Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_068462644.1 APY04_RS11160 aminodeoxychorismate synthase, component I
Query= BRENDA::F2L0W0 (295 letters) >NCBI__GCF_001541235.1:WP_068462644.1 Length = 614 Score = 56.2 bits (134), Expect = 2e-12 Identities = 62/207 (29%), Positives = 89/207 (42%), Gaps = 31/207 (14%) Query: 48 LRDHMERLLRSAKIIGL--DVPYTAEELSKAVVETVRANGFKEDLYIRPVAYISKPQISL 105 L H+ERL +SA D E L +AV + A G K L Sbjct: 424 LERHLERLAKSASYFAFVHDEAAAREALDRAVED---AGGDKR----------------L 464 Query: 106 DVRGL---QASVAIAAIPFGKYLKVEGVRAAVVSWRRVHTSMMPVMAKATGIYLNSIMAA 162 VR L +V++ P G +R AV S RV ++ + + K T L Sbjct: 465 RVRLLLTEDGAVSVTTTPLGAAAPDATMRFAVSS-SRVDSNDLFLFHKTTRRELYDREWQ 523 Query: 163 VEARARGYDEAIMLNAEGKVVEGSGENIFIVRRGVLMTPPLEDGILEGITRETVISIAGD 222 A G DE I LN G++ EGS ++FI R G L+TPPL G+L G R +++ Sbjct: 524 EYADKLGTDEVIYLNERGEIAEGSRMSVFIERDGTLLTPPLSAGLLPGTLRAELLAAG-- 581 Query: 223 LGIPLLEKSITREELYAADEAFFVGTA 249 E +T +L +AD A ++G + Sbjct: 582 ---KAREAVLTLADLESAD-AIYLGNS 604 Lambda K H 0.320 0.138 0.396 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: 351 Number of extensions: 20 Number of successful extensions: 1 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: 295 Length of database: 614 Length adjustment: 32 Effective length of query: 263 Effective length of database: 582 Effective search space: 153066 Effective search space used: 153066 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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