In Chebuu/fastalign:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

# library(fastalign)

Appendix

Annotations

THCAS

Features

Binding site 292 Substrate Binding site 417 Substrate Active site 484 Proton acceptor

Mutagenesis

92 H → A: "No effect"
108 R → A: "Strongly reduced catalytic activity"
110 R → A: "Strongly reduced catalytic activity"
114 H → A: "Loss of FAD binding and loss of catalytic activity. 2 Publications"
208 H → A: "No effect"
292 H → A: "Strongly reduced catalytic activity"
417 Y → F: "Reduced catalytic activity"
442 E → Q: "Slightly reduced catalytic activity"
484 Y → F: "Loss of catalytic activity"

Molecule processing

Signal peptide 1 – 28
Chain (THCAS) 29 – 545

Amino acid modifications

Disulfide bond 37 ↔ 99 1
Cross-link 114 ↔ 176 6-(S-cysteinyl)-8alpha-(pros-histidyl)-FAD (His-Cys)

Glycosylation sites

65 N-linked asparagine (GlcNAc...)
89 N-linked asparagine (GlcNAc...)
168 N-linked asparagine (GlcNAc...)
297 N-linked asparagine (GlcNAc...)
305 N-linked asparagine (GlcNAc...)
329 N-linked asparagine (GlcNAc...)
467 N-linked asparagine (GlcNAc...)
499 N-linked asparagine (GlcNAc...)

Domains and Repeats

Domain 77 – 251 FAD-binding

Compositional bias

Compositional bias 232 – 235 Poly-Gly

Genetic Code

Triplet Translations

Ala/A GCT, GCC, GCA, GCG
Arg/R CGT, CGC, CGA, CGG, AGA, AGG
Asn/N AAT, AAC
Asp/D GAT, GAC
Cys/C TGT, TGC
Gln/Q CAA, CAG
Glu/E GAA, GAG
Gly/G GGT, GGC, GGA, GGG
His/H CAT, CAC
Ile/I ATT, ATC, ATA
Leu/L TTA, TTG, CTT, CTC, CTA, CTG
Lys/K AAA, AAG
Met/M ATG
Phe/F TTT, TTC
Pro/P CCT, CCC, CCA, CCG
Ser/S TCT, TCC, TCA, TCG, AGT, AGC
Thr/T ACT, ACC, ACA, ACG
Trp/W TGG
Tyr/Y TAT, TAC
Val/V GTT, GTC, GTA, GTG
START ATG
STOP TAG, TGA, TAA

Codon Usage

[triplet] [frequency: per thousand] ([number])
UUU 33.5( 130) UCU 15.0( 58) UAU 30.7( 119) UGU 5.9( 23)
UUC 22.7( 88) UCC 9.3( 36) UAC 13.9( 54) UGC 8.3( 32)
UUA 20.6( 80) UCA 18.8( 73) UAA 1.5( 6) UGA 0.3( 1)
UUG 23.7( 92) UCG 6.2( 24) UAG 0.3( 1) UGG 17.8( 69)

CUU 20.9( 81) CCU 17.8( 69) CAU 19.6( 76) CGU 6.5( 25)
CUC 9.3( 36) CCC 4.6( 18) CAC 8.0( 31) CGC 2.3( 9)
CUA 7.2( 28) CCA 16.0( 62) CAA 27.1( 105) CGA 7.2( 28)
CUG 3.1( 12) CCG 1.3( 5) CAG 4.1( 16) CGG 1.5( 6)

AUU 37.7( 146) ACU 22.7( 88) AAU 46.7( 181) AGU 15.5( 60)
AUC 14.7( 57) ACC 9.8( 38) AAC 17.5( 68) AGC 5.7( 22)
AUA 24.3( 94) ACA 18.1( 70) AAA 43.1( 167) AGA 16.5( 64)
AUG 26.3( 102) ACG 2.6( 10) AAG 28.1( 109) AGG 6.7( 26)

GUU 28.6( 111) GCU 24.5( 95) GAU 37.7( 146) GGU 21.2( 82)
GUC 10.8( 42) GCC 5.2( 20) GAC 9.5( 37) GGC 9.0( 35)
GUA 11.6( 45) GCA 14.2( 55) GAA 37.9( 147) GGA 24.0( 93)
GUG 8.0( 31) GCG 6.5( 25) GAG 22.7( 88) GGG 7.2( 28)

Chebuu/fastalign documentation built on July 19, 2020, 8:39 p.m.