Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO353_14875 AO353_14875 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14875 Length = 305 Score = 130 bits (328), Expect = 3e-35 Identities = 75/241 (31%), Positives = 134/241 (55%), Gaps = 6/241 (2%) Query: 2 FQGSIVALITPFK-EGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60 + G A+ T F + +DYE +I V +G +++CGT GE+ +L+ EE ++E Sbjct: 7 WSGVFPAVTTQFNPDFSIDYEGTHKVISGLVRDGVSGLVICGTVGENTSLSTEEKISLVE 66 Query: 61 FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVV--VPYYNKPTQRGLYEHF 118 A AAGR+ VI+G + A + + VGADG +++ + Y +KP + HF Sbjct: 67 VAKDAAAGRVPVISGVAEFTSANASKVAKEIQRVGADGIMLMPALVYSSKPFETA--AHF 124 Query: 119 KTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLG 178 ++VA +D+P+++YN P +++ D + LA +C+N+V K+S+ + R ++ +G Sbjct: 125 RSVAASIDLPVMVYNNPPIYRNDVTPDILISLA-DCDNVVCFKDSSGDTRRFIDVRNEVG 183 Query: 179 ESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHD 238 + F + +G D + L +A+GA G +S +N P+E + L R A +G F+ A I+ + Sbjct: 184 DRFVLFAGLDDVVLESIAVGAVGWVSGMSNAFPKEGETLFRLARDGRFKEAMPIYEWFMP 243 Query: 239 L 239 L Sbjct: 244 L 244 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: 224 Number of extensions: 12 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 Aug 03 2021. The underlying query database was built on Aug 03 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