Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= SwissProt::H8WR05 (434 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 127 bits (319), Expect = 6e-34 Identities = 104/339 (30%), Positives = 146/339 (43%), Gaps = 39/339 (11%) Query: 46 YAPFPLTIARGEGAALWDADGHRYADFIAEYTAGVYGHSAPEIRDAVIEAMQGGINLTGH 105 YAP P+ +G G+ LWD G + DF GH P + A+ E Q +L+ Sbjct: 16 YAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLS-- 73 Query: 106 NLLEGRLARLICERFPQ---IEQLRFTNSGTEANLMALT----AALHFTGRRK--IVVFS 156 N + A ++ + E++ F NSG EAN AL AL+ G K I+ F Sbjct: 74 NTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFK 133 Query: 157 GGYHGGVL-------------GFGARPSPTTVPFDFLVLPYNDAQTARAQIERHGPEIAV 203 G+HG L GFG +P+ D YN+ + +A I Sbjct: 134 QGFHGRTLFTVSVGGQPAYSDGFGPKPA------DIDHAEYNNLDSLKALIS---DRTCA 184 Query: 204 VLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMT--SRLAPHGLANKLGIRSD 261 V++EP+QG G I P+F++ +RE Q ALLVFDEV T R LG+ D Sbjct: 185 VVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVTPD 244 Query: 262 LTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNVMTMAAGYAGLTKLFTP 321 + T K +GGG GA ++ T H T+ N + A G A T + TP Sbjct: 245 VLTTAKALGGGFPIGAMLTTTELAKHLVVGT----HGSTYGGNPLACAVGLAAFTTVNTP 300 Query: 322 EAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNA 360 E + ER + R LNA+ V + G G L+ A Sbjct: 301 EVLNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGA 339 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: 406 Number of extensions: 22 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: 434 Length of database: 405 Length adjustment: 32 Effective length of query: 402 Effective length of database: 373 Effective search space: 149946 Effective search space used: 149946 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: 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