Align Prephenate dehydratase; PDT; EC 4.2.1.51 (uncharacterized)
to candidate WP_041303735.1 BTUS_RS04750 prephenate dehydratase
Query= curated2:P21203 (285 letters) >NCBI__GCF_000092905.1:WP_041303735.1 Length = 293 Score = 187 bits (475), Expect = 2e-52 Identities = 112/288 (38%), Positives = 163/288 (56%), Gaps = 13/288 (4%) Query: 2 KVGYLGPAATFTHLA------VSSCFQNGAEHVAYRTIPECIDAAVAGEVDFAFVPLENA 55 ++ +LGP+ TFT A V + G E VA TI + +D +G F VP+EN+ Sbjct: 6 QLAFLGPSGTFTEEAARVMSGVLASDLPGEEWVACDTIADVLDLTASGATAFGVVPIENS 65 Query: 56 LEGSVNLTIDYLIHEQPLPIVGEMTLPIHQHLLVHPSRENAWKELDKIYSHSHAIAQCHK 115 LEGSVN+T+D+L HE L I E LP+ HLL P ++++ I SH A+AQC Sbjct: 66 LEGSVNITLDWLAHEGGLVIAAEAALPVSHHLLARPGVSG--EQIEGIVSHPQALAQCRG 123 Query: 116 FLHRHFPSVPYEYANSTGAAAKFVSDHPELNIGVIANDMAASTYELKIVKRDIQDYRDNH 175 +L HFP VP A ST AAA+ V PE ++ I +AA Y L+I+ +IQD +N Sbjct: 124 YLRNHFPGVPQYAAESTAAAAERVIRDPE-DLAAIGTRLAARIYGLEILASEIQDEANNR 182 Query: 176 TRFVILSPDENISFEVNSKLSSR---PKTTLMVMLPQDDQSGALHRVLSAFSWRNLNLSK 232 TRFV+++ + E + R KT+ ++ L +D GAL+ VL+ F+ +NL++ Sbjct: 183 TRFVLVAAQSRWTEEQQREFCRRHGASKTSALITL-GEDHPGALYEVLACFARERVNLTR 241 Query: 233 IESRPTKTGLGHYFFIIDIEKAFDDVLIPGAMQELEALGCKVRLLGAY 280 IESRPT+ GLG Y F +D+E + D + A++ + G VR LG Y Sbjct: 242 IESRPTRRGLGSYHFFVDMEGQWWDPAVIRAVEGIHETGAAVRDLGTY 289 Lambda K H 0.321 0.135 0.404 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: 197 Number of extensions: 11 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: 285 Length of database: 293 Length adjustment: 26 Effective length of query: 259 Effective length of database: 267 Effective search space: 69153 Effective search space used: 69153 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