Align Prephenate dehydratase; PDT; MjPDT; EC 4.2.1.51 (characterized)
to candidate WP_013430713.1 CALKRO_RS08950 prephenate dehydratase
Query= SwissProt::Q58054 (272 letters) >NCBI__GCF_000166775.1:WP_013430713.1 Length = 276 Score = 176 bits (445), Expect = 6e-49 Identities = 115/273 (42%), Positives = 164/273 (60%), Gaps = 15/273 (5%) Query: 5 VIYTLPKGTYSEKATKKFLDYIDGDYKIDYCNSIYDVFERVDNNG--LGVVPIENSIEGS 62 V Y P G+YS +A ++F + K+ C +I DVFE ++ N GVVP+ENSIEGS Sbjct: 3 VAYLGPIGSYSYEAARRFFG--EEREKLIACETIDDVFETIEENRAEFGVVPVENSIEGS 60 Query: 63 VSLTQDLLLQFKDIKILGELALDIHHNLIGYDKNK-IKTVISHPQALAQCRNYIKKHGWD 121 VS T D LL+ + I+ E+ L + H L ++ K I T+ SHPQA +QC +Y++K+ Sbjct: 61 VSTTLDYLLK-SQVYIVKEIVLKVEHYLSAREEKKQILTIASHPQAFSQCHDYLRKNFKQ 119 Query: 122 VKAVE--STAKAVKIVAESKDETLGAIGSKESAEHYNLKILDENIEDYKNNKTRFILIGK 179 K ++ ST+ A ++ AE E AI S +A NLKIL I ++ NN TRF +I K Sbjct: 120 AKLIQVSSTSYAARMCAEG--EVDAAICSSFAARQNNLKILAGPI-NHDNNYTRFFIISK 176 Query: 180 KVKFKYHPKNYKVSIVFELKEDKPGALYHILKEFAERNINLTRIESRPSKKRLGTYIFYI 239 F+ KN K SI+F DKPG+LY IL F ++NLT+IESRP+K LG Y+F++ Sbjct: 177 NANFEKGEKN-KTSIIFSTY-DKPGSLYKILAIFNLYDLNLTKIESRPAKTNLGEYVFFV 234 Query: 240 DFEN--NKEKLEEILKSLERHTTFINLLGKYPV 270 D + + E + + LK ++R +TF LLG Y V Sbjct: 235 DIDGFVDDEDVSDALKVVQRKSTFYKLLGSYSV 267 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: 221 Number of extensions: 16 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: 276 Length adjustment: 25 Effective length of query: 247 Effective length of database: 251 Effective search space: 61997 Effective search space used: 61997 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 Jul 26 2024. The underlying query database was built on Jul 25 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