Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_013009803.1 DACET_RS02325 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000025725.1:WP_013009803.1 Length = 422 Score = 199 bits (505), Expect = 2e-55 Identities = 132/412 (32%), Positives = 203/412 (49%), Gaps = 23/412 (5%) Query: 28 FEAQARYMPGANSRSVLFYAPF---PLTIARGEGAALWDADGHRYADFIAEYTAGVYGHS 84 FE +Y+PG + V + P+ + +G+ ++D +G Y D++ + + GH+ Sbjct: 4 FEESKKYIPGGVNSPVRAFGSVGGDPVIVKSAKGSKVYDENGKEYIDYVCSWGPMITGHA 63 Query: 85 APEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMALTAAL 144 P+I AV +A G + E +A+ IC P +E +R +SGTEA + A+ A Sbjct: 64 DPDIIKAVKDAADLGTSFGAPTKAELDIAKKICSMVPSVEMVRLVSSGTEALMSAIRLAR 123 Query: 145 HFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFDF----LVLPYNDAQT 189 +T R KI+ F G YHG G L F +PS VP DF LV YND ++ Sbjct: 124 AYTERDKIIKFEGCYHGHSDSLLVKAGSGALTFN-QPSSPGVPADFTKHTLVAQYNDIES 182 Query: 190 ARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS-RLA 248 + + + E+A +L+EP+ G + FL+ LR G +L+FDEV+T RLA Sbjct: 183 IKKLLAENKGEVACILIEPVAANMGVVLPAAGFLEDLRRVCDDEGVVLLFDEVITGFRLA 242 Query: 249 PHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNVMTM 308 G I+ D+TT+GK IGGG+ GAFGG++++M + P G + +GT + N + Sbjct: 243 AGGAQEYFNIKPDITTMGKIIGGGLPVGAFGGKSEIMKMLSP-DGAVYQAGTLSGNPLAT 301 Query: 309 AAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQGDVR 368 AAG L KL P+ L ++ + L + C G+ + I SL F G V Sbjct: 302 AAGLTMLNKLSQPDFYKNLRQKADTLFDGMADNCKKLGLDYAYNRIESLSCLFFKDGTVT 361 Query: 369 SSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF--VVLSLPLTDADIDRYVAA 418 S D D +L F +L+ I +P F + +S TD DI++ V A Sbjct: 362 SFADAMKTDTKLYAKYFHAMLDRGITIAPAQFEAMFVSAAHTDEDIEKTVKA 413 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: 403 Number of extensions: 17 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: 422 Length adjustment: 32 Effective length of query: 402 Effective length of database: 390 Effective search space: 156780 Effective search space used: 156780 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