Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_027177588.1 G496_RS0100775 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000429985.1:WP_027177588.1 Length = 366 Score = 154 bits (389), Expect = 6e-42 Identities = 110/346 (31%), Positives = 185/346 (53%), Gaps = 18/346 (5%) Query: 262 KAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSK 321 K + + +R I S+D+ IL+L+ +R A+ + IK E I E+E L ++ + Sbjct: 5 KQKDMSSIREKIDSLDTEILKLLNQRASASICVGEIKAGSSEQIFKPFREKEVLTGLIER 64 Query: 322 TT--LNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLR 379 + L L+ I+ I+S ++ + + LGP+G+FS L+ +G + L+ Sbjct: 65 NSGPLPAEHLEAIYREIISSSRRLQRPER-----VVYLGPEGTFSYFAGLEYLGRQAELQ 119 Query: 380 YCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVA 439 + ++I V GE D G+VP+ENS+ GTV +D + + V + E ++H ++ Sbjct: 120 PRNNFEDIFVSVSKGESDLGIVPLENSLKGTVGQNVDLFMRYPVFIQAEVYSRISHGIMG 179 Query: 440 KRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML---DDYSAAIMS 496 + +L +IK +YSH +A+ QC G++ + LP ST+ AA M+ +D AA+ + Sbjct: 180 -QTADLSKIKYVYSHSKALEQCSGWLRSNLPKAEQISVDSTAKAAEMVSQGEDNCAAVGN 238 Query: 497 ENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK--ITSLFFGVEDKPGALKDV 554 A + L++L + I+D+ N TRF +I + G+ EGK TSL F D+PGAL V Sbjct: 239 VKLANIFGLNILAEAIEDMPD-NWTRFLIIGAKPGK-EGKRDKTSLLFTTPDRPGALVSV 296 Query: 555 LEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPL---REEDLLD 597 L V K N+ KLESRP Y+FFV+++ L +++ L+D Sbjct: 297 LNVLSGKDINMTKLESRPFLGEKWKYMFFVDLQGDLGAEKQKSLID 342 Lambda K H 0.320 0.137 0.380 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: 429 Number of extensions: 16 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: 620 Length of database: 366 Length adjustment: 33 Effective length of query: 587 Effective length of database: 333 Effective search space: 195471 Effective search space used: 195471 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: 51 (24.3 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