Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_092350113.1 BLU87_RS14535 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_900107645.1:WP_092350113.1 Length = 427 Score = 209 bits (531), Expect = 2e-58 Identities = 127/388 (32%), Positives = 199/388 (51%), Gaps = 20/388 (5%) Query: 50 PLTIARGEGAALWDADGHRYADFIAEYTAGVYGHSAPEIRDAVIEAMQGGINLTGHNLLE 109 P+ IA+ G+ ++D DG+ Y D++ + + GH P++ +A+ + G + LE Sbjct: 35 PIFIAKAAGSKIYDVDGNEYIDYVGSWGPMILGHCHPKVVEAIQKTAASGASFGAPTPLE 94 Query: 110 GRLARLICERFPQIEQLRFTNSGTEANLMALTAALHFTGRRKIVVFSGGYHG-------- 161 LA ++CE +P IE++R +SGTEA + A+ A +TGR KI+ F G YHG Sbjct: 95 TELAEIVCEAYPNIEKVRMVSSGTEATMSAIRLARGYTGRDKILKFDGCYHGHADSLLVK 154 Query: 162 ---GVLGFGARPSPTTVPFDF----LVLPYNDAQTARAQIERHGPEIAVVLVEPMQGASG 214 G+ FG SP VP DF L YND + + + EIA +++E + G G Sbjct: 155 AGSGLATFGVPTSP-GVPADFAKYTLTANYNDLANVQELVAANKGEIACIILEAVAGNMG 213 Query: 215 CIPGQPDFLQALRESATQVGALLVFDEVMTS-RLAPHGLANKLGIRSDLTTLGKYIGGGM 273 C+P FLQ LR+ T G +L+ DEVMT R+A G + G+R DL LGK IGGG+ Sbjct: 214 CVPPVKGFLQELRDLCTAEGIILIIDEVMTGFRVAYGGAQERFGVRGDLVCLGKIIGGGL 273 Query: 274 SFGAFGGRADVMALFDPRTGPLAHSGTFNNNVMTMAAGYAGLTKLFTPEAAGALAERGEA 333 GAFGG+ ++M P G + +GT + N + M+AG A L L L E+ Sbjct: 274 PVGAFGGKREIMDSLSPE-GGVYQAGTLSGNPLAMSAGIATLKLLQQEGFYQQLEEKAAY 332 Query: 334 LRARLNALCANEGVAMQFTGIGSLMNAHFVQGDVRSSEDLAAVDGRLRQLLFFHLLNEDI 393 L + + N +A + +G + +F +G V + + A D F +L++ I Sbjct: 333 LEKGVQQVAGNSPIATCWQRVGGMFCTYFQEGPVNNFDAALASDTEAFGRYFRSMLDQGI 392 Query: 394 YSSPRGFVV--LSLPLTDADIDRYVAAI 419 +P F +S+ + D+D+ +AA+ Sbjct: 393 NLAPAQFEAGFISISHSKEDLDKTIAAL 420 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: 408 Number of extensions: 18 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