Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate GFF122 PGA1_c01240 electron transfer flavoprotein subunit alpha
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Phaeo:GFF122 Length = 308 Score = 128 bits (321), Expect = 3e-34 Identities = 93/304 (30%), Positives = 152/304 (50%), Gaps = 14/304 (4%) Query: 88 VTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVFVYDKPELKHFVIEP 146 + + KA A +G V L G + +E K GV KV V + L H + EP Sbjct: 14 LALDATAKAVTAAGKLGD-VTVLAAGASAAAAGEEAAKIAGVAKVLVAEDASLGHRLAEP 72 Query: 147 YANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTILEMKENTDLVQIRP 206 A ++ + I+ AT +++ PRVAA + +D + + + + RP Sbjct: 73 TAALIASLASDYE--HIVAPATTDAKNVLPRVAALLDVMVISDVSGVVDGDTFE----RP 126 Query: 207 AFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMDIEKAKLVSAIE-VMEV 265 + GN + Q V + + R F A G + I A+ E V + Sbjct: 127 IYAGNAV-QTVKSRDAKKVISFRTSTFDAAG----DGGSASVDTISAAENPGLSEWVEDK 181 Query: 266 IKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQI 325 + +L+ A +V+ GRGV E+D +I A+K+GA V +R +++G+ Q+ Sbjct: 182 VAASDRPELTSAGVVVSGGRGVGSEEDFKLIESLADKLGAAVGASRAAVDSGYAPNDWQV 241 Query: 326 GLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEIL 385 G +G+ V P+L +A+GISGA+Q AGM++S+ I+AIN D +APIF +A G+V DL++ + Sbjct: 242 GQTGKVVAPELYVAVGISGAIQHLAGMKDSKIIVAINKDEEAPIFQVADYGLVADLFQAV 301 Query: 386 PELL 389 PEL+ Sbjct: 302 PELI 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: 297 Number of extensions: 22 Number of successful extensions: 1 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