Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_020562931.1 A3OW_RS0108110 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000372865.1:WP_020562931.1 Length = 361 Score = 371 bits (952), Expect = e-107 Identities = 189/365 (51%), Positives = 249/365 (68%), Gaps = 4/365 (1%) Query: 1 MSEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWV 60 M L LR +ID +D IL LI++RA A+EVA K A+ E FYRP+RE+ V Sbjct: 1 MPSVTPLSELRDKIDRIDAEILRLINQRASYAKEVALTKIAA---GEVGTFYRPDRESLV 57 Query: 61 LKHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVI 120 L+ I ELN+GPL + R FRE+MS+CLALEQPL VA+LGPEGTF+Q AA KHFGH++ Sbjct: 58 LRRIHELNQGPLSDHTAVRFFRELMSACLALEQPLEVAFLGPEGTFTQQAAFKHFGHAIN 117 Query: 121 SKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHL 180 + P+A+I+E+F V +FGVVPVENSTEG +NHTLD FL + ICGEVE+++H +L Sbjct: 118 TVPVASINEIFNSVELNKCHFGVVPVENSTEGVINHTLDRFLTSPLKICGEVEVKVHQNL 177 Query: 181 LVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIA 240 + G T IT ++SH QSLAQCR WLD + P+ AV+SNA+AA+ ++AA+A Sbjct: 178 M-GHTESLSEITEVFSHQQSLAQCRYWLDKYLPHARLTAVASNAEAARLASVNKSTAAVA 236 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 G +AA++Y L + + IED P N+TRF++IG Q TG DKTS+++S N+PGAL++ L Sbjct: 237 GMVAAEVYQLPVIEKNIEDEPNNTTRFIVIGQQTSSSTGKDKTSLVISTGNQPGALYKAL 296 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 PF I + IE+RPSR G W YVFFID GH +DP + LE + LK+LGSY Sbjct: 297 EPFARFSIGMVNIESRPSRQGLWEYVFFIDIEGHSEDPNVAEALEILKGTVSMLKLLGSY 356 Query: 361 PKAVL 365 PKAVL Sbjct: 357 PKAVL 361 Lambda K H 0.319 0.133 0.390 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: 344 Number of extensions: 7 Number of successful extensions: 3 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: 365 Length of database: 361 Length adjustment: 29 Effective length of query: 336 Effective length of database: 332 Effective search space: 111552 Effective search space used: 111552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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