Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate 6936059 Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
Query= BRENDA::C7ACH5 (393 letters) >FitnessBrowser__SB2B:6936059 Length = 331 Score = 179 bits (453), Expect = 1e-49 Identities = 100/202 (49%), Positives = 127/202 (62%), Gaps = 6/202 (2%) Query: 194 VGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPLQPMSDI 253 +GASGY GA+L ++ PH+ + L VS S D GK +S L+P + L P++D Sbjct: 12 IGASGYTGAQLTALIDAEPHLQVQGLYVSEGSADKGKPLSSLYPVYSHL-KYCLSPLTDE 70 Query: 254 SEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYYGFTHQY 311 ++ + D V LAT H VS +LA F E G VFDLSGA+R D Y K+YGF H + Sbjct: 71 AKDAIVAEADAVALATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWYGFEHSH 130 Query: 312 PELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWPVINATS 371 PE+L +A YGLAEW + + +IAVPGCYPTA+ ALKPL A L + PVINA S Sbjct: 131 PEVLAKAVYGLAEWNADAVAATRMIAVPGCYPTASLTALKPL-KAMLTEAR--PVINAVS 187 Query: 372 GVSGAGRKAAISNSFCEVSLQP 393 GV+GAGRKA + SFCEVSL P Sbjct: 188 GVTGAGRKAQLHTSFCEVSLTP 209 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: 336 Number of extensions: 15 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: 331 Length adjustment: 29 Effective length of query: 364 Effective length of database: 302 Effective search space: 109928 Effective search space used: 109928 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