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 Ac3H11_2574 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2574 Length = 351 Score = 290 bits (743), Expect = 3e-83 Identities = 157/354 (44%), Positives = 220/354 (62%), Gaps = 10/354 (2%) Query: 12 VRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIMELNKGP 71 V+IDS+D+++L L+++RA A++V VK K E F+RP+R A V+ I N GP Sbjct: 1 VQIDSIDQQLLTLLNQRALVAEQVGEVK-----KREGTPFFRPDRVAQVIDKITHANPGP 55 Query: 72 LDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVF 131 L +A ++REIMS+CLALE P RVA LGPEGTF + AA++ FG + A DEVF Sbjct: 56 LKGPHVAAIWREIMSACLALESPQRVAVLGPEGTFCEQAAIEFFGGAADLMYCANFDEVF 115 Query: 132 REVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRI 191 AG+ +GVV VENSTEG V +LD FL + GEV L + H+LL T D I Sbjct: 116 HATAAGSAQYGVVGVENSTEGVVTRSLDLFLHTPTHVVGEVSLLVRHNLL-RTTNSLDGI 174 Query: 192 TRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLS 251 + +H Q+LAQC+ WL H P+ ER VSSNA+ A+ + AA++ + AA +GL Sbjct: 175 EAVLAHPQALAQCQAWLSKHLPHAERRPVSSNAEGARLATTNPAWAALSSERAATQFGLH 234 Query: 252 KLAEKIEDRPVNSTRFLII----GSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHSNG 307 ++ I+D N TRF II Q PP+G D TS++VS+ N+PGA+H+LL+P ++G Sbjct: 235 IVSHAIQDDAYNRTRFAIICLPHTLQTPPPSGKDCTSLVVSVPNQPGAVHDLLVPLKTHG 294 Query: 308 IDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 + +TR E+RP+R+G+W Y F+ID GH P + LE++ KVLG+YP Sbjct: 295 VSMTRFESRPARTGQWEYYFYIDLDGHPAQPHVARALEELRSLCAFYKVLGTYP 348 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: 350 Number of extensions: 12 Number of successful extensions: 4 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: 351 Length adjustment: 29 Effective length of query: 336 Effective length of database: 322 Effective search space: 108192 Effective search space used: 108192 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 09 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