Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate WP_084572759.1 DL86_RS06755 prephenate dehydratase
Query= BRENDA::P9WIC3 (321 letters) >NCBI__GCF_000746085.1:WP_084572759.1 Length = 279 Score = 199 bits (505), Expect = 8e-56 Identities = 123/284 (43%), Positives = 158/284 (55%), Gaps = 11/284 (3%) Query: 3 RIAYLGPEGTFTEAALVRMVAAGLVPETGPDALQRMPVESAPAALAAVRDGGADYACVPI 62 R YLGPE TFTEAAL + PET P SA AAL AVR G D A +P+ Sbjct: 4 RYGYLGPEATFTEAALRSL------PETAGAEYVAYP--SASAALGAVRSGAVDAAMLPL 55 Query: 63 ENSIDGSVLPTLDSLAIGVRLQVFAETTLDVTFSIVVKPGRNAADVRTLAAFPVAAAQVR 122 ENS++G V TL LQ+ AE L V F+++ PG ++ + A Q R Sbjct: 56 ENSVEGGVPATLREFVSDDPLQIVAEANLKVEFALMGNPGARVHTIKQVFTHSHAHGQCR 115 Query: 123 QWLAAHLPAADLRPAYSNADAARQVAD--GLVDAAVTSPLAAARWGLAALADGVVDESNA 180 +W LPAA S A AA ++A G AA+ + +AA R+GL LA + D +N Sbjct: 116 RWQREWLPAAQFESTPSTAAAALEIAQRGGRDIAAIAAVVAAERYGLEVLASDIGDRANV 175 Query: 181 RTRFVLVGRPGPPPARTGADRTSAV-LRIDNQPGALVAALAEFGIRGIDLTRIESRPTRT 239 TRFVL+ RPGP RTGADRTS V + ++PG LV L EF R + +TR+ESRP+ Sbjct: 176 VTRFVLLRRPGPLAPRTGADRTSIVAMASGDRPGWLVHVLDEFASREVPVTRVESRPSGE 235 Query: 240 ELGTYLFFVDCVGHIDDEAVAEALKAVHRRCADVRYLGSWPTGP 283 LG Y F +DC GH D V +AL ++ C VR+LGS+P GP Sbjct: 236 GLGRYHFLIDCEGHAVDPQVRDALVSLALHCRAVRFLGSYPRGP 279 Lambda K H 0.319 0.134 0.396 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: 251 Number of extensions: 16 Number of successful extensions: 4 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: 321 Length of database: 279 Length adjustment: 27 Effective length of query: 294 Effective length of database: 252 Effective search space: 74088 Effective search space used: 74088 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 (21.8 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