Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate Pf6N2E2_5719 D-lactate dehydrogenase (EC 1.1.1.28)
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5719 Length = 329 Score = 491 bits (1264), Expect = e-143 Identities = 246/327 (75%), Positives = 276/327 (84%) Query: 1 MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60 MR++FFSSQ YD +SF + G +L FQ A L DT LA+ EVVCAF+NDDLS PV Sbjct: 1 MRVIFFSSQTYDRDSFTKAPTPAGLQLQFQPARLNLDTVALAERHEVVCAFINDDLSAPV 60 Query: 61 LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120 LE+LA GGTRL+ALRSAGYNHVDL AA+ LGL +V VPAYSPHAVAEHAV LI+ LNR L Sbjct: 61 LEQLAEGGTRLIALRSAGYNHVDLLAAQRLGLSIVRVPAYSPHAVAEHAVALIMALNRCL 120 Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPR 180 HRAYNRTR+G+FSLHGLTGFDL GK VGVIGTGQIG TFARIMAGFGC+LLAYDPYPNP+ Sbjct: 121 HRAYNRTRDGNFSLHGLTGFDLVGKTVGVIGTGQIGATFARIMAGFGCQLLAYDPYPNPQ 180 Query: 181 IQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNA 240 ++ALG RYL L LLA++ I+SLHCPL +RHLI+AQ LA M+ GAMLINTGRG LV+ Sbjct: 181 VEALGARYLPLAELLAQAQIISLHCPLNEQSRHLINAQSLAAMQRGAMLINTGRGGLVDT 240 Query: 241 AALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLT 300 ALIEALKSGQLGYLGLDVYEEEA +FF+DRSD PLQDDVLARLL+FPNV+VTAHQAFLT Sbjct: 241 PALIEALKSGQLGYLGLDVYEEEAQLFFKDRSDLPLQDDVLARLLTFPNVIVTAHQAFLT 300 Query: 301 REALAAIADTTLDNIAAWQDGTPRNRV 327 EALAAIA TTLDNIAAW GTP+N V Sbjct: 301 HEALAAIAMTTLDNIAAWAAGTPQNLV 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: 424 Number of extensions: 8 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