Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate YP_004140865.1 Mesci_1660 NAD-binding D-isomer specific 2-hydroxyacid dehydrogenase protein
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000185905.1:YP_004140865.1 Length = 326 Score = 141 bits (355), Expect = 3e-38 Identities = 89/282 (31%), Positives = 154/282 (54%), Gaps = 14/282 (4%) Query: 47 IVSPTTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTV 106 IV + ++ + A+ L+ H AG D I +E AT G+ V V + + +VAE + Sbjct: 44 IVIVRAPLPPQLFDGAKLLRAAIRHGAGLDMIPMEAATAAGVLVANVPAVNARSVAEHVM 103 Query: 107 GLIINLMRKIHYADKFIRRGEW---ESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIAR 163 + + L+R D+ +R W HA + L GK +GI+G+GA+G+A+ Sbjct: 104 FVALALLRNFRVVDRDLRAKGWLAGREHANANS------ELAGKTIGIVGLGAVGQAVGH 157 Query: 164 RLIPFGVKLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERV 223 + G L + R + + K ++ ID L+E+SDI++L PLT +T +IN ER+ Sbjct: 158 -IAAHGFDLKVVATTRSMQPAPD-KVGFLSIDALVEQSDIIVLCCPLTPETRGLINRERI 215 Query: 224 KKLEGK-YLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPV-REHELFKYEWETVL 281 +++ + L+N+ RG +VD+ A+ EA+++ ++ G A DVF +P+ H F ++ ++ Sbjct: 216 ARMKPQALLINVSRGPVVDDDALIEALQKRRIGGAALDVFATQPLPSNHPYFGFD-NVIV 274 Query: 282 TPHYAGLALEAQEDVGFRAVENLLKVLRGEVPEDLVNKEVLE 323 TPH AG+ E+ +G A L VL G++P +L N EV++ Sbjct: 275 TPHMAGITEESMMRMGVGAAGEALLVLAGKLPVNLRNPEVVD 316 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: 222 Number of extensions: 11 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: 326 Length adjustment: 28 Effective length of query: 305 Effective length of database: 298 Effective search space: 90890 Effective search space used: 90890 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 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