Align Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized)
to candidate WP_011869215.1 MMARC5_RS07450 aspartate aminotransferase family protein
Query= SwissProt::H8WR05 (434 letters) >NCBI__GCF_000016125.1:WP_011869215.1 Length = 427 Score = 195 bits (495), Expect = 3e-54 Identities = 129/393 (32%), Positives = 192/393 (48%), Gaps = 19/393 (4%) Query: 24 SQRQFEAQARYMPGANSRSVLFYAPFPLTIARGEGAALWDADGHRYADFIAEYTAGVYGH 83 S+ FE +Y+ G + V + PFP + + L+D DG+ + D+ Y V GH Sbjct: 10 SKELFEESKKYLVGGVNSPVRSFKPFPFFVKSAKDCFLYDEDGNEFIDYCLAYGPMVLGH 69 Query: 84 SAPEIRDAVIEAMQGGINLTGHNLLEGRLARLICERFPQIEQLRFTNSGTEANLMALTAA 143 + I +AV M G + E LA+ + R P E +RF NSGTEA + A+ A Sbjct: 70 ANENILNAVKSQMDLGTAYGVPSEKEITLAKEVINRIPCAEMVRFVNSGTEATMGAIRLA 129 Query: 144 LHFTGRRKIVVFSGGYHG-----------GVLGFGARPSPTTVPFD----FLVLPYNDAQ 188 TGR KI+ F G +HG G L GA SP +P D L++P+ND Sbjct: 130 RGVTGRDKIIKFEGAFHGAHDYVLVKTGSGALTHGAPNSP-GIPEDTTKNTLLIPFNDED 188 Query: 189 TARAQIERHGPEIAVVLVEPMQGASGCIPGQPDFLQALRESATQVGALLVFDEVMTS-RL 247 R I + EIA +++EP+ G GCI Q +LQ LRE + G LL+FDEV+T RL Sbjct: 189 AVRKVISENKDEIACIILEPVMGNVGCILPQDGYLQFLREITEENGILLIFDEVITGFRL 248 Query: 248 APHGLANKLGIRSDLTTLGKYIGGGMSFGAFGGRADVMALFDPRTGPLAHSGTFNNNVMT 307 + G GI+SDL T+GK +GGG GA G+ + M F P +G + +GTFN N ++ Sbjct: 249 SKGGAQEYFGIKSDLATIGKILGGGFPIGAITGKKEYMEQFSP-SGQIYQAGTFNGNPVS 307 Query: 308 MAAGYAGLTKLFTPEAAGALAERGEALRARLNALCANEGVAMQFTGIGSLMNAHFVQGDV 367 + AG L L + ++ + L L V+ + + S+ +F + +V Sbjct: 308 VTAGIETLKNL-DDKFYKETTKKADILSNFLRETAEKYNVSTKVYNVASIFQIYFNEKEV 366 Query: 368 RSSEDLAAVDGRLRQLLFFHLLNEDIYSSPRGF 400 + ED + D F+ LL ++ +P F Sbjct: 367 VTYEDAKSSDTEKFMRYFYTLLENGVFVAPSQF 399 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: 368 Number of extensions: 12 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