Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_057509293.1 ABB28_RS14455 2-hydroxyacid dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >NCBI__GCF_001431535.1:WP_057509293.1 Length = 334 Score = 357 bits (915), Expect = e-103 Identities = 184/326 (56%), Positives = 227/326 (69%), Gaps = 5/326 (1%) Query: 1 MRILFFSSQAYDSESFQASNHR----HGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDL 56 M++ FS++ YDS S +N + HG E + A L TA LAQG + VC FVND L Sbjct: 1 MKVAVFSARPYDSRSLDEANQQAGAAHGVEFLYYDATLDVHTAALAQGCDAVCVFVNDRL 60 Query: 57 SRPVLERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTL 116 PVL+ L G R V LR AG+N+VDLAAAE LG V VPAYSP AVAEH + LI+TL Sbjct: 61 DAPVLQALHGMGVRAVLLRCAGFNNVDLAAAERLGFFVARVPAYSPEAVAEHTLALIMTL 120 Query: 117 NRRLHRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPY 176 NR+ HRA+NR REG+F L GL G LHGK G++GTG+IG ARI+ G GC +L +DPY Sbjct: 121 NRQTHRAFNRVREGNFMLEGLLGRTLHGKTAGIVGTGKIGLATARILHGMGCTVLGHDPY 180 Query: 177 PNPRIQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGA 236 P+P L G +++L LLA SDIVSLHCPLT TRHLI+ LA MKPGAML+NT RG Sbjct: 181 PSPDFAGL-GEFVSLQDLLARSDIVSLHCPLTIQTRHLINDDSLALMKPGAMLVNTSRGG 239 Query: 237 LVNAAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQ 296 LV+ A+I ALKS QLG+L +DVYE+E+ +FF+DRS Q + DDV RL++FPNV+VT HQ Sbjct: 240 LVDTDAVIRALKSRQLGHLAIDVYEQESALFFQDRSGQIIDDDVFQRLMTFPNVLVTGHQ 299 Query: 297 AFLTREALAAIADTTLDNIAAWQDGT 322 F T EAL IA+TTL N+ + GT Sbjct: 300 GFFTTEALQEIAETTLGNLGHFAAGT 325 Lambda K H 0.323 0.137 0.402 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: 16 Number of successful extensions: 3 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: 329 Length of database: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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