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_019556286.1 F612_RS0103095 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000381085.1:WP_019556286.1 Length = 363 Score = 187 bits (474), Expect = 9e-52 Identities = 124/365 (33%), Positives = 205/365 (56%), Gaps = 21/365 (5%) Query: 260 TKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVM 319 T + + E+R I +ID+ I LI +R A+++A IK + G+ ++ E+ +V+ Sbjct: 2 TTEQMQLTEIRNQIDTIDAQIQDLIGQRAACAQKVADIKTQ-GDNVDAVFYRPEREAQVL 60 Query: 320 S-----KTTLNP-VKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVG 373 T+L P ++ ++F IMS E T+A LGP+GS+S +K G Sbjct: 61 RAVKARNTSLLPDEEMAKLFREIMSACLALEQPT-----TVAYLGPEGSYSHASVIKQFG 115 Query: 374 SRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEV 433 S V ST +E+ + VE G+ YG+VP+ENS G V +AL+ D++V GE LE+ Sbjct: 116 SSVHSIAVSTIEEVFEAVEKGDASYGMVPVENSSEGVVKSTQNALVTTDLKVSGEVALEI 175 Query: 434 NHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM--LDDYS 491 +HCL++K K ++ I I +H QA+ QC +I N LP I S + AA+M D Sbjct: 176 HHCLLSKSK-TVENIHKIVAHQQALGQCEQWIKNNLPWAEIEAVASNALAAKMAKTDSAV 234 Query: 492 AAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK-ITSLFFGVEDKPGA 550 AAI SE AA+ Y+L++L I+D + N T+F+++ R + +S G+ T++ ++++ GA Sbjct: 235 AAIASEQAAQLYQLNILESHIED-QSDNSTKFWVVGRDATQSSGEDKTAMIVSMKNQSGA 293 Query: 551 LKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYK 606 L D+L F +G N+ ++ SRP+ DY FF++V +E+ L ++K + F+K Sbjct: 294 LLDILSCFSSRGINMTRIISRPSLDTTWDYQFFIDVMGHQEDENLKQALAEVKSKSAFFK 353 Query: 607 VVGVF 611 ++G F Sbjct: 354 LLGSF 358 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: 393 Number of extensions: 14 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: 620 Length of database: 363 Length adjustment: 33 Effective length of query: 587 Effective length of database: 330 Effective search space: 193710 Effective search space used: 193710 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 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