Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013722409.1 ALIDE2_RS14405 dihydrodipicolinate synthase family protein
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_000204645.1:WP_013722409.1 Length = 304 Score = 108 bits (270), Expect = 1e-28 Identities = 69/239 (28%), Positives = 115/239 (48%), Gaps = 1/239 (0%) Query: 2 FKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVVE 61 ++G PA+ T F N +D + A H+++QI G +GLV G+ GE+ TL+ +E V Sbjct: 6 WQGVFPAITTKFHPNERIDAEGTARHIDFQIRNGIHGLVTCGSLGEASTLTLEEKLEVAR 65 Query: 62 LCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFSA 121 + ++ AA RVPV+A +T EA+ A + G +V+ + A+ A Sbjct: 66 IALDAAASRVPVLANVSETSTREALRYIEGANKLGVAGFMVMPSVIYVADAREAMANVRA 125 Query: 122 VAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGKD 181 +A A + P+++YN P VD+ PE M AL + I +K++ G + R+++ R + G Sbjct: 126 MANAAQKPVMVYNNPVAYRVDLKPEHMLALADC-EWITAIKESCGDIRRITDLRNTVGDR 184 Query: 182 FVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240 + G D A A G G ++ PR M A + +AL + P+ Sbjct: 185 YQLFCGVDDLAYEALALGADGLLAGVGCAFPRETVALYDLMKAKRFDEALRLYQWMTPM 243 Lambda K H 0.317 0.133 0.384 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: 207 Number of extensions: 5 Number of successful extensions: 1 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: 294 Length of database: 304 Length adjustment: 27 Effective length of query: 267 Effective length of database: 277 Effective search space: 73959 Effective search space used: 73959 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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