Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate SMc00728 SMc00728 electron transfer flavoprotein alpha-subunit alpha-ETF flavoprotein
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Smeli:SMc00728 Length = 309 Score = 142 bits (357), Expect = 2e-38 Identities = 103/324 (31%), Positives = 169/324 (52%), Gaps = 30/324 (9%) Query: 74 ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132 I + DH + T KA AA IG V+ L+ G N+ A++ K GV KV Sbjct: 3 ILLLADHDNSHLSDQT----AKALTAAAKIGGDVHVLVAGQNVKGIAEQASKLSGVAKVL 58 Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTI 192 V + L + + EP A ++ +++ AT+VG+++ PRVAA + Sbjct: 59 VAEDASLANNLAEPLAALIVSLAGNY--DTVVAAATSVGKNVMPRVAA-----------L 105 Query: 193 LEMKENTDLVQI-------RPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGD 245 L++ + ++++++ RP + GN + + T + + TVR F A + Sbjct: 106 LDVAQVSEIIEVVSADTYRRPIYAGNAIQTVQTSEPQ-KVITVRTASFAAAQEGGS--AP 162 Query: 246 VEMMDIEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGV-KCEKDLDMIHEFAEKIG 304 VE + +SA V + + +L+ A+ I++ GR + EK ++I A+K+G Sbjct: 163 VETVAAAANPGLSA-HVSDALSSSDRPELTSAKIIISGGRALGSSEKFKEVILPVADKLG 221 Query: 305 ATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSD 364 A V +R ++AG+ Q+G +G+ V P L IA GISGA+Q AGM++S+ I+AIN D Sbjct: 222 AAVGASRAAVDAGYAPNDWQVGQTGKVVAPDLYIACGISGAIQHLAGMKDSKVIVAINKD 281 Query: 365 PKAPIFNIAHCGMVGDLYEILPEL 388 +APIF +A G+V DL+E+LPEL Sbjct: 282 EEAPIFQVADYGLVADLFEVLPEL 305 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: 268 Number of extensions: 16 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: 309 Length adjustment: 29 Effective length of query: 389 Effective length of database: 280 Effective search space: 108920 Effective search space used: 108920 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