Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate 7024199 Shewana3_1406 electron transfer flavoprotein, alpha subunit (RefSeq)
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__ANA3:7024199 Length = 308 Score = 134 bits (337), Expect = 4e-36 Identities = 91/296 (30%), Positives = 152/296 (51%), Gaps = 16/296 (5%) Query: 100 AAVIGHPVYALLMGTN---ITEKADELLKYGVDKVFVYDKPELKHFVIEPYANVLEDFIE 156 A IG V+ L++G + + A L GV +V V D + + E A +L D Sbjct: 25 ACAIGDDVHVLVVGHQCGAVAQAAQAL--QGVAQVLVADNSAYEAHLAENVAKLLVDLAP 82 Query: 157 KVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTILEMKENTDLVQIRPAFGGNIMAQI 216 S IL A++ G+ PRVAA ++ + + +RP + GN +A + Sbjct: 83 NY--SHILAAASSAGKDTLPRVAALLDVAQISEVIGVVSSDTF----VRPIYAGNALATV 136 Query: 217 VTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDIEKAKLVSAIEVMEVIKKEKGIDLSE 276 + + + TVR F A + N + ++K V + + +L Sbjct: 137 QSHDAI-KVMTVRASAFDAAAQGNS----AAVTTLDKVFEAKTQFVSQSLTVSARPELGN 191 Query: 277 AETIVAVGRGVKCEKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQIGLSGRTVKPKL 336 A IV+ GRG+ ++ M+ + A+K+GA V +R ++AG+ LQ+G +G+ V P L Sbjct: 192 AGIIVSGGRGMGSGENFGMLEQLADKLGAAVGASRAAVDAGFVPNDLQVGQTGKIVAPNL 251 Query: 337 IIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEILPELLTMI 392 IA+GISGA+Q AGM++++ I+AIN DP+APIF +A G+ DL++ +PEL++ + Sbjct: 252 YIAVGISGAIQHLAGMKDAKVIVAINKDPEAPIFQVADYGLEADLFDAVPELISTL 307 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: 289 Number of extensions: 12 Number of successful extensions: 2 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: 308 Length adjustment: 29 Effective length of query: 389 Effective length of database: 279 Effective search space: 108531 Effective search space used: 108531 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 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