Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013722399.1 ALIDE2_RS14335 5-dehydro-4-deoxyglucarate dehydratase
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_000204645.1:WP_013722399.1 Length = 303 Score = 121 bits (304), Expect = 2e-32 Identities = 90/297 (30%), Positives = 139/297 (46%), Gaps = 13/297 (4%) Query: 1 MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60 M G + IT F NG D K++AA +EW G++ L G TGE +L+ E+ ++ Sbjct: 10 MGSGLLSFPITDFDANGDFDAKSYAARLEWLAPFGASALFAAGGTGEYFSLTAGEYPAII 69 Query: 61 ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120 ++ +VP+IAGAG T AIE A A++AGA +L++ Y + +Q+GL AH Sbjct: 70 RTAVDTCRGKVPIIAGAG-GPTRFAIECAQAAEKAGAHGILLMPHYMTEASQEGLAAHVE 128 Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180 AV ++V ++IYN R V +PET+ L + + N++G KD G ++ ++ ++ G Sbjct: 129 AVCKSVDFGVIIYN---RGVSRYTPETVARLCERNPNLVGFKDGVGDIEGMASMFLAMGD 185 Query: 181 DFVQLSG---EDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALE-YQDR 236 L G + A + A G S N PR F A+ D A + +D Sbjct: 186 RLAYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPRTAMRFYEAVKNDDQATQHQLLKDF 245 Query: 237 LMPLHRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLM 293 MP + G YA+S + G R V P P + D A L+ Sbjct: 246 FMPYLKIRNRSAG-----YAVSIIKAGARIVGHPAGPVRPPLADLQPDEVEMLAALI 297 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: 213 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: 303 Length adjustment: 27 Effective length of query: 267 Effective length of database: 276 Effective search space: 73692 Effective search space used: 73692 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