Align Prephenate dehydratase; PDT; MjPDT; EC 4.2.1.51 (characterized)
to candidate NP_346859.1 CA_C0217 prephenate dehydratase PheA
Query= SwissProt::Q58054 (272 letters) >NCBI__GCF_000008765.1:NP_346859.1 Length = 275 Score = 130 bits (326), Expect = 4e-35 Identities = 87/282 (30%), Positives = 157/282 (55%), Gaps = 24/282 (8%) Query: 1 MNKAVIYTLPKGTYSEKATKKFLDYIDGDYKIDYCNSIYDVFERVDNN-GLGVVPIENSI 59 M KA + PKGT+SE A K++ + ID + ++ +C++I V + + + ++PIEN++ Sbjct: 1 MKKAAVLG-PKGTFSEFAVKEYKNKIDNNIEMIFCSTISKVVKAAEEECDIAIIPIENTL 59 Query: 60 EGSVSLTQDLLLQFKDIKILGELALDIHHNLIGYDK-NKIKTVISHPQALAQCRNYIKKH 118 +G V +T DLL + ++ I+ EL L I K +++ V + + QC +++KH Sbjct: 60 DGFVQVTLDLLSK-TNLNIIYELVLPIQFAFAANSKMEEVQRVYAQFKTQGQCCEFLEKH 118 Query: 119 G-WDVKAVESTAKAVKIVAESKDETLGAIGSKESAEHYNLKILDE------NIEDYKNNK 171 + + ES +++K + E G +G Y +K ++ N+ D + N+ Sbjct: 119 DEFKIITTESNGQSLKKLKE------GVLGEGAIVPAYAVKGTNKFKCNINNVTDSEGNE 172 Query: 172 TRFILIGKKVKFKYHPKNYKVS--IVFELKEDKPGALYHILKEFAERNINLTRIESRPSK 229 TRFI++ K+ K +Y K Y + I+ + DKPG L+ +L EF+ R+INLT I SRP+K Sbjct: 173 TRFIVLSKE-KVQYEGKGYYKTGIIISDANADKPGTLWRVLNEFSVRDINLTSIISRPTK 231 Query: 230 KRLGTYIFYIDFEN---NKEKLEEILKSLERHTTFINLLGKY 268 K LG Y F+I+ + +L E +++++ H+ + ++G Y Sbjct: 232 KGLGQYYFFIEVDGCYFKDNRLNEAVEAIKHHSV-VKVVGTY 272 Lambda K H 0.317 0.137 0.389 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: 207 Number of extensions: 15 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: 272 Length of database: 275 Length adjustment: 25 Effective length of query: 247 Effective length of database: 250 Effective search space: 61750 Effective search space used: 61750 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 (21.6 bits) S2: 47 (22.7 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