Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028583781.1 G494_RS0105885 D-amino-acid transaminase
Query= BRENDA::E6TUA8 (302 letters) >NCBI__GCF_000429965.1:WP_028583781.1 Length = 288 Score = 169 bits (429), Expect = 5e-47 Identities = 90/273 (32%), Positives = 161/273 (58%), Gaps = 7/273 (2%) Query: 6 IFSNGKFVTKQEAVISVYDHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIMLEI 65 ++ NG+++ + +A IS++D GFL+ D V+E V + + + HL+RL+ S + ++ Sbjct: 5 VYVNGRYLPEHQATISIFDRGFLFADAVYEVSAVLNNRLIENRNHLRRLHRSLDELAMDS 64 Query: 66 PYSKEDFQQIIVDTVRKNQLESGYIRVVVSRGPGNLGLDPSRCSAPHVIVIAEELALFPK 125 P + + + + +R+N+L G + + +SRG + + P ++ + L Sbjct: 65 PLTDPEIVAVQEELIRRNELREGVVYLQISRGAADRDFVFPTGAQPTMVAFTQVKPLLSS 124 Query: 126 ELYELGLTVASVASRR-NRPDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQGYVT 184 E G++V + R RPD IK++ L + + K++A QAGA +AL+++ +GY+T Sbjct: 125 PQAEEGISVITTPDIRWGRPD-----IKTVGLLASSMAKMQALQAGADDALLVDSEGYIT 179 Query: 185 EGSADNIFIVK-NNTIITPPVYLGALEGITRNAIIDLAKECGYEMKETPFTRHDVYVADE 243 EGSA N +IV +NTI+T + L GITR++I++LA+E G ++E PF+ + A E Sbjct: 180 EGSACNAYIVTTDNTIVTRHLSQAILPGITRSSILELAREAGLSIEERPFSVSEALAARE 239 Query: 244 VFLTGTAAEVIAVVEVDKRMISDGKPGKVTNHL 276 F+TG+AA V+ VV++D R ++ G+PG +T L Sbjct: 240 AFVTGSAAFVLPVVKIDNRQLNRGRPGPLTTRL 272 Lambda K H 0.318 0.136 0.385 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: 221 Number of extensions: 11 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: 302 Length of database: 288 Length adjustment: 26 Effective length of query: 276 Effective length of database: 262 Effective search space: 72312 Effective search space used: 72312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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