Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate PP_4201 PP_4201 Electron transfer flavoprotein subunit alpha
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Putida:PP_4201 Length = 309 Score = 142 bits (357), Expect = 2e-38 Identities = 105/321 (32%), Positives = 165/321 (51%), Gaps = 16/321 (4%) Query: 74 ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132 I V ++ G + P T + A A IG V+ L+ G N+ A+ K GV KV Sbjct: 3 ILVVAEYEAGAVAPATLNTVAAA----AKIGGDVHVLVAGQNVGGVAESAAKIAGVAKVL 58 Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKP-SSILVGATNVGRSLAPRVAARYRTGLTADCT 191 V D H + E NV +E K S +L AT G+++ PRVAA ++ Sbjct: 59 VADNAAYAHVLPE---NVAPLIVELAKGYSHVLAPATTNGKNILPRVAALLDVDQISEII 115 Query: 192 ILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDI 251 +E + RP + GN +A V + + TVR F A VE + Sbjct: 116 SVESADTFK----RPIYAGNAIAT-VQSSAAIKVITVRTTGFDAVAAEGGS-AAVEAVGA 169 Query: 252 EKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACTR 311 +SA E+ K ++ +L+ A+ +V+ GRG+ + ++ A+K+GA V +R Sbjct: 170 AHNAGISAFVGEELAKSDRP-ELTAAKIVVSGGRGMGNGDNFKHLYSLADKLGAAVGASR 228 Query: 312 PGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFN 371 ++AG+ +Q+G +G+ V P+L IA+GISGA+Q AGM++S+ I+AIN D +APIF Sbjct: 229 AAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQ 288 Query: 372 IAHCGMVGDLYEILPELLTMI 392 +A G+V DL+E +PEL ++ Sbjct: 289 VADYGLVADLFEAVPELEKLV 309 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: 307 Number of extensions: 18 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