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OPENSEQ.org
cIp_1_40_cIV_B_60
Genes: A B A+B
Length: 438 298 697
Sequences: 2218 1458 283
Seq/Len: 5.06 4.89 0.41
MirrorTree (Pazo et al. 2001) 0.18
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 0.01 0.00 0.00
10 0.02 0.00 0.00
20 0.02 0.00 0.01
100 0.04 0.00 0.04
∞ 0.12 0.00 0.38
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
288_Q 100_F 1.25 0.33 0.00
288_Q 262_A 1.20 0.30 0.00
127_A 118_L 1.19 0.29 0.00
113_L 84_I 1.16 0.27 0.00
107_L 216_A 1.15 0.27 0.00
42_K 143_I 1.11 0.24 0.00
45_L 237_Q 1.09 0.23 0.00
274_E 217_F 1.05 0.22 0.00
86_Q 254_A 0.99 0.19 0.00
371_F 96_V 0.99 0.18 0.00
269_G 141_L 0.98 0.18 0.00
45_L 73_A 0.97 0.18 0.00
46_K 217_F 0.97 0.18 0.00
53_V 113_V 0.97 0.18 0.00
387_L 268_Y 0.96 0.17 0.00
120_L 199_V 0.96 0.17 0.00
71_P 108_V 0.96 0.17 0.00
339_D 238_E 0.95 0.17 0.00
326_G 199_V 0.92 0.15 0.00
14_E 108_V 0.91 0.15 0.00
428_K 63_L 0.90 0.15 0.00
53_V 24_A 0.90 0.15 0.00
54_I 24_A 0.89 0.15 0.00
308_D 233_F 0.89 0.14 0.00
223_T 224_V 0.89 0.14 0.00
130_G 90_N 0.89 0.14 0.00
214_K 270_A 0.88 0.14 0.00
14_E 84_I 0.88 0.14 0.00
218_I 187_T 0.88 0.14 0.00
120_L 236_D 0.88 0.14 0.00
278_E 224_V 0.86 0.13 0.00
153_R 274_G 0.86 0.13 0.00
258_V 97_P 0.85 0.13 0.00
271_T 53_S 0.85 0.13 0.00
156_G 195_V 0.85 0.13 0.00
50_P 52_A 0.84 0.13 0.00
172_H 119_V 0.83 0.12 0.00
236_D 191_V 0.83 0.12 0.00
149_I 47_M 0.83 0.12 0.00
364_A 171_E 0.83 0.12 0.00
254_I 113_V 0.82 0.12 0.00
119_I 143_I 0.82 0.12 0.00
274_E 46_G 0.82 0.12 0.00
121_A 196_G 0.82 0.12 0.00
55_E 53_S 0.82 0.12 0.00
166_D 141_L 0.82 0.12 0.00
218_I 106_I 0.82 0.12 0.00
187_A 267_K 0.81 0.12 0.00
124_A 70_I 0.81 0.12 0.00
160_K 112_L 0.81 0.12 0.00
380_E 187_T 0.81 0.12 0.00
218_I 46_G 0.80 0.12 0.00
188_L 270_A 0.80 0.12 0.00
335_V 56_L 0.80 0.12 0.00
150_K 191_V 0.80 0.12 0.00
320_G 51_P 0.79 0.11 0.00
42_K 205_A 0.78 0.11 0.00
40_T 123_A 0.78 0.11 0.00
300_L 255_Y 0.78 0.11 0.00
217_T 266_E 0.78 0.11 0.00
165_T 199_V 0.78 0.11 0.00
72_T 136_P 0.78 0.11 0.00
122_G 100_F 0.78 0.11 0.00
328_V 240_V 0.78 0.11 0.00
100_S 218_A 0.78 0.11 0.00
72_T 255_Y 0.77 0.11 0.00
243_T 211_A 0.77 0.11 0.00
147_Q 199_V 0.77 0.11 0.00
170_D 123_A 0.76 0.10 0.00
223_T 70_I 0.76 0.10 0.00
273_R 191_V 0.76 0.10 0.00
90_I 140_D 0.76 0.10 0.00
145_L 53_S 0.75 0.10 0.00
384_V 143_I 0.75 0.10 0.00
158_L 90_N 0.75 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
4043 0.98 cIp_1_20_cIV_B_40 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4042 0.89 cIp_1_60_cIV_B_40 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4041 0.41 cIp_1_40_cIV_B_60 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4037 0.96 cIp_1_40_cIV_B_20 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4036 1.09 cIp_1_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4035 0.89 cIp_1_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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