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_014449221.1 LFE_RS05290 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000284315.1:WP_014449221.1 Length = 361 Score = 291 bits (746), Expect = 1e-83 Identities = 157/357 (43%), Positives = 221/357 (61%), Gaps = 6/357 (1%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 + L LR ID +D RI+ L+ +RA A V K KA F+ RE +L I Sbjct: 3 EDLGNLRNSIDEIDTRIVGLLRDRAAIAARVGDYK-----KARALPFHVVSREREILDRI 57 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 EL P E + +FREI+S+CL+LE+P+ ++Y+GP T++ AALKHFGHS+ P Sbjct: 58 TELESAPFPKESIRTIFREILSACLSLEEPVVISYMGPPATYTHQAALKHFGHSLKHVPA 117 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 A + EVFR V +G +GVVP+ENSTEG VN+TLD+ +E D+ ICGE+ L IHH LL Sbjct: 118 ATVREVFRAVESGEALYGVVPIENSTEGMVNNTLDTLVESDLRICGEIILPIHHCLLT-R 176 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMA 244 T I +Y+H Q+LAQCR +L P+ +SN A + + +SAAIAG+MA Sbjct: 177 ATSAKEIRTVYAHPQALAQCRIYLSNALPDASTGETTSNTKAVEMALEDPHSAAIAGEMA 236 Query: 245 AQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFH 304 A++Y + + IED P N TRFL+IG+ + T D+TSI+VS+ ++ GAL E+L Sbjct: 237 AEVYNIPIFSRHIEDFPDNQTRFLVIGTIDPGKTRKDQTSIMVSILDRVGALSEILSLIA 296 Query: 305 SNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 + GI+LTR+E+RPSR W Y+FF+D GH D I+ +L K+ +++LGSYP Sbjct: 297 TEGINLTRLESRPSRKKAWDYIFFMDIEGHQADENIRQLLTKLQTLCPYVRILGSYP 353 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: 335 Number of extensions: 9 Number of successful extensions: 2 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