Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_057509293.1 ABB28_RS14455 2-hydroxyacid dehydrogenase
Query= BRENDA::H9JRZ9 (432 letters) >NCBI__GCF_001431535.1:WP_057509293.1 Length = 334 Score = 118 bits (295), Expect = 3e-31 Identities = 85/269 (31%), Positives = 130/269 (48%), Gaps = 19/269 (7%) Query: 153 DALVVRSATQVTKEVLDA--GVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSA 210 DA+ V ++ VL A G+ ++ V AG +N+D+ +A + G V P + + Sbjct: 50 DAVCVFVNDRLDAPVLQALHGMGVRAVLLRCAGFNNVDLAAAERLGFFVARVPAYSPEAV 109 Query: 211 CELTCTLMLVLARHVVPASTALKAGRWDRALYTGSELAGKTLAILGLGRVGREVATRMYA 270 E T L++ L R A ++ G + G L GKT I+G G++G A ++ Sbjct: 110 AEHTLALIMTLNRQTHRAFNRVREGNFMLEGLLGRTLHGKTAGIVGTGKIGLATARILHG 169 Query: 271 FGMNIIGFDPFVSADQCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVLKQCK 330 G ++G DP+ S D + L+D+ +D ++LH PL TR+ IN D L K Sbjct: 170 MGCTVLGHDPYPSPDFAGLGEF--VSLQDLLARSDIVSLHCPLTIQTRHLINDDSLALMK 227 Query: 331 KGVKIINVGRGGLIQETDFLQALKSGKVGGAALDVFEQEPP-----------TDPVTLEI 379 G ++N RGGL+ ++ALKS ++G A+DV+EQE D V + Sbjct: 228 PGAMLVNTSRGGLVDTDAVIRALKSRQLGHLAIDVYEQESALFFQDRSGQIIDDDVFQRL 287 Query: 380 IQQPAVIATPHLGASTKEAQVRVGQEIAE 408 + P V+ T H G T EA QEIAE Sbjct: 288 MTFPNVLVTGHQGFFTTEAL----QEIAE 312 Lambda K H 0.320 0.135 0.387 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: 282 Number of extensions: 20 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: 432 Length of database: 334 Length adjustment: 30 Effective length of query: 402 Effective length of database: 304 Effective search space: 122208 Effective search space used: 122208 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: 50 (23.9 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