Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate SMa0819 SMa0819 FixB electron transfer flavoprotein alpha chain
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Smeli:SMa0819 Length = 353 Score = 231 bits (588), Expect = 3e-65 Identities = 122/324 (37%), Positives = 183/324 (56%), Gaps = 6/324 (1%) Query: 71 YRGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGT----NITEKADELLKY 126 YR + V+++ GQ+HPV+ EL+G+ R+LA +G + +++G + Y Sbjct: 12 YRNVWVFIELEHGQVHPVSIELLGEGRKLADKLGVHLAGVVIGPPGGQGTANAIADAFAY 71 Query: 127 GVDKVFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGL 186 G D ++ + P L H+ EP+ L D + KP +L+GAT +GR LA VA +TGL Sbjct: 72 GADLSYLVESPLLAHYRNEPFTKALTDLVLANKPEILLLGATTLGRDLAGSVATTLKTGL 131 Query: 187 TADCTILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDV 246 TADCT L + + L RP FGG+++ I T RPQ TVR V P+RVN P G + Sbjct: 132 TADCTELNVDSDGSLAATRPTFGGSLLCTIYTLKCRPQMATVRPSVMATPQRVNRPTGSI 191 Query: 247 EMMDIEKAKLVSAIEVMEVIKKEKGI--DLSEAETIVAVGRGVKCEKDLDMIHEFAEKIG 304 D++ + A +V+ +L+ A+ +VA G G+ ++L ++ + A +G Sbjct: 192 IRHDLKMLEEEIATKVLAFFSDCDSTIANLAYADVVVAGGLGLGAVQNLQLLKDLARTLG 251 Query: 305 ATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSD 364 C+RP ++ GW QIG +G T++PKL IA GISGAVQ G++ S+ I+AIN+D Sbjct: 252 GDFGCSRPLVQKGWMPFDRQIGQTGNTIRPKLYIAAGISGAVQHRVGVEGSDLIVAINTD 311 Query: 365 PKAPIFNIAHCGMVGDLYEILPEL 388 P APIF+ AH G+V D LP L Sbjct: 312 PNAPIFDFAHLGVVADAISFLPAL 335 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: 362 Number of extensions: 13 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: 353 Length adjustment: 30 Effective length of query: 388 Effective length of database: 323 Effective search space: 125324 Effective search space used: 125324 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