Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_027490233.1 LRK54_RS01370 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_021560695.1:WP_027490233.1 Length = 482 Score = 154 bits (390), Expect = 4e-42 Identities = 93/292 (31%), Positives = 146/292 (50%), Gaps = 14/292 (4%) Query: 52 GLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVD 111 G+P FP ++ +T + L K A + Y ++G LR A+A+ + + S D Sbjct: 126 GIPDHRHFPHDVWRRLTAQTLRKSAREPFAYAPSQGIPALREAIAQHVAFARAVACSADD 185 Query: 112 IMITSGSQQALDLIGRVFINPGDI-VVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVD 170 +++TSG+QQA DLI R+ + PG V VE P Y AF + +P+DDEG+ V+ Sbjct: 186 VVVTSGAQQAFDLIARLLVTPGQTKVAVEEPGYPPLRAAFAAAGARLLPLPVDDEGLCVE 245 Query: 171 LLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGE 230 L E V+++ P+ Q+P MS +RR LL+ A + +IVED+ GE Sbjct: 246 RLPED----------VRIISVTPSHQSPTDAAMSLRRRAALLDFARRHRAVIVEDDYDGE 295 Query: 231 LRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCT 290 R+ G P+ ++ D + V Y+GTFSK + P R G++ A L K VD Sbjct: 296 FRFGGRPLDALQTLDGDALVFYVGTFSKSMFPSLRKGFVVAPAWAHSGLVTVKHCVDSHC 355 Query: 291 NPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKP 342 + +Q ++ GHL H+ ++ Y RR A+L L+ + RW +P Sbjct: 356 DSLTQSALAAFIRDGHLARHLRHMRPIYAERRAALLDGLQRVLG---RWLQP 404 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: 441 Number of extensions: 23 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: 482 Length adjustment: 33 Effective length of query: 384 Effective length of database: 449 Effective search space: 172416 Effective search space used: 172416 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