Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013840613.1 DESRU_RS02800 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000215085.1:WP_013840613.1 Length = 392 Score = 366 bits (939), Expect = e-106 Identities = 189/387 (48%), Positives = 260/387 (67%), Gaps = 6/387 (1%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 F+++ +K+S +RE+LK+ E VIS AGGLPAPE FP+E + E VL+ A ALQ Sbjct: 5 FAERVGQIKSSVIREILKVTEQPGVISFAGGLPAPEMFPLEEMKEALGRVLDGGNASALQ 64 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 YGTT+G+ PLR L M K+ I +I+IT+GSQQALDL+ ++FI+PGD VVVE+P Sbjct: 65 YGTTEGYLPLREYLTAAMEKK-GIATRPAEILITNGSQQALDLLAKLFIDPGDRVVVESP 123 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 +YL A+Q F+ Y+ +FV +P DD G+ + LE+ L+E + KL+Y PTF+NP G Sbjct: 124 SYLGAIQVFRSYQAQFVSVPTDDGGIELAALEKALEE-----NRPKLIYITPTFKNPTGE 178 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 TMS +RR+++ EL +Y ++ED+PYGELRY GE + P+KA+D R++YL TFSK +A Sbjct: 179 TMSLERRRQVAELLEKYQVPLIEDDPYGELRYQGESIPPLKAFDKGNRIIYLSTFSKTVA 238 Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321 PG R+GWI P L+ KL +AKQ DL T Q Y+ + HI I + Y R Sbjct: 239 PGLRLGWIVTGPELMAKLVLAKQGTDLHTGTLVQQAVHYYLTHYDVTGHIQAIRDEYGRR 298 Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 R+ ML+A++ P G WT+PEGGMF+WVTLP+ + T L+L++AVA+ VAYVPGEAFFA Sbjct: 299 RNTMLEAMDRRFPRGASWTEPEGGMFLWVTLPQQLKTDLLLKEAVAEKVAYVPGEAFFAQ 358 Query: 382 RDVKNTMRLNFTYVPEEKIREGIKRLA 408 N +RLNF+ +I EGI+RLA Sbjct: 359 GGGHNCLRLNFSNSLPSQIEEGIERLA 385 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: 469 Number of extensions: 20 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: 392 Length adjustment: 31 Effective length of query: 386 Effective length of database: 361 Effective search space: 139346 Effective search space used: 139346 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 Jul 25 2024. The underlying query database was built on Jul 25 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