Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate HSERO_RS14225 HSERO_RS14225 protein fixB
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__HerbieS:HSERO_RS14225 Length = 364 Score = 228 bits (582), Expect = 2e-64 Identities = 132/347 (38%), Positives = 201/347 (57%), Gaps = 14/347 (4%) Query: 49 KKGPEGVLILEEDEKVAIDKSLYRGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVY 108 +KG +G L+E K Y+G+ V+++H G++HPV++EL+G+ R+LA +G + Sbjct: 10 RKGGKGKYELDERLKA------YQGVWVFIEHERGEVHPVSWELLGEGRKLADQLGVSLS 63 Query: 109 ALLMGTN---ITEKADELLKYGVDKVFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILV 165 +++G + ++ +G D ++ P L + +P+ L D + + +P +L+ Sbjct: 64 GVVLGAPDLATRQFCEQAFHHGADSCYLMADPTLSAYRNQPFTKGLTDLVNRYQPEILLL 123 Query: 166 GATNVGRSLAPRVAARYRTGLTADCTILEMK-ENTDLVQIRPAFGGNIMAQIVTENTRPQ 224 GAT GR LA VA +TGLTADCT L + EN + RP FGG+++ I+T N RPQ Sbjct: 124 GATAQGRDLAGSVATTLKTGLTADCTGLTIDMENRSMAASRPTFGGSLLCTILTLNYRPQ 183 Query: 225 FCTVRYKVFTAPERVNEPWGDV---EMMDIEKAKLVSAIEVMEVIKKEKGIDLSEAETIV 281 TVR +V PE G + + +E + +E + +++K L A+ IV Sbjct: 184 MATVRPRVMAMPEPDRSRSGQIIEHPLCLVESDIITKVLEYIPDNQQDKP-QLPFADIIV 242 Query: 282 AVGRGVKCEKDLDMIHEFAEKIGATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALG 341 A GRG+K ++ +I + A +GA V TRP ++A W A Q+G SG+TV+PKL IA G Sbjct: 243 AGGRGMKRAENFQLIWDLAMVLGAEVGATRPVVQANWVQAERQVGQSGKTVRPKLYIAAG 302 Query: 342 ISGAVQFAAGMQNSEYIIAINSDPKAPIFNIAHCGMVGDLYEILPEL 388 ISGA+Q GM +S+ IIAINSDP APIF+ A G+VG+ ILP L Sbjct: 303 ISGAIQHRVGMADSDVIIAINSDPNAPIFDFASYGIVGNAMTILPAL 349 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: 395 Number of extensions: 14 Number of successful extensions: 4 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: 364 Length adjustment: 31 Effective length of query: 387 Effective length of database: 333 Effective search space: 128871 Effective search space used: 128871 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