Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate PfGW456L13_1233 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
Query= BRENDA::C7ACH5 (393 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1233 Length = 344 Score = 152 bits (383), Expect = 2e-41 Identities = 85/197 (43%), Positives = 117/197 (59%), Gaps = 5/197 (2%) Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253 VG +GY G EL+ + +HP + +T ++AG ++D++P L+G D + DI Sbjct: 7 VGGTGYTGVELLRLLAQHPQAEVVVIT---SRSEAGLAVADMYPNLRGHYDGLAFSVPDI 63 Query: 254 SEFSPGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQYPE 313 DVVF AT H V+H LA + L AG V DLS FR+ DA + K+YG H PE Sbjct: 64 KTLG-ACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAPE 122 Query: 314 LLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATSGV 373 LL++A YGL E ++K+A LIAVPGCYPTA QL PL++A L D + + SGV Sbjct: 123 LLDEAVYGLPEVNREQIKKARLIAVPGCYPTATQLGFLPLLEAGLADAAHL-IADCKSGV 181 Query: 374 SGAGRKAAISNSFCEVS 390 SGAGR A++ + + E S Sbjct: 182 SGAGRGASVGSLYSETS 198 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: 349 Number of extensions: 14 Number of successful extensions: 4 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: 344 Length adjustment: 30 Effective length of query: 363 Effective length of database: 314 Effective search space: 113982 Effective search space used: 113982 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