Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_083769300.1 AFER_RS11020 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000023265.1:WP_083769300.1 Length = 373 Score = 94.0 bits (232), Expect = 5e-24 Identities = 79/262 (30%), Positives = 119/262 (45%), Gaps = 17/262 (6%) Query: 5 VVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAVQGAD 64 V I G+G IG S AL L R G A I +++ RE AT AV A+ Sbjct: 58 VGIVGLGHIGASLALRLGRRGPLAVI---DEDPEAVAWVRER----TSATVGWDAVSAAE 110 Query: 65 LILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPAHPIA 124 +++VA P G +L ++ + +V D S K VV AA L + + HP+A Sbjct: 111 IVVVATPTPVVGDVLCALGER-GARGLVLDVASVKRPVVDAAPAGL-----RHLSVHPMA 164 Query: 125 GREKHGPEAALAELYEGKK---VVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHDA 181 GRE HG +A +++G V+ + ++D A GAV+ L HD Sbjct: 165 GREGHGAASADPSIWDGASWAFVLHGSESDDDVATALEFVFGDAGAGAVV-ALDATAHDE 223 Query: 182 VFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANRD 241 A VSHLPH+LA A+ + A + + RD TR+A S ++ + NRD Sbjct: 224 TLAVVSHLPHLLAAAMGRVLVADSGHPAAWWLGSGSLRDATRVARSDGARVAEMVVPNRD 283 Query: 242 ALLTEVDAYLLQLQNIRAMIAA 263 AL + + +L+ + A + A Sbjct: 284 ALTSAASVFRAELERLVADLEA 305 Lambda K H 0.320 0.132 0.376 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: 273 Number of extensions: 13 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: 295 Length of database: 373 Length adjustment: 28 Effective length of query: 267 Effective length of database: 345 Effective search space: 92115 Effective search space used: 92115 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 (21.9 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