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 CA265_RS11630 CA265_RS11630 prephenate dehydratase
Query= SwissProt::P57472 (385 letters) >FitnessBrowser__Pedo557:CA265_RS11630 Length = 277 Score = 136 bits (342), Expect = 8e-37 Identities = 79/266 (29%), Positives = 141/266 (53%), Gaps = 5/266 (1%) Query: 110 GPKGSYSHIAAYKYADLNFQKCITNECSTFEEVVLSVENNQSDYAVLPIENTCSGSINEV 169 G K S+ AAYK+ + + T EC++F+E +E N +D+ V+ IEN+ +GS+ Sbjct: 11 GIKASFHEEAAYKFFGKDIE---TVECNSFKETCDKLEKNDADFVVMAIENSIAGSLLPN 67 Query: 170 FDILKKTNLFIIGEINIFINHNLLTLKKIELNKIKTIYSHPQPFQQCSDFIKKFPEWKIK 229 + +++ ++GE+ + I +L+ L ++ IK + SHP +QC DF +P KI Sbjct: 68 YTLIRDFGFSVVGEVYLPIQLHLMALPGVKFEDIKVVTSHPIAIRQCIDFFYDYPHIKIV 127 Query: 230 YTKSTADAMKKIKKYNDVTNAALGSEIGSKIYGLEILMKNLANKENNITRFILLNRNPKK 289 + TA K+I++ A+ + + +++Y L IL + + + + N TRF++L ++ Sbjct: 128 ESNDTAACAKRIQEEQLTDTMAIANSLAAELYSLNILERRVESNKKNYTRFLILKKDKTD 187 Query: 290 ISKNIPTTTTLIFTTGQEAGSLSKVLSILQEKKLIMKKLTSQKIYKNPWEEMFYIDIQVN 349 K I ++ F G +AGSL+ VL+I E+ + + K+ S + E FY+D++ Sbjct: 188 EGKKI-NKASICFQVGHKAGSLATVLNIFAEQDVSLTKIQSMPVLGKRNEYYFYVDLEWP 246 Query: 350 LSSTLMQDALEKIKKITRFIKILGCY 375 S+ A+ K K T ILG Y Sbjct: 247 -STEKYDKAIRKALKYTSNFNILGEY 271 Lambda K H 0.318 0.134 0.374 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: 258 Number of extensions: 8 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: 385 Length of database: 277 Length adjustment: 28 Effective length of query: 357 Effective length of database: 249 Effective search space: 88893 Effective search space used: 88893 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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