Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::C7ACH5 (393 letters) >FitnessBrowser__azobra:AZOBR_RS07795 Length = 350 Score = 120 bits (302), Expect = 5e-32 Identities = 82/198 (41%), Positives = 115/198 (58%), Gaps = 9/198 (4%) Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253 +GASGY GAELV + RHP + I ALT Q AGK ++++ P L G +LP + I Sbjct: 13 LGASGYTGAELVRMLLRHPGVEICALTAERQ---AGKPMAEVFPHL-GQFNLP--GLVKI 66 Query: 254 SEFS-PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYP 312 E + +D VF A H + ++ L V DLS FR++D Y +YG H+ Sbjct: 67 EEVAWDKLDAVFCALPHGTTQEVIAG-LPRHIKVVDLSADFRLSDPAEYATWYGHEHRAV 125 Query: 313 ELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATSG 372 EL ++ AYGL E+ +++A ++A PGCYPT + LAL PL+ ++++ VI+A SG Sbjct: 126 ELQKEVAYGLTEFNRQGVRKARVVANPGCYPTCSLLALLPLLMDEMIEPG-GIVIDAKSG 184 Query: 373 VSGAGRKAAISNSFCEVS 390 VSGAGR A N F EVS Sbjct: 185 VSGAGRDAKQQNLFTEVS 202 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: 343 Number of extensions: 21 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: 350 Length adjustment: 30 Effective length of query: 363 Effective length of database: 320 Effective search space: 116160 Effective search space used: 116160 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 Sep 17 2021. 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