Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ac3H11_4483 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4483 Length = 504 Score = 224 bits (570), Expect = 7e-63 Identities = 142/458 (31%), Positives = 230/458 (50%), Gaps = 5/458 (1%) Query: 7 EASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYE 66 +A + A+ + +PA + +E + D L + P V+ + +EV +++ + Sbjct: 23 QAEVVQALGQAVPAHALLWHSEDTTPYECDGLTAYRQRPLVVCLPETYDEVQAVLRACHR 82 Query: 67 HNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFV 126 +PVV RG+GTGL G +P G+ L N IL L E+ T V+ GV + +S+ Sbjct: 83 LQVPVVARGAGTGLSGGAMPHAMGVTLSLAKFNRILNLSPESRTAVVQSGVRNLAISEAA 142 Query: 127 EENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGK 185 ++L+Y PDP + A TI GN++ N+GG+ +KYG+T V + GE +E G + Sbjct: 143 APHNLYYAPDPSSQIACTIGGNVAENSGGVHCLKYGLTVHNVLKVKGFTVEGEPVEFGSE 202 Query: 186 IVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIK 245 + +S GY L VIGSEG L VIT+ ++L+P P++ ++ F+++ A V +I Sbjct: 203 AL-DSPGYDLLAAVIGSEGMLAVITEVTVRLIPKPQLARCIMASFDDVRKAGDAVAAVIA 261 Query: 246 SKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCL 305 + IP +E M++ EDF+ + D ++ A +L DG T E+VE E ++ + Sbjct: 262 AGIIPAGLEMMDKPMTAAVEDFVHAGY-DLTAEAILLCESDG-TPEEVEEEIGRMSEVLR 319 Query: 306 AEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLA 365 A GA + + + WS R A + + D +PR R+A+ + ++ Sbjct: 320 AAGATAISVSRDEAERLRFWSGRKNAFPASGRISPDYMCMDSTIPRKRLADILLAIQEME 379 Query: 366 KEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGI 425 K+ +R + HAGDGNLH + D AD + + ++ G V+GEHG+ Sbjct: 380 KKYQLRCANVFHAGDGNLHPLILFD-ANDADQLHRCELFGADILETSVAMGGTVTGEHGV 438 Query: 426 GYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 G K + F E A M G+K FDP LLNP KV Sbjct: 439 GVEKLNSMCVQFTAEENAQMFGLKHAFDPAGLLNPGKV 476 Lambda K H 0.318 0.136 0.388 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: 526 Number of extensions: 33 Number of successful extensions: 6 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: 466 Length of database: 504 Length adjustment: 34 Effective length of query: 432 Effective length of database: 470 Effective search space: 203040 Effective search space used: 203040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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