Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_041098940.1 SUTH_RS09870 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000828635.1:WP_041098940.1 Length = 297 Score = 331 bits (848), Expect = 1e-95 Identities = 162/284 (57%), Positives = 214/284 (75%), Gaps = 4/284 (1%) Query: 4 KVVIFGVGLIGGSFALALRRAGQAAH----IVGVGRSLQSLERARELGIIDAVATDAASA 59 K+VI GVGLIGGSFALAL+++ A +VG+GR+ LE+A++LG+IDA+ATD ASA Sbjct: 5 KIVICGVGLIGGSFALALKKSALALRRNLQVVGMGRTRAPLEQAQQLGVIDAIATDWASA 64 Query: 60 VQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIP 119 + GADL+L+ PV Q +++++APHL+P IVTD GSTKSDVVAAAR ALG++I QF+P Sbjct: 65 LDGADLVLLGMPVGQMPAVMSALAPHLQPHTIVTDGGSTKSDVVAAARAALGNKIGQFVP 124 Query: 120 AHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEH 179 HPIAG EK G AA ++LY K+VV+T LPEN A D++ V W CGA + +L+PQEH Sbjct: 125 GHPIAGAEKSGVAAAQSDLYVDKRVVLTPLPENSAGDLKAVRTVWELCGAKVSQLAPQEH 184 Query: 180 DAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLAN 239 D VFA+VSHLPH+LAFALV D A +P++ LF +AA GFRDFTRIA+S PEMWRDI +AN Sbjct: 185 DRVFAAVSHLPHLLAFALVHDFAQRPNSDQLFGFAAGGFRDFTRIASSHPEMWRDICIAN 244 Query: 240 RDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283 R ALL E+DAY+++L R ++A D G+E ++ +A+ R W Sbjct: 245 RQALLQELDAYMVELMRTRVLLAGADAAGLETLFLTARARRDAW 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: 277 Number of extensions: 10 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: 297 Length adjustment: 26 Effective length of query: 269 Effective length of database: 271 Effective search space: 72899 Effective search space used: 72899 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 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