Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate WP_092483748.1 BM299_RS10480 electron transfer flavoprotein subunit alpha/FixB family protein
Query= BRENDA::H6LBB1 (418 letters) >NCBI__GCF_900115975.1:WP_092483748.1 Length = 325 Score = 216 bits (550), Expect = 8e-61 Identities = 115/318 (36%), Positives = 188/318 (59%), Gaps = 6/318 (1%) Query: 72 RGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKYGVDKV 131 +GI V+ + +GQI VTFEL+ + R++A +G + A+L+G + + A L +YG DKV Sbjct: 3 KGIWVFAEQRDGQIKKVTFELLSEGRKIADQLGEELGAVLLGNGVADLAASLGEYGADKV 62 Query: 132 FVYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCT 191 +V D L+++ + Y NV+ D +++ PS +L+G T GR LA +VA R TGL DCT Sbjct: 63 YVADSDALENYTTDGYTNVIADLVKQYAPSVLLMGCTVTGRDLAAQVAQRLETGLMTDCT 122 Query: 192 ILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDI 251 +E+ + LV RP + G + + RP T+R F E E++++ Sbjct: 123 GMEIADG-QLVFTRPIYAGKAIVKAACPEARPVMATIRPNTFAVQAGAKE----AEIINV 177 Query: 252 EKAKLVSAIEVMEVIKK-EKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACT 310 + +++++ + +L+EA+ IV+ GRG+K ++ ++ E A+ +GA V + Sbjct: 178 TPNTGNIRQVIKDIVRQVSERPELTEADIIVSGGRGMKGPENFKLLEELADVLGAAVGAS 237 Query: 311 RPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIF 370 R ++AGW Q+G +G+TV P L IA GISGA+Q AGM +++ I+AIN D +A IF Sbjct: 238 RAAVDAGWIPQSFQVGQTGKTVSPVLYIACGISGAIQHLAGMSSAKCIVAINKDEEANIF 297 Query: 371 NIAHCGMVGDLYEILPEL 388 +A G+VGDL+E++P L Sbjct: 298 KVADYGIVGDLFEVVPIL 315 Lambda K H 0.319 0.137 0.395 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: 347 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: 418 Length of database: 325 Length adjustment: 30 Effective length of query: 388 Effective length of database: 295 Effective search space: 114460 Effective search space used: 114460 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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