Align Prephenate dehydratase; PDT; EC 4.2.1.51 (uncharacterized)
to candidate WP_005813040.1 DHAF_RS15220 prephenate dehydratase
Query= curated2:P43909 (279 letters) >NCBI__GCF_000021925.1:WP_005813040.1 Length = 286 Score = 154 bits (389), Expect = 2e-42 Identities = 99/281 (35%), Positives = 155/281 (55%), Gaps = 15/281 (5%) Query: 1 MKIAYLGPRGSFCSVVAEAAFKSEE--------LYSYATILDVIEAYNEGECDFALVPIE 52 M I YLGP+GSF + ++ L + TI ++ A E + A VP+E Sbjct: 2 MNIGYLGPKGSFSEEALQLFLTTQSDLLEPPLNLIPFTTIPKLLIACQNLEIEGAFVPLE 61 Query: 53 NSTEGTVNMSIDKIFHDSNAKVVAEFVLPISQNLLAVSKEQ--KIEHIYSHPQALAQTRV 110 NSTEG V +++D + + ++ EF+ P+ Q L+ +I+ +YSH QAL Q R Sbjct: 62 NSTEGQVGVTMDMLGQTESLYIMREFIFPVDQCLITAQPLHLAQIKQVYSHEQALGQCRD 121 Query: 111 YLRKFYPQAQVEITESTSAAAEFVKNNPDLPAAAVANSFAAKMYDLEFIAENIQDLAGNS 170 +L QA+ + ST+ A + NPD P AA+ AA++Y+L +E IQD N+ Sbjct: 122 FLETHLAQAEQHSSPSTAEAVTKIAQNPDQPWAAIGPRRAAEIYNLHCKSEKIQDSMLNA 181 Query: 171 TRFWLLGKEKQSFDLNQTKDKVTLALTLPDNLPGALHKAISVFAWRDIDMTKIESRPLRT 230 TRF +G ++N+ +DK +L L + + PGAL A+ FA R+I++++IESRP + Sbjct: 182 TRFIFVGHHLA--EMNE-EDKTSL-LIITGDTPGALAHALQEFALRNINLSRIESRPSKK 237 Query: 231 RLGQYFFIIDLENNATNSLKIPYALEELAGLGVNVRLLGNY 271 +LG+Y F +D++ S I AL L GV+ +LLG+Y Sbjct: 238 KLGEYVFFVDIDGYVF-SPSIQEALWALKDKGVSTKLLGSY 277 Lambda K H 0.317 0.133 0.373 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: 180 Number of extensions: 8 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: 279 Length of database: 286 Length adjustment: 26 Effective length of query: 253 Effective length of database: 260 Effective search space: 65780 Effective search space used: 65780 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 (21.7 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