Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_068463039.1 APY04_RS11295 NAD-dependent formate dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_001541235.1:WP_068463039.1 Length = 401 Score = 145 bits (365), Expect = 2e-39 Identities = 88/243 (36%), Positives = 141/243 (58%), Gaps = 7/243 (2%) Query: 54 ITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLM 113 +T E L+ A++LK+ G D++DL+ A K G+ V +V+ S +VAE V +I++L+ Sbjct: 104 LTEERLKKAKKLKLAITAGIGSDHVDLDAAMKNGVTVAEVTYSNSISVAEHVVMMILSLV 163 Query: 114 RKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLY 173 R + +++++G W I +R L G VG +G G IG A+ RRL PF VKL+ Sbjct: 164 RNYLPSYEWVKKGGWN----IADCVERSYDLEGMNVGTVGAGRIGLAVLRRLKPFDVKLH 219 Query: 174 YWSRHR-KVNVEKELKARY-MDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE-GKY 230 Y RHR VEKEL Y D++ L++ D+V + PL +T H+ + + + K++ G Y Sbjct: 220 YTDRHRLPKEVEKELGLIYHKDVESLVKVCDVVTINAPLHSETEHLFDAKMISKMKHGAY 279 Query: 231 LVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLAL 290 L+N R +VD AV +A++ G+L GYA DV+ +P + ++ +TPH +G +L Sbjct: 280 LINTARAKIVDRDAVVKALESGQLAGYAGDVWFPQPAPKDHPWRKMPHHGMTPHISGTSL 339 Query: 291 EAQ 293 AQ Sbjct: 340 SAQ 342 Lambda K H 0.319 0.139 0.393 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: 316 Number of extensions: 19 Number of successful extensions: 4 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: 333 Length of database: 401 Length adjustment: 30 Effective length of query: 303 Effective length of database: 371 Effective search space: 112413 Effective search space used: 112413 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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