Align Prephenate dehydratase; PDT; MjPDT; EC 4.2.1.51 (characterized)
to candidate WP_011867826.1 MMARC5_RS00250 prephenate dehydratase
Query= SwissProt::Q58054 (272 letters) >NCBI__GCF_000016125.1:WP_011867826.1 Length = 269 Score = 249 bits (637), Expect = 3e-71 Identities = 139/262 (53%), Positives = 180/262 (68%), Gaps = 6/262 (2%) Query: 10 PKGTYSEKATKKFLDYIDGDYKIDYCNSIYDVFERVDNNG--LGVVPIENSIEGSVSLTQ 67 PKG+Y+EKA F I+ D +I + +SIY+VF+ V+ N GVVP ENSI GSVSLTQ Sbjct: 7 PKGSYTEKAAVTFSKAIN-DNEIQFEDSIYNVFKAVETNSEFFGVVPSENSIGGSVSLTQ 65 Query: 68 DLLLQFKDIKILGELALDIHHNLIGYDKNKIKTVISHPQALAQCRNYIKKHGWDVKAVES 127 DLLL+F +KI+GE+ + I+H LIG D K+ V++HPQAL QC +YI K+ W++ V+S Sbjct: 66 DLLLEFP-VKIIGEVDVSINHCLIGIDIKKVTEVLAHPQALTQCGHYITKNNWNITPVDS 124 Query: 128 TAKAVKIVAESKDETLGAIGSKESAEHYNLKILDENIEDYKNNKTRFILI-GKKVKFKYH 186 AKA KIV+E KDE L AI E+AE Y LK+LDENI+DYKNN TRF LI K FK + Sbjct: 125 NAKAAKIVSEKKDEKLAAICGVENAEIYGLKVLDENIQDYKNNTTRFFLICNKNNDFKTN 184 Query: 187 PKNYKVSIVFELKEDKPGALYHILKEFAERNINLTRIESRPSKKRLGTYIFYIDFENNKE 246 K KVSIV E+ ++ PGA Y +L F RN+NLTRIESRPSKK +G Y+FYID+E ++ Sbjct: 185 LKPNKVSIVIEINKNMPGAFYEVLGVFKYRNVNLTRIESRPSKKEIGNYVFYIDYEFYED 244 Query: 247 KLEEILKSLERHTTFINLLGKY 268 +L+ L + LG Y Sbjct: 245 N-AALLRDLRMWALNVIELGNY 265 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: 251 Number of extensions: 11 Number of successful extensions: 5 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: 269 Length adjustment: 25 Effective length of query: 247 Effective length of database: 244 Effective search space: 60268 Effective search space used: 60268 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