Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate RR42_RS04575 RR42_RS04575 electron transfer flavoprotein subunit beta
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Cup4G11:RR42_RS04575 Length = 311 Score = 133 bits (335), Expect = 6e-36 Identities = 99/296 (33%), Positives = 157/296 (53%), Gaps = 13/296 (4%) Query: 100 AAVIGHPVYALLMGTNITEKADELLKY-GVDKVFVYDKPELKHFVIEPYANVLEDFIEKV 158 AA G V+ L+ G N A K GV KV + D P+ + E NV E + Sbjct: 25 AAQCGGDVHVLVAGANAAAAAAAAAKIAGVSKVLLADAPQFADGLAE---NVAEQVLAIA 81 Query: 159 KP-SSILVGATNVGRSLAPRVAARYRTGLTADCTILEMKENTDLVQIRPAFGGNIMAQIV 217 S IL A+ G+++ PRVAA+ +D T ++ + + RP + GN ++ IV Sbjct: 82 SDYSHILAPASAYGKNILPRVAAKLDVAQLSDITKVDSPDTFE----RPIYAGNAIS-IV 136 Query: 218 TENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDIEKAKLVSAIEVMEVIKKEKGIDLSEA 277 + + + TVR F A + VE + +S EV K ++ +L+ A Sbjct: 137 QSSDKVKVITVRGTGFDAAA-ADGGSAAVENLPAVADAGISQFVSREVTKSDRP-ELTAA 194 Query: 278 ETIVAVGRGVKC-EKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQIGLSGRTVKPKL 336 + IV+ GRGV E ++ A+K+ A + +R ++AG+ Q+G +G+ V P+L Sbjct: 195 KIIVSGGRGVGSGENYTKVLTPLADKLNAAMGASRAAVDAGFVPNDYQVGQTGKIVAPQL 254 Query: 337 IIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEILPELLTMI 392 IA+GISGA+Q AGM++S+ I+AIN D +APIF++A G+VGDL ++PEL+ + Sbjct: 255 YIAVGISGAIQHLAGMKDSKVIVAINKDAEAPIFSVADYGLVGDLNTVVPELVAAL 310 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: 283 Number of extensions: 17 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: 311 Length adjustment: 29 Effective length of query: 389 Effective length of database: 282 Effective search space: 109698 Effective search space used: 109698 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