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OPENSEQ.org
ctICvsp150_3
Genes: A B A+B
Length: 120 204 303
Sequences: 316 46881 197
Seq/Len: 2.63 229.81 0.65
MirrorTree (Pazo et al. 2001) 0.21
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 0.06 0.58 0.01
2 0.06 0.58 0.01
5 0.07 0.58 0.02
10 0.07 0.58 0.02
20 0.07 0.58 0.07
100 0.07 0.59 0.31
∞ 0.07 0.60 0.61
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
14_R 136_K 1.29 0.48 0.00
14_R 191_H 1.28 0.47 0.00
52_E 165_D 1.12 0.34 0.00
43_T 45_I 1.10 0.33 0.00
5_R 110_L 1.08 0.31 0.00
12_K 37_Q 1.06 0.30 0.00
94_T 164_E 1.02 0.27 0.00
54_E 185_E 1.01 0.27 0.00
54_E 184_L 0.94 0.22 0.00
54_E 109_E 0.94 0.22 0.00
88_D 122_E 0.91 0.20 0.00
62_S 171_S 0.91 0.20 0.00
34_I 142_I 0.90 0.20 0.00
95_A 42_R 0.89 0.19 0.00
65_A 52_L 0.88 0.18 0.00
19_K 133_Q 0.87 0.18 0.00
8_L 103_Q 0.86 0.18 0.00
103_S 75_A 0.84 0.17 0.00
54_E 95_S 0.83 0.17 0.00
95_A 170_L 0.83 0.17 0.00
5_R 94_E 0.82 0.16 0.00
30_A 161_E 0.82 0.16 0.00
26_A 68_S 0.81 0.15 0.00
102_P 39_D 0.80 0.15 0.00
63_S 126_E 0.79 0.14 0.00
8_L 111_R 0.78 0.14 0.00
109_S 150_V 0.78 0.14 0.00
86_S 83_L 0.78 0.14 0.00
52_E 67_E 0.78 0.14 0.00
78_S 93_I 0.78 0.14 0.00
35_T 45_I 0.77 0.14 0.00
70_P 65_C 0.76 0.14 0.00
9_L 187_M 0.76 0.14 0.00
16_A 115_D 0.76 0.13 0.00
56_L 55_Y 0.76 0.13 0.00
109_S 80_R 0.76 0.13 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.60 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
9477 0.65 ctICvsp150_3 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9476 0 ctICvsp150_2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
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