Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate 199470 SO0275 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
Query= BRENDA::C7ACH5 (393 letters) >FitnessBrowser__MR1:199470 Length = 326 Score = 182 bits (463), Expect = 9e-51 Identities = 101/208 (48%), Positives = 131/208 (62%), Gaps = 6/208 (2%) Query: 188 MLNTLNVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 247 M N +GASGY GA+L V+ ++I L VS S D G+ ++DL+P I +L L Sbjct: 1 MKNIAIIGASGYTGAQLTALVHAESELSIQGLYVSENSLDKGRALADLYPVYSHI-ELTL 59 Query: 248 QPMSDISEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYY 305 P+++ ++ + D V LAT H VS LA F G VFDLSGA+R +D Y K+Y Sbjct: 60 SPLTEEAKANIVAEADAVVLATEHSVSLHLAAWFYSQGLAVFDLSGAYRFSDVAQYPKWY 119 Query: 306 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 365 GF H+YPE+L +A YGLAEW + +IAVPGCYPTA+ ALKPL + L + +P Sbjct: 120 GFEHEYPEVLAKAVYGLAEWNAKDVAATKMIAVPGCYPTASLTALKPLKN---LLTSAYP 176 Query: 366 VINATSGVSGAGRKAAISNSFCEVSLQP 393 VINA SGV+GAGRKA + SFCEVSL P Sbjct: 177 VINAVSGVTGAGRKAQLHTSFCEVSLTP 204 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: 327 Number of extensions: 12 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: 326 Length adjustment: 29 Effective length of query: 364 Effective length of database: 297 Effective search space: 108108 Effective search space used: 108108 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