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OPENSEQ.org
cIp_5_4_cIV_A_4
Genes: A B A+B
Length: 207 558 722
Sequences: 1036 4375 557
Seq/Len: 5 7.84 0.77
MirrorTree (Pazo et al. 2001) 0.10
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 0.01 0.01
2 0.00 0.01 0.02
5 0.00 0.02 0.04
10 0.00 0.03 0.05
20 0.00 0.03 0.08
100 0.00 0.05 0.18
∞ 0.01 0.08 0.73
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
44_I 51_V 1.09 0.36 0.00
123_L 485_W 1.09 0.35 0.00
165_I 290_I 1.08 0.34 0.00
51_R 348_A 1.05 0.32 0.00
46_L 391_V 1.03 0.31 0.00
23_N 488_I 1.02 0.30 0.00
22_E 143_A 0.94 0.25 0.00
105_S 488_I 0.92 0.23 0.00
21_R 381_F 0.91 0.22 0.00
38_A 147_A 0.89 0.22 0.00
105_S 423_G 0.89 0.22 0.00
51_R 367_I 0.89 0.21 0.00
25_V 458_L 0.88 0.21 0.00
82_L 294_I 0.86 0.20 0.00
46_L 427_G 0.86 0.20 0.00
154_T 314_A 0.86 0.20 0.00
109_V 188_V 0.84 0.19 0.00
56_C 141_G 0.84 0.19 0.00
111_P 229_W 0.84 0.19 0.00
99_E 302_I 0.84 0.19 0.00
107_I 205_L 0.84 0.19 0.00
121_F 214_L 0.83 0.18 0.00
170_V 488_I 0.83 0.18 0.00
137_I 151_A 0.82 0.18 0.00
108_G 143_A 0.82 0.18 0.00
79_V 133_L 0.82 0.18 0.00
154_T 439_Q 0.81 0.17 0.00
42_G 507_V 0.81 0.17 0.00
109_V 64_Y 0.80 0.17 0.00
38_A 399_D 0.80 0.17 0.00
130_G 141_G 0.80 0.17 0.00
24_D 41_I 0.80 0.17 0.00
114_N 289_I 0.80 0.17 0.00
109_V 55_M 0.79 0.16 0.00
38_A 491_I 0.78 0.16 0.00
17_I 179_M 0.78 0.16 0.00
111_P 421_V 0.78 0.16 0.00
123_L 529_T 0.77 0.15 0.00
17_I 392_V 0.77 0.15 0.00
124_F 425_F 0.77 0.15 0.00
137_I 139_V 0.76 0.15 0.00
83_L 393_L 0.76 0.15 0.00
67_V 454_I 0.76 0.15 0.00
64_I 353_I 0.76 0.15 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
3980 0.77 cIp_5_4_cIV_A_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3979 0.59 cIp_5_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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