Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_033102282.1 JG50_RS0116910 FAD-binding protein
Query= BRENDA::H6LBS1 (466 letters) >NCBI__GCF_000763315.1:WP_033102282.1 Length = 470 Score = 292 bits (748), Expect = 1e-83 Identities = 173/460 (37%), Positives = 261/460 (56%), Gaps = 12/460 (2%) Query: 10 DIAAIKELI---PAERVFVGTEIGEDFSHDELGSIHSY-PEVLIKVTSTEEVSKIMKYAY 65 D + +KELI ERV + + ++ D S +Y P+V++ S E+++IMK A Sbjct: 4 DPSIVKELIRITDEERVLLSLDERYTYAFD--ASFGTYLPDVVVFPQSATEIAEIMKLAN 61 Query: 66 EHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKF 125 IPV RG GT L G +P+ GGI+L T MN +L +D +NL VEPG+ EL + Sbjct: 62 REQIPVTPRGGGTSLSGGPLPVAGGIVLAMTRMNKLLRIDRDNLIAFVEPGITTAELQRE 121 Query: 126 VEENDLFYPPDPGEKS-ATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGG 184 E+ LFYPPDP + +TI GN++ N+GG +KYGVT+ YV GL VV GEII GG Sbjct: 122 AEKAGLFYPPDPSSSNVSTIGGNLAENSGGPHGLKYGVTKHYVIGLEVVTPQGEIIRTGG 181 Query: 185 KIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKII 244 VKN +GY L L++GSEGTL +ITKA+L+L+P P +L+ F+ I D+ + I+ Sbjct: 182 MTVKNVTGYDLTSLIVGSEGTLGIITKAVLRLIPKPPARKALMAIFDEIVDSGRAISGIL 241 Query: 245 KSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLC 304 K+ +P +E M++ +I E++ P ++ A +LL DG+ V+ E A +C Sbjct: 242 KNGILPAKLEMMDQASIRAVENYQPSGLPLDAA-AILLLEVDGH-PAAVDEEIRKAAQIC 299 Query: 305 LAEGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHD 363 A++V + + +W AR AI + T++ E D VPR++I E +E Sbjct: 300 RQYAAREVRLAADEAERAELWKARKLVSPAISQVKPTKISE-DATVPRSKIPEMLERLRQ 358 Query: 364 LAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEH 423 + ++ + + FGHAGDGNLH + D D ++ EA+ ++ A+ G +SGEH Sbjct: 359 IREKYQLHLVVFGHAGDGNLHPNIIADSR-DRDEMKRVEEAVAEIFKAAVELGGTLSGEH 417 Query: 424 GIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 GIG K ++ + G+ L +M IKQ +DP N+LNP K+ Sbjct: 418 GIGTMKPAFMEMELGSAGLDMMRRIKQAWDPNNILNPFKI 457 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: 502 Number of extensions: 24 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: 466 Length of database: 470 Length adjustment: 33 Effective length of query: 433 Effective length of database: 437 Effective search space: 189221 Effective search space used: 189221 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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