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_027721085.1 H589_RS0105335 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000425265.1:WP_027721085.1 Length = 367 Score = 236 bits (601), Expect = 9e-67 Identities = 135/361 (37%), Positives = 205/361 (56%), Gaps = 7/361 (1%) Query: 2 SEADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVL 61 S + L +LR IDSLD IL+L+++RA + V +K S + ++P RE VL Sbjct: 4 SSKNNLGSLREEIDSLDSEILELLNKRAAASLSVGAIKAGSSDQ-----IFKPFREQEVL 58 Query: 62 KHIMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVIS 121 + + N GPL +E + ++REI+SS L++P RV YLGPEGTFS A L+H G Sbjct: 59 QGLTGRNPGPLPSEHLEAIYREIISSSRRLQRPERVVYLGPEGTFSYFAGLQHMGRQADM 118 Query: 122 KPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLL 181 P +++F V G + G++P+ENS +G V +D F+ + + I E+ RI H L Sbjct: 119 IPKNNFEDIFVAVSKGEADLGIIPLENSLKGTVGQNVDLFMRYPVYIQAELYHRISHG-L 177 Query: 182 VGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRV-KSEWNSAAIA 240 + + D I +YSH+++L QC WL A+ P V V V S A AA+ V S+ AA+ Sbjct: 178 ISKGVGLDEIKTVYSHSKALEQCTGWLRANLPGVPLVPVDSTAQAAQMVADSDEPIAALG 237 Query: 241 GDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELL 300 A ++GL +AE IED N TRFLIIG + DKT+I+ + ++PGAL +L Sbjct: 238 HVKLANIFGLHVVAEAIEDLSDNWTRFLIIGPKPGKEGKRDKTTILFTTPDRPGALVSVL 297 Query: 301 MPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 + I++T++E+RP KW Y+FF+D G + ++++E + + K+LGSY Sbjct: 298 NELYGKDINMTKLESRPFLGEKWKYMFFVDLQGDLRAEEYESLIEDLKSRCLTFKILGSY 357 Query: 361 P 361 P Sbjct: 358 P 358 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: 313 Number of extensions: 14 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: 367 Length adjustment: 30 Effective length of query: 335 Effective length of database: 337 Effective search space: 112895 Effective search space used: 112895 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