Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_015739145.1 ADEG_RS05810 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000024605.1:WP_015739145.1 Length = 367 Score = 219 bits (557), Expect = 1e-61 Identities = 125/283 (44%), Positives = 167/283 (59%), Gaps = 2/283 (0%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60 M KVVI GVGLIGGS LALRR G+A +VG+GRS + L +A+ LG +D+ TD A V Sbjct: 1 MLGKVVIVGVGLIGGSLGLALRRRGKAREVVGIGRSAERLRQAQALGAVDSFTTDLAEGV 60 Query: 61 QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120 +GADL++VA P+ P + ++APHLEP +VTD GSTK ++V AA F+ Sbjct: 61 RGADLVVVATPIGIIVPTMHALAPHLEPGTVVTDVGSTKREIVEAAERLAAKHSFAFVGG 120 Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180 HP+AG E+ G E A L+E ++T P+ + VA A GA + P HD Sbjct: 121 HPMAGSERTGVENADPYLFENAYYILTPTPKTPPEAISRVAELVEAVGARKVEIPPDLHD 180 Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240 A+VSHLPH LA AL + IA+ P + AA GFRD TR+AA P +WRDI L N Sbjct: 181 YYVAAVSHLPHCLASALCNLIASLPEKEAILPLAAGGFRDTTRVAAGDPVLWRDILLTN- 239 Query: 241 DALLTEVDAYLLQ-LQNIRAMIAAGDGPGIEKIYASAQHARQQ 282 A L E+ A LL+ LQ + ++A D G+E+ AQ R++ Sbjct: 240 TAPLRELLALLLRVLQELEELLAKKDARGLEEWLRRAQILRKE 282 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: 299 Number of extensions: 13 Number of successful extensions: 1 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: 367 Length adjustment: 28 Effective length of query: 267 Effective length of database: 339 Effective search space: 90513 Effective search space used: 90513 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