Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_063836917.1 BS73_RS05050 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000744815.1:WP_063836917.1 Length = 541 Score = 128 bits (322), Expect = 4e-34 Identities = 97/303 (32%), Positives = 137/303 (45%), Gaps = 12/303 (3%) Query: 52 GLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVD 111 GLP FP A ++ L L Y +G LR ALAE + +R ++ + Sbjct: 135 GLPDLSLFPRAAWAAAQRDALAALPHAVLDYPDPRGLPALRTALAELLARRRNVAVGPDS 194 Query: 112 IMITSGSQQALDLIGRVFINPGD-IVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVD 170 +++ G QAL LIGRV G V VE P + + +P+D EG V Sbjct: 195 VVVVFGVAQALTLIGRVLRARGHRTVAVEEPGSPQENALLRQSGLDIAALPVDAEGPDV- 253 Query: 171 LLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGE 230 L + G + +V P Q P GV + RR LL A D L++ED+ G+ Sbjct: 254 ------AALRRSGARAAVV--TPAHQFPTGVACAPGRRAELLSWARSVDGLLIEDDYDGD 305 Query: 231 LRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCT 290 RY PV ++ E V Y G+ SK LAPG R+GW+ P L+ ++ AK+ DL Sbjct: 306 FRYDRAPVGALQGLAPE-LVAYTGSVSKSLAPGLRLGWLVPPPGLLAEVVEAKRVADLGN 364 Query: 291 NPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWV 350 Q ++V G D + Y+ RRDA++ ALE P GVR T G+ + Sbjct: 365 PVPEQAALAEFVRSGRYDRQLRRCGRTYRERRDALISALEAGFP-GVRITGIAAGLHLIA 423 Query: 351 TLP 353 LP Sbjct: 424 ELP 426 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: 496 Number of extensions: 26 Number of successful extensions: 4 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: 541 Length adjustment: 33 Effective length of query: 384 Effective length of database: 508 Effective search space: 195072 Effective search space used: 195072 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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