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_092052376.1 BQ4888_RS00675 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900111775.1:WP_092052376.1 Length = 357 Score = 303 bits (777), Expect = 4e-87 Identities = 160/360 (44%), Positives = 227/360 (63%), Gaps = 6/360 (1%) Query: 4 ADQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKH 63 AD L ALR ID +D+ ILDL+++RA EV + K + FY P RE + + Sbjct: 3 ADNLSALRQAIDDIDDHILDLLNQRASVVVEVGKAKAG-----QSKDFYVPSRERAIYER 57 Query: 64 IMELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKP 123 + N GP +E + ++FREI+S+ L+LEQP++VA+LGP+GTF+ AAA++ FG S P Sbjct: 58 LTAANPGPFPSEAIRKVFREIISASLSLEQPMKVAFLGPQGTFTHAAAMQQFGFSAQLMP 117 Query: 124 MAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVG 183 +I +F EV G +GVVPVENSTEG V+HTLD F+E ++ I E+ L I H L+ Sbjct: 118 QKSIPAIFEEVARGRAPYGVVPVENSTEGVVSHTLDMFMESELKINAEIMLGISHFLMSR 177 Query: 184 ETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDM 243 TD I ++ SH Q LAQCRKWL+ + P+V V V S A AA+ + + AIA +M Sbjct: 178 SGRMTD-IKKVVSHPQPLAQCRKWLEENLPDVPLVDVGSTALAAQMALEDESFGAIASEM 236 Query: 244 AAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPF 303 AA LYGL + E+IED P N TRFL+IG+ +G DKTS++ +++++PG L+ +L PF Sbjct: 237 AATLYGLQVVKERIEDNPNNFTRFLVIGTNTPERSGRDKTSLMFNIKDQPGILYRMLEPF 296 Query: 304 HSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363 I+L++IE+RP + W Y+FF+D GH D I + ++ LKVLGSYP+A Sbjct: 297 SKREINLSKIESRPMKKKAWEYIFFLDIEGHIDDEPITAAVTELRDYCQFLKVLGSYPRA 356 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: 323 Number of extensions: 11 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: 357 Length adjustment: 29 Effective length of query: 336 Effective length of database: 328 Effective search space: 110208 Effective search space used: 110208 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