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_025273042.1 HALAL_RS0105495 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000527155.1:WP_025273042.1 Length = 319 Score = 143 bits (360), Expect = 7e-39 Identities = 100/276 (36%), Positives = 140/276 (50%), Gaps = 17/276 (6%) Query: 97 VAYLGPEGTFSQAA------ALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENST 150 + YLGP GTF++AA + +H H V PMA+I +V + G V+ G VP+ENS Sbjct: 3 IGYLGPSGTFTEAALHDLPDSERH--HPV---PMASIPDVLDALHNGEVDAGFVPLENSH 57 Query: 151 EGAVNHTLDSFLEHD-IVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLD 209 EG VN TLD L D +VI EV+ + L KT + I SH +LAQ R +L Sbjct: 58 EGTVNPTLDRLLHGDPVVITAEVDYPVSFVLATATPNKT--VGTIASHPHALAQVRGFLR 115 Query: 210 AHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLI 269 + +P + S A A V+ A + G + L I D P +TRF++ Sbjct: 116 SSFPEARIIETLSTAAGADAVRKSEADACVCGPHTTEQSDLVIRYHDIGDNPNAATRFVL 175 Query: 270 IGSQEVP--PTGDDKTSIIVSMRN-KPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYV 326 + P PTG D TS+ V +R+ + GAL +L F GI+LT+IE+RP+ G Y Sbjct: 176 LRRPTPPAEPTGHDVTSLAVFLRHDQVGALVTVLQQFAERGINLTKIESRPTGEGLGHYT 235 Query: 327 FFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362 F +DC GH D I + L I ++ LGSY + Sbjct: 236 FLLDCTGHLHDARIGDALAGIKRSGAGVRYLGSYER 271 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: 299 Number of extensions: 12 Number of successful extensions: 5 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: 319 Length adjustment: 29 Effective length of query: 336 Effective length of database: 290 Effective search space: 97440 Effective search space used: 97440 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