Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_027179917.1 G496_RS0114610 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000429985.1:WP_027179917.1 Length = 397 Score = 354 bits (909), Expect = e-102 Identities = 176/392 (44%), Positives = 262/392 (66%), Gaps = 5/392 (1%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 F+ + + S +RE+LK+ E +IS AGGLP PE FPVE + + +VL + + LQ Sbjct: 5 FADRMQTVHRSFIREILKVTEDPSIISFAGGLPNPELFPVEAMRKAASDVLAESGKEVLQ 64 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 Y TT+G+ PLR +A+ + I + DI++T+GSQQ LDL+G+VF+N GD V++E P Sbjct: 65 YSTTEGYQPLRKFIADRYKSEKGIEVDPEDILLTTGSQQCLDLLGKVFLNSGDRVIIERP 124 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 YL A+Q+F +++PEFV + L+++G ++ LE+ L KVK+ Y +P FQNP+G+ Sbjct: 125 GYLGAIQSFSFFQPEFVTVGLENDGPDLNELEKILAM-----DKVKMFYAVPNFQNPSGL 179 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 T S ++RK + EL +E D L +ED+PYGELR+ GE P+ + + LG+FSKI A Sbjct: 180 TYSAEKRKAVAELMAESDTLFIEDDPYGELRFMGEHQTPLSKGYLKDNCVLLGSFSKIAA 239 Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321 PGFR+GW+ AE + KL IAKQ+ DL T+ SQ I +++++ +D HI I E Y+ + Sbjct: 240 PGFRLGWVVAESEVRDKLVIAKQASDLHTSTVSQRIMYRFMKDNDIDAHIEKIRERYRRQ 299 Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 R+ M++ +E++ PEGV TKPEGGMF+W+TLPEG+ + +L+ AVA VA+VPG F+ Sbjct: 300 RETMVECIEKYFPEGVEITKPEGGMFLWITLPEGMSSMDLLDTAVAHKVAFVPGRPFYVD 359 Query: 382 RDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 +NT RLNF+ EE I EGIKR+A+ +K+ Sbjct: 360 GSGENTFRLNFSNSDEEHIEEGIKRMADCLKD 391 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: 462 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 397 Length adjustment: 31 Effective length of query: 386 Effective length of database: 366 Effective search space: 141276 Effective search space used: 141276 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