Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_011938637.1 GURA_RS08815 phosphoglycerate dehydrogenase
Query= BRENDA::F8A9V0 (325 letters) >NCBI__GCF_000016745.1:WP_011938637.1 Length = 541 Score = 160 bits (404), Expect = 9e-44 Identities = 95/249 (38%), Positives = 140/249 (56%), Gaps = 16/249 (6%) Query: 70 LLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG 129 ++A G D++DI+ A G+ VVN P + ++ A+H +A++L+ R + +A+ ++ G Sbjct: 67 MVARAGVGIDNVDIDYASSKGVIVVNAPFGNTNSAAEHAMALLLSFCRNITKANASLKSG 126 Query: 130 DFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI-----VENV 184 ++ G +L GK AGVIGLGK+G VATRLKAF C VLG DPYI + V+ V Sbjct: 127 EWKRAPFTGVELKGKTAGVIGLGKVGGRVATRLKAFECDVLGCDPYIAVKRAHDLGVKLV 186 Query: 185 DLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKS 244 + + DII+ H PL E +M E+ MK G IL+N ARGG+I+ +ALL ALK Sbjct: 187 SHEEIYKNCDIITFHTPLNEETRNMVGEKEIAMMKDGVILINAARGGIINEQALLNALKG 246 Query: 245 GKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEE 304 GK+ GAA+DV+ +E K L +L+ +V+T H T EA N+ Sbjct: 247 GKVFGAAMDVW-----------SEEPPKSETLKELISQDKLVVTPHLGANTFEAQINVAV 295 Query: 305 TTVENILEW 313 + IL + Sbjct: 296 DVSKEILNY 304 Lambda K H 0.321 0.140 0.407 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: 375 Number of extensions: 17 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: 325 Length of database: 541 Length adjustment: 32 Effective length of query: 293 Effective length of database: 509 Effective search space: 149137 Effective search space used: 149137 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 09 2024. The underlying query database was built on Sep 17 2021.
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