Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_027180549.1 G496_RS0118275 aminotransferase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000429985.1:WP_027180549.1 Length = 313 Score = 139 bits (349), Expect = 1e-37 Identities = 83/270 (30%), Positives = 145/270 (53%), Gaps = 7/270 (2%) Query: 24 DHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEIPYSLDEVTNIVVETIRQN 83 DH GDGVFE ++ +G +++L H+ R+ SAKSI LE P S DE+ I++E R + Sbjct: 49 DHLVHRGDGVFETMKFVNGKLYQLDPHVRRMKRSAKSIYLEPPCSWDELKEIIIEVSRAS 108 Query: 84 KLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQLSLFPQEYYEKGIPVVTVATRRNR 143 + +G +R+++ RG G G+ C ++ V+ L P E+YEKGI + + Sbjct: 109 ECESGLVRVLLGRGCGGFGISTQECPVSSLYVVVYNLKPKPDEWYEKGITAFKTSIPAKQ 168 Query: 144 PDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAEGSGDNVFIVKGNKLITPP 203 + + +K+++YL N+L++ EA+ G + G++AEG+ +NV IV+ + I P Sbjct: 169 SYLAT--IKTIDYLPNVLMKREAEEKGFDFPFCFDHMGFLAEGATENVCIVEPSGTIHVP 226 Query: 204 SSAGALEGITRNAILEI--GEKLGYDVREELFTRHDVYVADEVFLTGTAAEVIAVTTVDG 261 AL G T LE+ GE D+ + +V +A EV + GT + ++V + Sbjct: 227 QFTNALAGTTLLRALELISGE---VDIDYRAISEEEVLLAKEVIVCGTTLDAVSVVRYNT 283 Query: 262 RTIGLGQTGPHTNRLLEEFRKLVVEDGEKI 291 + I + GP + R+ E ++ + ++G K+ Sbjct: 284 KPIHDVRPGPVSKRMRELLKEDIAKNGYKL 313 Lambda K H 0.317 0.138 0.389 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: 227 Number of extensions: 10 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: 298 Length of database: 313 Length adjustment: 27 Effective length of query: 271 Effective length of database: 286 Effective search space: 77506 Effective search space used: 77506 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 (21.6 bits) S2: 48 (23.1 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