Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein
Query= BRENDA::H6LBS1 (466 letters) >NCBI__GCF_900115975.1:WP_092483962.1 Length = 458 Score = 295 bits (756), Expect = 2e-84 Identities = 172/463 (37%), Positives = 258/463 (55%), Gaps = 7/463 (1%) Query: 6 VEASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAY 65 ++ + IK ++ +E V E +S+D P +++ + EV++I++ A Sbjct: 1 MDKDTVKKIKSVVGSEYVLESPEERICYSYDGTAR-RGIPALVVLPGNAREVAEIVRLAN 59 Query: 66 EHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKF 125 E P+ RG+GTGL G VP G+ + + MN ILE+ ++L VEPGV+ L + Sbjct: 60 EKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLLAVVEPGVVTGRLHRA 119 Query: 126 VEENDLFYPPDPGE-KSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGG 184 VE+ LFYPPDP ++ TI GN++ NAGG RA KYGVTRDYV GL VV GEII GG Sbjct: 120 VEKEGLFYPPDPSSLQTCTIGGNVAENAGGPRAFKYGVTRDYVLGLEVVTPTGEIINTGG 179 Query: 185 KIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKII 244 + VKN +GY L L+ GSEGTL +IT+ L+L+P P+ + L + + DAA V +I Sbjct: 180 RTVKNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRAVQTALAVYNRVEDAASTVTAMI 239 Query: 245 KSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLC 304 + IP +E M+R TI E++L P + A +L+ DG QV E + V + C Sbjct: 240 RRGIIPATLELMDRITIRCVENYLRLGLP-MDAGAILLIEVDG-LPAQVAEEMKLVEDAC 297 Query: 305 LAEGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHD 363 + + ++ +W AR A AI + T++ E D VPR++I E +E Sbjct: 298 RQNSCRALQTATDAAERERLWKARRAVSTAIVQIKPTKISE-DATVPRSKIPEMVERLKS 356 Query: 364 LAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEH 423 + ++ + +P FGHAGDGNLH + D+ + E K +A+ ++ AL G +SGEH Sbjct: 357 IGEKYGLHLPVFGHAGDGNLHPNILVDKRDPVEME-KAEKAVQEIFRAALDLGGTLSGEH 415 Query: 424 GIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466 G+G K+ YL + G + M IK+ DP+N+LNP K+ Q+ Sbjct: 416 GVGLLKKPYLEWEAGAGGIEYMKAIKKAVDPRNVLNPGKIFQV 458 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: 496 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: 458 Length adjustment: 33 Effective length of query: 433 Effective length of database: 425 Effective search space: 184025 Effective search space used: 184025 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 Apr 09 2024. 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