Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011763917.1 AZO_RS00910 cytochrome c550
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000061505.1:WP_011763917.1 Length = 285 Score = 148 bits (373), Expect = 2e-40 Identities = 97/288 (33%), Positives = 152/288 (52%), Gaps = 13/288 (4%) Query: 7 FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEIP 66 +L+G ++P DEA+VS D G+L+GDG +E + VYS FRL EHL RL + ++ L P Sbjct: 5 YLDGRYLPLDEARVSPMDRGFLFGDGAYEVVPVYSRRPFRLAEHLGRLARTLAAMRLPNP 64 Query: 67 YSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAG---NLGLDPDSCKKPNVVVIAEQLSLF 123 +S +E + V + N + I L V+RGA N D +P V +++E L Sbjct: 65 HSDEEWADRVTTLVAGNPWEDQSIYLQVTRGADAVRNHAFPKDV--RPTVFMLSEPLLTP 122 Query: 124 PQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYV 183 E G+ V+ A R L +KS++ L N L+R G E ++ D G++ Sbjct: 123 APELLASGVAAVSAADFR----WLRCDLKSVSLLANCLLRQYGFDQGCAETVLFRD-GFL 177 Query: 184 AEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADE 243 EGS N+F+V+ +L+ PP S L GIT + +LE+ G + +V ADE Sbjct: 178 TEGSASNIFVVRDGRLLAPPKSHLMLAGITYDVVLELAAAHGLPLEVREILDAEVRSADE 237 Query: 244 VFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRL---LEEFRKLVVEDG 288 +++T + EV+A+T +DGR +G G GP ++ +EF+ V+ G Sbjct: 238 LWMTSSTKEVLAITRLDGRPVGSGAPGPLGRQMYAWYQEFKNTVMRSG 285 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: 190 Number of extensions: 7 Number of successful extensions: 2 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: 285 Length adjustment: 26 Effective length of query: 272 Effective length of database: 259 Effective search space: 70448 Effective search space used: 70448 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