Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_028950107.1 Q385_RS0102260 aminodeoxychorismate lyase
Query= BRENDA::E6TUA8 (302 letters) >NCBI__GCF_000619805.1:WP_028950107.1 Length = 249 Score = 98.6 bits (244), Expect = 1e-25 Identities = 75/236 (31%), Positives = 126/236 (53%), Gaps = 15/236 (6%) Query: 28 LYGDGVFEGIRVYDGNIFKLTE-HLKRLYESAQSIMLEIPY-SKEDFQQIIVDTVRKNQL 85 +YG+GVFE R Y+ + K + H +RL + A L+IP+ +KED+ I V + Sbjct: 21 MYGEGVFETFR-YNQKLPKYIDYHYERLIKGAS--FLKIPHITKEDYIYYINQAVNSVEE 77 Query: 86 ESGYIR-VVVSRGPGNLGLDPSRCSAPHVIVIAEELALFPKELYELGLTVASVASRRNRP 144 + Y++ +++S G L P + + ++V+ + P + +T+ R + Sbjct: 78 KDLYVKTILLSEGNSYYPLQPYKSN---LLVVVK-----PYQTINSPITLTVSPYRVHSK 129 Query: 145 DVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQGYVTEGSADNIFIVKNNTIITPPV 204 D L +IKS NYL NILVK A + G +A++LN+ +TE S+ NIF +K + TP + Sbjct: 130 DPLL-KIKSTNYLRNILVKRYAQEKGFFDAIILNEDDCITETSSANIFWIKGRYLYTPSL 188 Query: 205 YLGALEGITRNAIIDLAKECGYEMKETPFTRHDVYVADEVFLTGTAAEVIAVVEVD 260 G LEGI+R I++ AK G+ + E F D+ A+ +FL+ ++ V +D Sbjct: 189 DCGVLEGISRRKILEEAKNQGFIVVEGMFNLKDLKDANIIFLSNALHGIMKVENID 244 Lambda K H 0.318 0.136 0.385 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: 175 Number of extensions: 9 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: 302 Length of database: 249 Length adjustment: 25 Effective length of query: 277 Effective length of database: 224 Effective search space: 62048 Effective search space used: 62048 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: 47 (22.7 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