Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_006747659.1 THITH_RS07705 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000227685.2:WP_006747659.1 Length = 293 Score = 241 bits (615), Expect = 1e-68 Identities = 121/288 (42%), Positives = 178/288 (61%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60 M +++VIFGVGLIGGS ALALR AG +VG R+ +LE A+ LG+ID TD A Sbjct: 1 MIQRLVIFGVGLIGGSLALALREAGAVGEVVGCSRNPANLEEAQRLGVIDRWTTDPVEAC 60 Query: 61 QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120 + AD+ ++A P+ + A++A H A++TD GS+K V+ A R G F+ Sbjct: 61 RDADVGVLAVPLGSMQGLAAALAGHWPKDALLTDVGSSKQAVIEAVRSGFGQLPRNFVAG 120 Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180 HPIAG EK G AA L+ + V++T E + + + + WRA GA + ++P HD Sbjct: 121 HPIAGTEKSGVAAAFPSLFRNRLVILTPADETNPIAADRIGSMWRAAGARVEFMTPAHHD 180 Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240 V A+ SHLPHVLA+ALV+ +A + + +F YAA GFRDFTRIA+S P +WRDI +ANR Sbjct: 181 HVLAATSHLPHVLAYALVESLARRSESDEIFHYAAGGFRDFTRIASSDPVVWRDICVANR 240 Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWAAAIE 288 DA+L ++ + L ++R +I GD P +E + A+ AR +++ ++ Sbjct: 241 DAILDVLERFQRDLDSLREVIVRGDAPTLEARFRYAKQARDRFSEKMQ 288 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: 234 Number of extensions: 9 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: 293 Length adjustment: 26 Effective length of query: 269 Effective length of database: 267 Effective search space: 71823 Effective search space used: 71823 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: 48 (23.1 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