Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate GFF3991 Psest_4064 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__psRCH2:GFF3991 Length = 329 Score = 488 bits (1256), Expect = e-143 Identities = 248/327 (75%), Positives = 270/327 (82%) Query: 1 MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60 MRI FSS+AYD +SF A+N HGF+LHF + L DTA LA G EVVC FVND LS PV Sbjct: 1 MRITLFSSKAYDRDSFLAANQAHGFDLHFLETRLDPDTAALAAGAEVVCPFVNDVLSAPV 60 Query: 61 LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120 LERLAAGGTRL+ALRSAGYNHVDL A+ LGLPVV VPAYSPHAVAEH V LIL LNRRL Sbjct: 61 LERLAAGGTRLIALRSAGYNHVDLPCAKRLGLPVVRVPAYSPHAVAEHTVALILALNRRL 120 Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPR 180 RAYNR REG+FSL GLTGFDL GKRVGV+G+GQIG FARIM GFGCE+ YDPYPNP Sbjct: 121 PRAYNRIREGNFSLQGLTGFDLVGKRVGVVGSGQIGAVFARIMLGFGCEVQLYDPYPNPE 180 Query: 181 IQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNA 240 ++ LG RY+ALD LLA SDIVSLHCPLTA T HLI+ Q LATMKP AMLINTGRGAL++ Sbjct: 181 LERLGMRYVALDELLASSDIVSLHCPLTAQTHHLINQQSLATMKPRAMLINTGRGALIDT 240 Query: 241 AALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLT 300 ALI ALKSGQLGYLGLDVYEEEA +FFED S PLQDDVLARLLSFPNV+VTAHQAFLT Sbjct: 241 PALIGALKSGQLGYLGLDVYEEEAGLFFEDHSGLPLQDDVLARLLSFPNVIVTAHQAFLT 300 Query: 301 REALAAIADTTLDNIAAWQDGTPRNRV 327 EAL+AIA TTL N+AAWQ G N+V Sbjct: 301 EEALSAIAGTTLGNVAAWQAGQTSNQV 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: 404 Number of extensions: 12 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