Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_24905 AO356_24905 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24905 Length = 305 Score = 124 bits (311), Expect = 3e-33 Identities = 72/238 (30%), Positives = 132/238 (55%), Gaps = 6/238 (2%) Query: 2 FQGSIVALITPFKEG-EVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60 + G A+ T F + ++ E +I + +G ++VCG+ GE+ +L+ EE V E Sbjct: 7 WSGVFPAVTTQFNDDFSINLEKTHQVISNVIRDGVSGLVVCGSVGENTSLSAEEKIAVTE 66 Query: 61 FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVV--VPYYNKPTQRGLYEHF 118 AV + GR+ VI G + +A + ++VG DG +++ + Y +KP + EHF Sbjct: 67 VAVDASRGRVPVICGVAEFTSVQAAKVANAVRKVGVDGVMLMPALVYGSKPFETA--EHF 124 Query: 119 KTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLG 178 + VA+ D+P+++YN P +++ D + LA +C+N+V K+S+ + R ++ +G Sbjct: 125 RYVARHADVPLMVYNNPPIYKNDVTPDILISLA-DCDNVVCFKDSSGDTRRFIDVRNEVG 183 Query: 179 ESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYL 236 + F + +G D + L +A+GA+G +S +NV P+E + + R A G F A I+ +L Sbjct: 184 DRFVLFAGLDDVVLESLAVGAEGWVSGMSNVFPKEGETIFRLARAGRFAEAMPIYEWL 241 Lambda K H 0.318 0.136 0.390 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: 193 Number of extensions: 6 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: 294 Length of database: 305 Length adjustment: 27 Effective length of query: 267 Effective length of database: 278 Effective search space: 74226 Effective search space used: 74226 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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