Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate Pf1N1B4_5613 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5613 Length = 318 Score = 135 bits (341), Expect = 1e-36 Identities = 93/295 (31%), Positives = 157/295 (53%), Gaps = 10/295 (3%) Query: 100 AAVIGHPVYALLMGTNITEKADELLKY-GVDKVFVYDKPELKHFVIEPYANVLEDFI--E 156 AA IG ++ L+ G + A+ K GV KV V D + + E A ++ + + Sbjct: 30 AAKIGGDIHVLVAGAFVGSVAEAAAKIAGVAKVLVADNAAYAYQLPENVAPLVAGLVIEQ 89 Query: 157 KVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTILEMKENTDLVQIRPAFGGNIMAQI 216 + S +L AT+ G+++ PRVAA+ ++ +E + RP + GN +A Sbjct: 90 RTIYSHVLASATSNGKNILPRVAAQLDADQISEIISVESADTFK----RPIYAGNAIAT- 144 Query: 217 VTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDIEKAKLVSAIEVMEVIKKEKGIDLSE 276 V N + TVR F P VE + +S E+ K ++ +L+ Sbjct: 145 VQSNAAVKVITVRATGFD-PVAAEGGSAAVEAVAAAHDAGISTFVGEELAKSDRP-ELTA 202 Query: 277 AETIVAVGRGVKCEKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQIGLSGRTVKPKL 336 A+ +V+ GRG++ + ++ A+K+GA V +R ++AG+ +Q+G +G+ V P+L Sbjct: 203 AKIVVSGGRGMQNGDNFKHLYALADKLGAAVGASRAAVDAGFVPNDMQVGQTGKIVAPQL 262 Query: 337 IIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEILPELLTM 391 IA+GISGA+Q AGM++S+ I+AIN D +APIF +A G+V DL+E +PE+ + Sbjct: 263 YIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQVADYGLVADLFEAIPEMAAL 317 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: 298 Number of extensions: 15 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: 318 Length adjustment: 29 Effective length of query: 389 Effective length of database: 289 Effective search space: 112421 Effective search space used: 112421 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