Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate GFF3198 PS417_16375 2-hydroxyacid dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__WCS417:GFF3198 Length = 329 Score = 495 bits (1275), Expect = e-145 Identities = 246/327 (75%), Positives = 277/327 (84%) Query: 1 MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60 MR++ FSSQ YD +SF G EL FQ A L DT LA+ EVVCAF+NDDLS PV Sbjct: 1 MRVILFSSQTYDRDSFLGEPLPPGLELQFQPARLNLDTVALAEHHEVVCAFINDDLSAPV 60 Query: 61 LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120 LE LA GGTRL+ALRSAGYNHVDLA A+ LGL +V VPAYSPHAVAEHAV LIL LNRRL Sbjct: 61 LEHLAKGGTRLIALRSAGYNHVDLACAKRLGLTIVRVPAYSPHAVAEHAVALILALNRRL 120 Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPR 180 HRAYNRTR+GDFSLHGLTGFDL GK VGV+GTGQIG TFA+IMAGFGC+LLAYDP+PNP+ Sbjct: 121 HRAYNRTRDGDFSLHGLTGFDLVGKTVGVVGTGQIGATFAKIMAGFGCQLLAYDPFPNPQ 180 Query: 181 IQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNA 240 +QALG RY++L LLA++ I+SLHCPLTAD++HLI+A+ LA M+PGAMLINTGRG LV+ Sbjct: 181 VQALGTRYVSLPELLAQAQIISLHCPLTADSKHLINARSLAQMQPGAMLINTGRGGLVDT 240 Query: 241 AALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLT 300 ALIEALK GQLGYLGLDVYEEEA +FFEDRSD PLQDDVLARLL+FPNV++TAHQAFLT Sbjct: 241 PALIEALKDGQLGYLGLDVYEEEAQLFFEDRSDLPLQDDVLARLLTFPNVIITAHQAFLT 300 Query: 301 REALAAIADTTLDNIAAWQDGTPRNRV 327 REALAAIA TTL NIAAW DG +N V Sbjct: 301 REALAAIAGTTLANIAAWADGRAQNLV 327 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: 434 Number of extensions: 6 Number of successful extensions: 1 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: 329 Length adjustment: 28 Effective length of query: 301 Effective length of database: 301 Effective search space: 90601 Effective search space used: 90601 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 17 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