Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_028950807.1 Q385_RS0106035 D-2-hydroxyacid dehydrogenase
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_000619805.1:WP_028950807.1 Length = 319 Score = 168 bits (426), Expect = 1e-46 Identities = 104/301 (34%), Positives = 171/301 (56%), Gaps = 15/301 (4%) Query: 14 IEVLKNAGFEVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRAGVG 73 + + ++ G+ VY ++ +E VKD + I++ +K + + V+ A LK+I A G Sbjct: 17 LNIFRDFGYLEVYPITKTKEETIERVKDKN-IVITNKVVIDKDVMNNAHYLKLICVAATG 75 Query: 74 LDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCM 133 +N+D+ A+++GI V N G S+ SV + ++F + + + D ++ G ++K Sbjct: 76 YNNVDIDYAKQKGIAVANVAGYSTNSVVQHTFAMLFYLLENLRYYDDYVKLGEYSKSPIF 135 Query: 134 GI------ELEGKTIGVVGFGRIGYQVAKIANALGMKVLFYDPY-PNEERAKEVGGKFAD 186 EL GKT G++G G IG +VA++A + G V++Y N +A G Sbjct: 136 THLDRPFWELNGKTWGIIGLGTIGKRVAQVAESFGCDVIYYSTSGKNINQAYPHKG---- 191 Query: 187 LETLLKESDVVTLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEG 246 L+ LL SDVV++H PL + T +LI +++KLMK TAIL+N RG +V+ L KAL EG Sbjct: 192 LDELLSISDVVSIHAPLNEYTKNLITYDKIKLMKKTAILLNLGRGGIVNEKDLAKALDEG 251 Query: 247 WIAGAGLDVFEEEPLPADHPLTKL---DNVVLTPHIGASTVEAQMRAGVEVAEKIVEALK 303 IAGAGLDV E+EP+ D+ L + D +++TPHI +++EA+ E+ I ++ Sbjct: 252 LIAGAGLDVLEKEPISPDNLLLHIKNKDRLLITPHIAWTSIEARQTLVKEIYLNIEAFIR 311 Query: 304 G 304 G Sbjct: 312 G 312 Lambda K H 0.317 0.136 0.378 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: 220 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: 304 Length of database: 319 Length adjustment: 27 Effective length of query: 277 Effective length of database: 292 Effective search space: 80884 Effective search space used: 80884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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