Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_108403031.1 B9Z44_RS14805 alanine racemase
Query= BRENDA::Q04HB7 (371 letters) >NCBI__GCF_003063475.1:WP_108403031.1 Length = 353 Score = 125 bits (314), Expect = 2e-33 Identities = 103/326 (31%), Positives = 165/326 (50%), Gaps = 20/326 (6%) Query: 16 SSLAYNVQYTKQVSGAKTLWLAVKSNAYGHGLLQVSKIARECGVDGLAVSVLDEGIAIRQ 75 ++L N + + G K + +K+NAYGHG ++ ++ E D AV+ L+EG+ +R+ Sbjct: 12 NALLSNYKKLRTFHGGKA-FAVLKANAYGHGAVRCAR-KLEMDADAFAVAFLEEGLELRE 69 Query: 76 AGIDDFILIL-GPIDVKYAPIASKYHFLTTVSSLDWLKSADKILGKEK-LSVNLAVDTGM 133 AGI IL+L G DVK A+ + F VS + L+ ++ + L+V L ++TGM Sbjct: 70 AGIQKPILLLEGVFDVKELRKAANHGFWVVVSRHEQLEMIEQCSSAMRGLNVWLKLETGM 129 Query: 134 NRIGVRSKKDLKDEIEFLQE--HSDHFSYDGIFTHFASSDNPDDHYFQRQKNRWYELIDG 191 NR+G+ D E++ + + TH A +D D + +Q + G Sbjct: 130 NRLGL----DGSLACEYIARLCATKAVAKVSFMTHLACADVEGDDFSTKQIEKLMNATRG 185 Query: 192 LIMPRYVHVMNSGAAMYHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDKLKPVFELKSA 251 L + NS A + +K P + AR+G +YGV P V G L+PV ELKS Sbjct: 186 LDCE--LSFCNS-AGVLSAKGPP--SDWARLGIAMYGVNP---VPGSSFSLEPVMELKSQ 237 Query: 252 LTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGWLAEYQDFQLLIDGQKCRQVGQI 311 + VK + AGEG+ YG SRD+ +G + +GY DG+ +L+DG+ + +G I Sbjct: 238 IFDVKNVKAGEGVGYGCTVRVSRDSRVGIVALGYADGYPRNAMGCSVLVDGRLTKTLGVI 297 Query: 312 AMDQMMVALP--HEYPIGTEVTLIGK 335 +MD + V + G++V L GK Sbjct: 298 SMDMLAVDITDLENSGQGSQVELWGK 323 Lambda K H 0.319 0.137 0.410 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: 322 Number of extensions: 13 Number of successful extensions: 5 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: 371 Length of database: 353 Length adjustment: 29 Effective length of query: 342 Effective length of database: 324 Effective search space: 110808 Effective search space used: 110808 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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