Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate 351333 BT1805 electron transfer flavoprotein alpha-subunit (NCBI ptt file)
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Btheta:351333 Length = 339 Score = 202 bits (513), Expect = 2e-56 Identities = 123/326 (37%), Positives = 189/326 (57%), Gaps = 12/326 (3%) Query: 76 VYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKYGVDKVFVYD 135 VY + EG + V+ EL+ K R LA + + A++ GT + E ++L YGVDK+ V+D Sbjct: 6 VYCEIEEGIVADVSLELLTKGRSLANELNCQLEAVVAGTGLKEIEKQILPYGVDKLHVFD 65 Query: 136 KPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTILEM 195 L + P+ ++L + ++ +P L+GAT +GR L PRV++ +GLTADCT LE+ Sbjct: 66 AEGLYPYTSLPHTSILVNLFKEEQPQICLMGATVIGRDLGPRVSSALTSGLTADCTSLEI 125 Query: 196 KENTD----------LVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGD 245 ++ D L QIRPAFGGNI+A IV RPQ TVR V G+ Sbjct: 126 GDHEDKKEGKVYKNLLYQIRPAFGGNIVATIVNPEHRPQMATVREGVMKKEIVSPAYQGE 185 Query: 246 VEMMDIEK--AKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKI 303 V D++K A ++V+E ++ +L + I+A G GV +++ D++ A+++ Sbjct: 186 VIRHDVKKYVADTDYVVKVIERHVEKAKNNLKGSPIIIAGGYGVGSKENFDLLFSLAKEL 245 Query: 304 GATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINS 363 A V +R ++AG+ + QIG +G TV+PKL IA GISG +Q AGMQ S II+IN+ Sbjct: 246 HAEVGASRAAVDAGFAEHDRQIGQTGVTVRPKLYIACGISGQIQHIAGMQESGIIISINN 305 Query: 364 DPKAPIFNIAHCGMVGDLYEILPELL 389 DP API IA + G + E++P+++ Sbjct: 306 DPDAPINTIADYVINGTIEEVVPKMI 331 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: 387 Number of extensions: 23 Number of successful extensions: 3 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: 339 Length adjustment: 30 Effective length of query: 388 Effective length of database: 309 Effective search space: 119892 Effective search space used: 119892 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: 50 (23.9 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