258_V 83_N 0.82 0.11 0.00
141_A 34_S 0.82 0.11 0.00
365_I 103_A 0.82 0.11 0.00
49_G 73_L 0.82 0.11 0.00
365_I 79_X 0.82 0.11 0.00
141_A 88_V 0.82 0.11 0.00
26_A 10_N 0.82 0.11 0.00
3_A 114_A 0.82 0.11 0.00
24_A 114_A 0.82 0.11 0.00
511_M 100_L 0.81 0.11 0.00
116_A 20_I 0.81 0.11 0.00
416_I 95_I 0.81 0.11 0.00
460_I 13_L 0.81 0.11 0.00
477_A 96_I 0.81 0.11 0.00
31_T 54_K 0.81 0.11 0.00
198_S 32_E 0.81 0.11 0.00
403_Y 19_I 0.81 0.11 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
4474 0.34 cIV_A_20_cI_A_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4471 3.35 cIV_A_20_cI_A_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
4470 3.05 cIV_A_10_cI_A_20_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
4468 2.76 cIV_A_40_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4466 0.34 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4460 3.04 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.27 Done - Shared
4458 3.54 cIV_A_4_cI_A_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4456 0 cIV_A_80_cI_A_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) Killed - Shared
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