Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013092763.1 BC1002_RS24880 dihydrodipicolinate synthase family protein
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_000092885.1:WP_013092763.1 Length = 305 Score = 101 bits (252), Expect = 2e-26 Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 5/241 (2%) Query: 2 FKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVVE 61 + G PA+ T F + S+D V + +G +G+V GT GE+ +LS E +V+E Sbjct: 7 WSGVFPAVSTQFKPDFSLDIDGTHRVVSNLVKDGVSGMVVCGTVGENTSLSTSEKLQVIE 66 Query: 62 LCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTP--YYNKPTQKGLFAHF 119 + + +VPV+AG T+ A + A G D ++V+ Y KP + AHF Sbjct: 67 AARDASGGQVPVVAGVAEFTTEFARQTVREAARVGVDGVMVMPALVYSAKPHETA--AHF 124 Query: 120 SAVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCG 179 +VA + LP++IYN PP D++P+ + AL +NI+ KD++G R + R + G Sbjct: 125 RSVATSTDLPVMIYNNPPIYKNDVTPDVLIALQDC-ENIVCFKDSSGDTRRFIDLRNAVG 183 Query: 180 KDFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMP 239 FV +G D + A G G +S +N P+ + +AL MP Sbjct: 184 DRFVLFAGLDDVVVESIAVGAEGWVSGMSNAFPKEGETLFRLATQKRFDEALALYSWFMP 243 Query: 240 L 240 L Sbjct: 244 L 244 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: 188 Number of extensions: 12 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: 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 ( 7.3 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