Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_066327576.1 BLR17_RS04940 dihydrodipicolinate synthase family protein
Query= BRENDA::Q8RBI5 (297 letters) >NCBI__GCF_900100165.1:WP_066327576.1 Length = 304 Score = 107 bits (267), Expect = 3e-28 Identities = 64/211 (30%), Positives = 110/211 (52%), Gaps = 2/211 (0%) Query: 4 FKGSCVAIVTPFT-ENGVNFDKLGELIEWHIKEGTDAILICGTTGEASTMTDEEQKEAIK 62 + G A+ T FT ++ ++F+ ++ I G I++ GT GEAST+ +EE+ + ++ Sbjct: 5 WSGVMPAVTTKFTADDKLDFNMFEVNLKAQIDAGVSGIILGGTLGEASTLLEEEKTQLVR 64 Query: 63 FTVEKVAKRIPVIAGTGSNNTAHAIELSEYAQSVGADALLVITPYYNKTTQKGLVAHFTE 122 TV KV ++PVI T AI + A+ GA L+++ P K T V +F+E Sbjct: 65 ETVRKVDGKVPVIMNIAEQTTRAAIIAANKAEEDGATGLMMLPPMRYKATDHETVTYFSE 124 Query: 123 IARHVDIPIIIYNVPSRTSLNMLPETYLEVKKKAENVVGVKEASGDISQIAEIARIMGKS 182 +A+ +PI+IYN P + + + + E+ K +N+ VKE++ DIS + I G Sbjct: 125 VAKSTSLPIMIYNNPVDYKIEVTLDMFEEM-LKYDNIQAVKESTRDISNVTRIINRFGSR 183 Query: 183 FEIYSGNDDQVIPIMSLGGLGVISVTANIIP 213 +I SG D + + +G G +S + P Sbjct: 184 LKILSGVDTLALESLFMGSDGWVSGLVDAFP 214 Lambda K H 0.315 0.134 0.373 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: 204 Number of extensions: 6 Number of successful extensions: 2 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: 297 Length of database: 304 Length adjustment: 27 Effective length of query: 270 Effective length of database: 277 Effective search space: 74790 Effective search space used: 74790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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