Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_027457275.1 K420_RS0105975 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000519045.1:WP_027457275.1 Length = 427 Score = 198 bits (504), Expect = 2e-55 Identities = 135/416 (32%), Positives = 201/416 (48%), Gaps = 23/416 (5%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGV 80 ++ F +++PG + V + PL +G GA + DADG Y D++ + + Sbjct: 5 NEELFARAQKHIPGGVNSPVRAFRSVGGTPLFFQKGVGAKVQDADGKWYTDYVGSWGPMI 64 Query: 81 YGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMAL 140 GH+ PE+ AV A+ G++ E +A L+C+ P ++ +R +SGTEA + A+ Sbjct: 65 LGHAHPEVIAAVQAAVVDGLSFGAPTEREVEIADLLCDMVPSLDMVRLVSSGTEATMSAI 124 Query: 141 TAALHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPF----DFLVLPYN 185 A +TGR +V F G YHG G+L FG PS VP +VL YN Sbjct: 125 RLARGYTGRDILVKFEGCYHGHADSLLVKAGSGLLTFG-NPSSGGVPAGTAETTMVLTYN 183 Query: 186 DAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS 245 D Q + HG +IA V+VEP+ G I +FL+A+R+ Q GA+L+FDEVMT Sbjct: 184 DPQGLAEAFKTHGDKIAAVIVEPVVGNMNLIAPTAEFLKAMRDLTAQYGAVLIFDEVMTG 243 Query: 246 -RLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNN 304 R+ GI DL+T GK +GGGM GAFGG+ +M P GP+ +GT + N Sbjct: 244 FRVGLQSAQGLFGITPDLSTFGKVVGGGMPMGAFGGKRAIMEKIAP-LGPVYQAGTLSGN 302 Query: 305 VMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQ 364 + AAG A L + P +L + +AL L GV IG + +F + Sbjct: 303 PIATAAGLATLKLIQAPGFYESLTAKTKALCDGLVGAAKKHGVLFSAQNIGGMFGLYFAE 362 Query: 365 GDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVV--LSLPLTDADIDRYVAA 418 + + + A D F ++ Y +P F +S T+ADI +AA Sbjct: 363 ACPSTYDAVLACDKEAFNRFFHAMIAAGHYFAPSAFEAGFVSAAHTEADIAGTIAA 418 Lambda K H 0.322 0.138 0.408 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: 453 Number of extensions: 25 Number of successful extensions: 4 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: 434 Length of database: 427 Length adjustment: 32 Effective length of query: 402 Effective length of database: 395 Effective search space: 158790 Effective search space used: 158790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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