Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_050465615.1 AKL27_RS25035 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_001189915.1:WP_050465615.1 Length = 405 Score = 422 bits (1086), Expect = e-123 Identities = 212/398 (53%), Positives = 275/398 (69%), Gaps = 2/398 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F ++ DPIL + + F D K NL +G+YY+++G +P LQ V +AEA L A+ Sbjct: 9 LFTAIEMAPRDPILGITDAFNADQNPHKTNLGVGVYYDDNGKVPLLQCVRKAEAELAAKL 68 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 YLP++GL Y A+ L+FGA V++++R T+Q LGG+GALK+GADFLK + P Sbjct: 69 -APRTYLPIDGLATYDKAVQELVFGAGSAVVQEKRAITVQALGGTGALKLGADFLKHFSP 127 Query: 121 -ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179 ++ VW+SDP+WENH A+F AGF V+ YP+YD AT GV F +LA LK++ A S+VLLH Sbjct: 128 ADTQVWISDPSWENHRALFEMAGFTVNNYPYYDPATRGVNFAGMLAALKSMAAGSVVLLH 187 Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239 CCHNPTGADLT DQW VIE++ +R L+PFLD+AYQGFG G+EED +R A AG P Sbjct: 188 ACCHNPTGADLTADQWTEVIEVVTSRGLVPFLDMAYQGFGDGIEEDGKVVRRFAEAGGPL 247 Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299 VSNSFSK FSLYGERVG LS++ +E A RVL QLK VR NYS+PP G QVVA L Sbjct: 248 FVSNSFSKSFSLYGERVGALSIVAASSEEAARVLSQLKRVVRTNYSNPPIHGGQVVATAL 307 Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359 L+ W E+ EMR RI MRQ LVK L + P +FD+++ QRGMFSY+GL+ AQV Sbjct: 308 AAPELRKLWEDELAEMRVRIREMRQLLVKKLKEKAPAHDFDFVIKQRGMFSYSGLTKAQV 367 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 +RLR EF +Y + +GR+CVA LNT N+ V A A V+ Sbjct: 368 ERLRTEFSIYAVDTGRICVAALNTKNIDAVVDAIAKVL 405 Lambda K H 0.320 0.135 0.401 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: 407 Number of extensions: 16 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: 397 Length of database: 405 Length adjustment: 31 Effective length of query: 366 Effective length of database: 374 Effective search space: 136884 Effective search space used: 136884 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 (21.8 bits) S2: 50 (23.9 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