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OPENSEQ.org
cIp_9_10_cIV_I_40_human
Genes: A B A+B
Length: 210 378 580
Sequences: 1803 4493 207
Seq/Len: 8.59 11.89 0.36
MirrorTree (Pazo et al. 2001) 0.40
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.06
∞ 0.02 0.00 0.35
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
52_T 245_F 1.30 0.33 0.00
164_A 318_R 1.25 0.30 0.00
66_R 330_A 1.24 0.29 0.00
63_E 327_L 1.17 0.25 0.00
186_E 333_L 1.14 0.24 0.00
53_D 197_L 1.06 0.20 0.00
91_L 304_I 1.06 0.20 0.00
56_A 39_A 1.05 0.20 0.00
202_N 204_G 1.05 0.20 0.00
199_I 361_T 1.04 0.19 0.00
72_L 18_L 1.04 0.19 0.00
194_K 119_L 1.03 0.19 0.00
68_L 245_F 1.03 0.19 0.00
12_A 191_A 1.03 0.19 0.00
53_D 118_I 1.01 0.18 0.00
194_K 94_L 0.99 0.17 0.00
164_A 41_L 0.99 0.17 0.00
68_L 50_F 0.98 0.17 0.00
94_R 260_N 0.98 0.17 0.00
186_E 155_Y 0.97 0.16 0.00
112_I 181_F 0.94 0.15 0.00
183_Y 330_A 0.92 0.15 0.00
186_E 343_V 0.92 0.15 0.00
65_F 36_L 0.91 0.14 0.00
199_I 204_G 0.90 0.14 0.00
57_R 299_L 0.90 0.14 0.00
202_N 252_D 0.90 0.14 0.00
148_T 352_Q 0.90 0.14 0.00
202_N 54_H 0.89 0.13 0.00
169_P 301_L 0.88 0.13 0.00
203_I 49_L 0.87 0.13 0.00
72_L 93_C 0.87 0.13 0.00
182_L 50_F 0.87 0.13 0.00
72_L 179_F 0.86 0.13 0.00
66_R 334_I 0.86 0.13 0.00
134_T 82_L 0.86 0.13 0.00
199_I 176_T 0.86 0.13 0.00
201_A 374_N 0.86 0.13 0.00
194_K 369_I 0.86 0.12 0.00
186_E 140_F 0.86 0.12 0.00
202_N 40_C 0.85 0.12 0.00
201_A 30_W 0.85 0.12 0.00
101_L 103_Y 0.85 0.12 0.00
93_P 245_F 0.84 0.12 0.00
57_R 46_T 0.84 0.12 0.00
155_F 96_L 0.84 0.12 0.00
199_I 44_Q 0.84 0.12 0.00
164_A 167_G 0.84 0.12 0.00
32_V 167_G 0.84 0.12 0.00
208_L 369_I 0.83 0.12 0.00
201_A 321_S 0.83 0.12 0.00
66_R 296_L 0.83 0.12 0.00
208_L 361_T 0.83 0.12 0.00
58_T 192_L 0.82 0.12 0.00
130_A 334_I 0.82 0.11 0.00
99_H 318_R 0.82 0.11 0.00
203_I 328_L 0.82 0.11 0.00
130_A 192_L 0.82 0.11 0.00
82_I 180_T 0.81 0.11 0.00
135_D 303_M 0.81 0.11 0.00
208_L 94_L 0.81 0.11 0.00
80_A 300_I 0.81 0.11 0.00
199_I 54_H 0.81 0.11 0.00
170_N 31_W 0.81 0.11 0.00
175_T 369_I 0.80 0.11 0.00
71_T 194_T 0.80 0.11 0.00
183_Y 293_A 0.80 0.11 0.00
195_W 167_G 0.79 0.11 0.00
164_A 30_W 0.79 0.11 0.00
53_D 28_S 0.79 0.11 0.00
77_R 361_T 0.79 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
5835 0.27 cIp_9_4_cytb_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5645 0.47 cIp_9_40_cIV_I_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5624 0.36 cIp_9_10_cIV_I_40_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5623 0.46 cIp_9_40_cIV_I_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5622 0.47 cIp_9_4_cIV_I_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
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