Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_010937296.1 DET_RS08305 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::C7ACH5 (393 letters) >NCBI__GCF_000011905.1:WP_010937296.1 Length = 341 Score = 135 bits (339), Expect = 2e-36 Identities = 79/198 (39%), Positives = 108/198 (54%), Gaps = 13/198 (6%) Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253 + +GYAG EL + HP + + ++T + AGK +SD P L + DLP I Sbjct: 9 INVTGYAGLELARILASHPSVELCSVTGRSL---AGKKLSDAFPYLHSL-DLP------I 58 Query: 254 SEFSPG-VDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYP 312 +E G VD+ F+A H+ L P L G V D+S FR+ D Y+ +YGF H P Sbjct: 59 TESLEGEVDIAFMALPHKEGASLVPDLLSKGMRVIDISADFRLKDPPLYQAWYGFEHPCP 118 Query: 313 ELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATSG 372 ELL +A YGL E + A L+A PGCYPT+A L L P DL++ N +++A SG Sbjct: 119 ELLAEAVYGLPELKRKDIASARLVANPGCYPTSAILGLAPAFKMDLIEPN--AIVDAKSG 176 Query: 373 VSGAGRKAAISNSFCEVS 390 +SG+GR N FCE S Sbjct: 177 LSGSGRTPTAKNIFCEAS 194 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: 310 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: 393 Length of database: 341 Length adjustment: 30 Effective length of query: 363 Effective length of database: 311 Effective search space: 112893 Effective search space used: 112893 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