Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_027721027.1 H589_RS0105035 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000425265.1:WP_027721027.1 Length = 396 Score = 326 bits (835), Expect = 9e-94 Identities = 167/396 (42%), Positives = 252/396 (63%), Gaps = 5/396 (1%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 F+ + + S +RE+LK+ E +IS AGGLP PE FPV + +V+E+ Q+LQ Sbjct: 5 FADRMATVHRSFIREILKVTEDQSIISFAGGLPNPELFPVADLQAAAVKVMEESGPQSLQ 64 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 Y TT+GF PLR +A+ +++ I +S +I+ITSGSQQ LDL+G+VF+N GD V++E P Sbjct: 65 YSTTEGFQPLRQFIADRYKEKKGIDVSADEILITSGSQQCLDLLGKVFLNKGDNVIIERP 124 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 YL A+Q+F ++ F+ + L+D+G + LE L + + K+ Y + FQNP+G+ Sbjct: 125 GYLGAIQSFSMFQSNFLTVGLEDDGPDLAELEMVLDQNDS-----KMFYAVTNFQNPSGL 179 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 T S ++R+ + +L D L VED+PYGELR+ GE KP+ + + LG+FSK+ A Sbjct: 180 TYSPEKRQGVADLLKGRDVLFVEDDPYGELRFMGEFHKPVVRGYLKDDGVLLGSFSKVAA 239 Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321 PGFR+GW+ + K+ IAKQ+ DL T+ F+Q + +YV +LD+HI I + Y + Sbjct: 240 PGFRLGWMVCSGEMRDKMIIAKQASDLHTSTFAQRVIHRYVTDNNLDDHIEKIRQRYGNQ 299 Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 R+ M+K++E+F P + T+PEGGMF+WVTLPE + + ++A+ VA+VPG F+ Sbjct: 300 REVMVKSIEKFFPAEAKVTQPEGGMFLWVTLPESVSAMELFDEAIKNKVAFVPGRPFYVD 359 Query: 382 RDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417 +NT RLNF+ E +I EGIKRL IKE + K Sbjct: 360 GTGENTFRLNFSNSDETRIEEGIKRLGSGIKEFLTK 395 Lambda K H 0.318 0.137 0.398 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: 448 Number of extensions: 13 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: 417 Length of database: 396 Length adjustment: 31 Effective length of query: 386 Effective length of database: 365 Effective search space: 140890 Effective search space used: 140890 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: 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