Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013520672.1 ALIDE2_RS21035 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000204645.1:WP_013520672.1 Length = 393 Score = 317 bits (811), Expect = 5e-91 Identities = 173/390 (44%), Positives = 246/390 (63%), Gaps = 9/390 (2%) Query: 25 KALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGT 84 +A M S +RE+LK+ E +ISLAGGLP+P+TFP+E A VL A ALQY Sbjct: 9 RAAKMNPSVIREILKVTEKPGIISLAGGLPSPKTFPIESFAAAAASVLANEGASALQYAA 68 Query: 85 TKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYL 144 ++G PLR A+A ++ +D+ +V +IT+GSQQALDL +V I+ G V+VE PTYL Sbjct: 69 SEGHAPLREAIAGFLP--WDVHPDQV--LITTGSQQALDLAAKVLIDAGSRVLVETPTYL 124 Query: 145 AALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMS 204 ALQAF EP+ V + DDEG+ +D L K K + +Y +P FQNP G TMS Sbjct: 125 GALQAFAPMEPQVVSVASDDEGVLIDDLAAKAGS---GADKARFLYVLPNFQNPTGRTMS 181 Query: 205 EKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGF 264 E RR+ L A+E ++EDNPYG+L + P KP+ A + EG +Y+G+FSK+LAPG Sbjct: 182 EARREALSARAAELGLPLIEDNPYGDLWFDKAPPKPLAARNPEG-CLYMGSFSKVLAPGL 240 Query: 265 RIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDA 324 R+G++ A + KL AKQ+ DL T F+Q + + ++ G LD H+P I + YK + A Sbjct: 241 RLGYLVAPRQMYPKLLQAKQAADLHTPSFNQRLVAEVLKNGFLDRHVPTIRQLYKRQCQA 300 Query: 325 MLKALEEFMPE-GVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRD 383 M+ ALE+ M GV W +P+GGMF+W+ LPEG+ +L +AV + VA+VPG AF+A + Sbjct: 301 MVAALEKEMQGLGVTWNRPDGGMFLWLRLPEGMSALELLPRAVERNVAFVPGAAFYAQQA 360 Query: 384 VKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 + T+RL+F EE+I+ + LA I+E Sbjct: 361 DERTLRLSFVTASEEQIQTAVAALAAAIRE 390 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: 422 Number of extensions: 23 Number of successful extensions: 5 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: 393 Length adjustment: 31 Effective length of query: 386 Effective length of database: 362 Effective search space: 139732 Effective search space used: 139732 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