Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_012405377.1 BPHY_RS30745 aspartate aminotransferase family protein
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000020045.1:WP_012405377.1 Length = 447 Score = 481 bits (1237), Expect = e-140 Identities = 244/428 (57%), Positives = 298/428 (69%), Gaps = 1/428 (0%) Query: 4 AAIDQALADAYRRFTDANPASQRQFEAQARYMPGANSRSVLFYAPFPLTIARGEGAALWD 63 A + +A + A F +NP S+ MPG N+RSVLF++PFPLTIARGEG LWD Sbjct: 14 AELTRAASLASGAFAKSNPKSEAAHLEALSVMPGGNTRSVLFFSPFPLTIARGEGKRLWD 73 Query: 64 ADGHRYADFIAEYTAGVYGHSAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQI 123 DGH Y DF+AEYT +YGHS P IR A++EA+ G+NLTGHN LE LARL+ ERF + Sbjct: 74 VDGHAYTDFLAEYTTAMYGHSHPVIRAAIVEALDNGLNLTGHNTLEVPLARLLQERFDSV 133 Query: 124 EQLRFTNSGTEANLMALTAALHFTGRRKIVVFSGGYHGGVLGFGARPSPTTVPFDFLVLP 183 E LRFTNSGTE+NLMA+ A+L FTGR+K++ F GGYHGGVL FG+ S VP DF+V P Sbjct: 134 ESLRFTNSGTESNLMAIAASLIFTGRKKVIAFKGGYHGGVLTFGSGNSAVNVPHDFVVAP 193 Query: 184 YNDAQTARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVM 243 YND A HG +IA V+VEPMQ A GCI G+P+FL+ LR + ALL+ DEV+ Sbjct: 194 YNDLSAVEAAFAAHGDDIAAVIVEPMQVAGGCIVGEPEFLKGLRALTQRHDALLILDEVV 253 Query: 244 TSRLAPHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPR-TGPLAHSGTFN 302 TSRL+ G LGIR DLTT GKYIGGGMSFGAFGGR DVMA FDPR G H+GTFN Sbjct: 254 TSRLSGGGRQALLGIRPDLTTFGKYIGGGMSFGAFGGRKDVMAQFDPRLPGATPHAGTFN 313 Query: 303 NNVMTMAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHF 362 NNV++MAAGYAGL++L+TP AA AL E+GE LRAR+N LC V MQFTGIGSLMN H Sbjct: 314 NNVLSMAAGYAGLSRLYTPGAAAALNEKGERLRARINGLCRERQVQMQFTGIGSLMNLHA 373 Query: 363 VQGDVRSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGFVVLSLPLTDADIDRYVAAIGSF 422 + S +DL+ D L+ L FFH++ Y + RGF+VL+L + D+ R A+ SF Sbjct: 374 GTQPIHSVDDLSEADAPLKDLFFFHMIERGCYVARRGFIVLTLAHDEGDLRRLEEAVTSF 433 Query: 423 IGGHGALL 430 I + ALL Sbjct: 434 IDRYAALL 441 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: 562 Number of extensions: 17 Number of successful extensions: 2 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: 447 Length adjustment: 32 Effective length of query: 402 Effective length of database: 415 Effective search space: 166830 Effective search space used: 166830 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