Align prephenate dehydrogenase (NADP+) (EC 1.3.1.13) (characterized)
to candidate WP_093395041.1 BM091_RS08660 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= BRENDA::A0A101IGG2 (310 letters) >NCBI__GCF_900114975.1:WP_093395041.1 Length = 309 Score = 157 bits (397), Expect = 3e-43 Identities = 97/282 (34%), Positives = 149/282 (52%), Gaps = 11/282 (3%) Query: 15 IVGGTGGTGSWFAKYFKEHGFLVSIWGPSGKVEVAERLGVKFARDLMAEVAKSDVVLLSV 74 I+GG G G +FA+ F + G+ V + S V +G + + + + +SD+VL SV Sbjct: 16 IIGGLGEMGQFFARLFSKRGYRVLV---SDVVLKKNHVGTPVSSEEIFQ--QSDIVLFSV 70 Query: 75 PIKETAKVVEEVAPRMRPGSLLMDVTSLKAEPMKAMLRWAPDGVEVLGTHPMFGPTIPTI 134 P+ T +++E APR L+MDV+SLK +P+KAML+ V+G HPMFG ++ Sbjct: 71 PLHRTVEIIESYAPRFGKDQLVMDVSSLKVQPIKAMLKGV---ASVVGLHPMFGGSVRNA 127 Query: 135 RGQTVILVPAAGRCDEWLLPMEEIFQEDGARVEVLGAEEHDRIMAVVQALTHFAYISIGS 194 GQT++ P + WL+ E+ +E G +V E HDR+MAV+Q L H + G Sbjct: 128 CGQTLVACPVRVDREGWLVVKEQFLRE-GLKVVECSPEHHDRMMAVIQVLFHLCTMLKGR 186 Query: 195 TLRSLDFDIAHSRRLMSPVYEIMIDFVGRILAQSPELYSSI-QENPEAKRVREAYIEECQ 253 +R + DI + R SPVY + I +GR+ AQ+P LY++I Q NP + + +E Sbjct: 187 VIREMGIDIEETLRFTSPVYRLEISILGRMFAQNPWLYAAISQLNPHTGEIIDHLLEGLS 246 Query: 254 RLSKLADTGNSEGFMEAMRSAADHF-DEREVALARSDRLISL 294 + G E F+E R A H D A S +L+ + Sbjct: 247 LFREYYRKGALEKFVEEFRDTATHLGDFCNRAFEESSQLVEI 288 Lambda K H 0.320 0.135 0.399 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: 225 Number of extensions: 14 Number of successful extensions: 5 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: 310 Length of database: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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: 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