Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate WP_011159234.1 TX73_RS18870 prephenate dehydratase
Query= BRENDA::Q5NLV8 (337 letters) >NCBI__GCF_000195775.1:WP_011159234.1 Length = 280 Score = 245 bits (625), Expect = 1e-69 Identities = 141/274 (51%), Positives = 179/274 (65%), Gaps = 11/274 (4%) Query: 60 VAFQGAPGCNSNIAIQDLFPDSLPLPCFSFADALTAVKEGRAGRAMIPIENSLNGRVADM 119 +AFQG PG NS+IAI D +P + +PC +F DAL+A+ G A MIPIENS+ GRVAD+ Sbjct: 3 IAFQGEPGANSHIAISDAYPTAEAMPCATFEDALSAISSGEADLGMIPIENSVAGRVADI 62 Query: 120 HFLLPESGLTIQAEYFLPINHCLVAPKGA--GEITHVLSHPQALGQCRHWLQAHNLRALA 177 H LLP S L I E+FLPI H LVA GA +I V SH ALGQCR ++ L+ + Sbjct: 63 HHLLPTSKLFIVGEWFLPIRHQLVAVPGAKLEDIKTVESHVHALGQCRRIIRKFGLKPIV 122 Query: 178 HADTAGAAAEVADRKQAGLAALSPALAAKLYGLEILEKGIADGDTNITRFVVLA-EADTA 236 DTAG+A +A+R AA+S LAAK+YGL+IL + I D N TRFVVLA E A Sbjct: 123 AGDTAGSARIIAERGDKTCAAISSRLAAKIYGLDILAEDIEDEAHNTTRFVVLAREPRWA 182 Query: 237 LQDLPPIRQNLSGKMMTSLLFTVKNTPSALLNAIKGFGDNQVNMTKLESYQHGASFSATQ 296 +Q SGK++T+ +F V+N P+AL A+ GF N VNMTKLESY +F ATQ Sbjct: 183 VQG--------SGKLVTTFVFRVRNLPAALYKALGGFATNGVNMTKLESYMVDGNFFATQ 234 Query: 297 FYADVEGEPSEDNVARALDILQENACDLRILGVY 330 FYADVEG P + N+A ALD L+ + + RI+GVY Sbjct: 235 FYADVEGHPEDRNLAFALDELKFFSREFRIVGVY 268 Lambda K H 0.318 0.132 0.382 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: 232 Number of extensions: 9 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: 337 Length of database: 280 Length adjustment: 27 Effective length of query: 310 Effective length of database: 253 Effective search space: 78430 Effective search space used: 78430 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