Align Prephenate dehydratase; PDT; MjPDT; EC 4.2.1.51 (characterized)
to candidate WP_048102761.1 MBAR_RS10240 prephenate dehydratase
Query= SwissProt::Q58054 (272 letters) >NCBI__GCF_000195895.1:WP_048102761.1 Length = 293 Score = 195 bits (495), Expect = 1e-54 Identities = 125/287 (43%), Positives = 171/287 (59%), Gaps = 28/287 (9%) Query: 10 PKGTYSEKATKKF-LDYIDGDYKIDYCNSIYDVFERV--DNNGLGVVPIENSIEGSVSLT 66 P+G+YSEKA + + L + + KI Y I D F V + L +VPIENSIEGSV +T Sbjct: 8 PEGSYSEKAAQIWTLRHRLDNVKIQYFADIEDAFLAVIQGKSDLSIVPIENSIEGSVGIT 67 Query: 67 QDLLLQFKDIKILGELALDIHHNLIGYD-KNKIKTVISHPQALAQCRNYIKKH--GWDVK 123 DLLL+ ++I+GE+ + I H L+ KIK V+SHPQ LAQCR+++KK+ +++ Sbjct: 68 LDLLLE-NGVEIVGEIVVKIEHCLLSKGGPEKIKVVLSHPQGLAQCRHFLKKYFPEAELR 126 Query: 124 AVESTAKAVKIVAESKDETLGAIGSKESAEHYNLKILDENIEDYKNNKTRFILIGKKVKF 183 + ST+ A ++ E E + AI S E+AE Y LK+L NI+D K N TRFI + K Sbjct: 127 STGSTSHAARLAGEF--EEMAAIASPEAAECYRLKVLLPNIQDRKENYTRFIALQAAGKI 184 Query: 184 KYH------------PKN-----YKVSIVFELKEDKPGALYHILKEFAERNINLTRIESR 226 P+N +K SI+ L++D+PGALY IL FA+ INLTRIESR Sbjct: 185 SDEQVLCSTEDKTGKPENSSHSAFKTSIIVYLEKDRPGALYEILGAFAKNKINLTRIESR 244 Query: 227 PSKKRLGTYIFYIDFENN--KEKLEEILKSLERHTTFINLLGKYPVF 271 PSKK LG Y FYIDFE + +E+ LK +E + +LG YP F Sbjct: 245 PSKKELGDYYFYIDFEGHTGDALIEKTLKDIENKIDTLKILGSYPAF 291 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: 247 Number of extensions: 17 Number of successful extensions: 6 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: 293 Length adjustment: 26 Effective length of query: 246 Effective length of database: 267 Effective search space: 65682 Effective search space used: 65682 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