Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_017597712.1 D471_RS0105545 PLP-dependent aminotransferase family protein
Query= SwissProt::H3ZPL1 (417 letters) >NCBI__GCF_000341125.1:WP_017597712.1 Length = 410 Score = 342 bits (876), Expect = 2e-98 Identities = 178/387 (45%), Positives = 247/387 (63%), Gaps = 2/387 (0%) Query: 29 MKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGF 88 M ASE+R L + +V+SLAGG+P P++ IGE+ ++V+ + ALQYG+ +G Sbjct: 1 MVASEVRALFAVASRPEVVSLAGGMPNVAALPLDQIGELVRDVVAEEGQAALQYGSAQGD 60 Query: 89 TPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148 LR + ++M I S D++ T GSQQALDLI RVF++PGD+++ EAPTY+ A+ Sbjct: 61 PVLREQICDYMTLE-GITASPDDVIVTVGSQQALDLITRVFVDPGDVVLCEAPTYVTAIN 119 Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208 F ++ + + +D+ G+ + L+E L +EG++VK YTIP FQNPAG+TM +RR Sbjct: 120 TFAAFQADIRHVAMDENGVLPEELDEALTRAAREGRRVKFFYTIPNFQNPAGITMTAERR 179 Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268 R+LE+ ++D ++VEDNPYG LRY G+P + A G VIYLG+ SK L+PG RIGW Sbjct: 180 ARVLEICERHDVLVVEDNPYGLLRYDGDPQPTLYA-QGTGNVIYLGSLSKTLSPGLRIGW 238 Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRRDAMLKA 328 A KL +A +S L +TF+Q++ +Y+ + I Y RRDAML A Sbjct: 239 ALAPAPVRAKLVLAAESAMLSHSTFNQLVVRRYLRTFPWREQIKTFNTMYGERRDAMLGA 298 Query: 329 LEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTM 388 LE MP G WT+PEGG FVWATLPEGID K ML +AVA+ VAYVPG FFA + M Sbjct: 299 LEAMMPAGCTWTRPEGGFFVWATLPEGIDAKAMLPRAVAERVAYVPGTGFFADGRGRADM 358 Query: 389 RLNFTYVPEEKIREGIKRLAETIKEEM 415 RL+F Y E+IREG++RL I+ E+ Sbjct: 359 RLSFCYPTPEQIREGVRRLVGAIEGEL 385 Lambda K H 0.318 0.137 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 477 Number of extensions: 34 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 410 Length adjustment: 31 Effective length of query: 386 Effective length of database: 379 Effective search space: 146294 Effective search space used: 146294 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory