Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_092482993.1 BM299_RS08220 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::C7ACH5 (393 letters) >NCBI__GCF_900115975.1:WP_092482993.1 Length = 347 Score = 132 bits (332), Expect = 2e-35 Identities = 77/197 (39%), Positives = 110/197 (55%), Gaps = 5/197 (2%) Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253 +GA+GYAGAELV ++ HPH + ALT + GK +++P L V L + + D+ Sbjct: 8 IGATGYAGAELVRILSAHPHAELVALTTQSYG---GKAFCEVYPHLYKHVALECREL-DL 63 Query: 254 SEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYPE 313 + DV+F A H +A + L G DL FR + + YE++Y H PE Sbjct: 64 PALAEQADVIFAALPHGHVVPVAREVLARGKKFIDLGADFRFDSSEVYEQWYKVEHTAPE 123 Query: 314 LLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATSGV 373 LL QA YGL E K+K A+L+ PGCYPT+ L L PL+ + L+D V+++ SGV Sbjct: 124 LLRQAVYGLPEVHREKIKTASLVGNPGCYPTSVILGLAPLLRSGLVDTGT-VVVDSKSGV 182 Query: 374 SGAGRKAAISNSFCEVS 390 SGAGR ++ F EV+ Sbjct: 183 SGAGRGLSLGTHFAEVN 199 Lambda K H 0.320 0.136 0.403 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: 342 Number of extensions: 13 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: 393 Length of database: 347 Length adjustment: 30 Effective length of query: 363 Effective length of database: 317 Effective search space: 115071 Effective search space used: 115071 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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