Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_019864113.1 METMI_RS0100120 phosphoglycerate dehydrogenase
Query= BRENDA::F8A9V0 (325 letters) >NCBI__GCF_000384075.1:WP_019864113.1 Length = 527 Score = 155 bits (391), Expect = 3e-42 Identities = 94/242 (38%), Positives = 134/242 (55%), Gaps = 20/242 (8%) Query: 63 LHS-YGVGLLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHR 121 LHS + L+ G D++DI A LGI V+N P + A+ +A +++L R L Sbjct: 60 LHSAVNLKLIGRAGIGVDNVDIPLATELGIIVMNTPDANATTTAELAIAHLMSLSRHLPA 119 Query: 122 AHDKVRLGDFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI- 180 A VR G ++ LMG ++ K G++G G IGR+V+ R +V+ YDP++ PEI Sbjct: 120 ADRSVRAGKWERSKLMGTEVAHKTLGIVGFGTIGRIVSQRGVGLKMEVIAYDPFVAPEIF 179 Query: 181 ----VENVDLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTK 236 VE+V LD L+++AD I++HCPL + H+ + MK +++N ARGGLID Sbjct: 180 TELGVESVSLDDLVSRADYITLHCPLIEKTRHIIGGKQLALMKKETMVINCARGGLIDET 239 Query: 237 ALLEALKSGKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTR 296 AL EALK+G++ GAALDVYE E P + LL L N+V T H T Sbjct: 240 ALYEALKNGQIAGAALDVYENE--------------PPAGSPLLALDNIVFTPHLGASTI 285 Query: 297 EA 298 EA Sbjct: 286 EA 287 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: 363 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: 325 Length of database: 527 Length adjustment: 31 Effective length of query: 294 Effective length of database: 496 Effective search space: 145824 Effective search space used: 145824 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 Sep 24 2021. 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