Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase
Query= BRENDA::H6LBS1 (466 letters) >NCBI__GCF_000009985.1:WP_043745229.1 Length = 469 Score = 176 bits (445), Expect = 2e-48 Identities = 140/431 (32%), Positives = 215/431 (49%), Gaps = 21/431 (4%) Query: 48 LIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGG--IMLETTLMNNILELD 105 +++ ST EV+++++ IP+V +G TGL G VP G +++ T + I +D Sbjct: 41 VVRPGSTAEVAEVVRLCAAAGIPMVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVD 100 Query: 106 TENLTVTVEPGVLLMELSKFVEENDLFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTR 164 + T+T E G +L L + EE +P G E S I GNISTNAGG ++YG TR Sbjct: 101 PVDFTLTAEAGCVLANLQQAAEEAGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTR 160 Query: 165 DYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTL 224 D V GL VVL +G + ++ K+++GY+L+ L IG+EGTL ++T +LKL P P+ Sbjct: 161 DLVLGLEVVLPDGRVWNGLKRLRKDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPR--- 217 Query: 225 SLLIPFENISDAAGIVPKIIKSKAIP----TAIEFMERQTI-LFAEDFLGKKFPDSSSNA 279 + F ++D +P +++ TA E + R+ + L G + P ++ + Sbjct: 218 EIATAFVALADLEAALPLFSRARTASGDSVTACELVPRRGLELGMRHVPGVRAPFAAFHD 277 Query: 280 Y-ILLTFDGNTKEQVEAEYETVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKA 337 + +LL + + E + +G A D I ++ ++ W R A EA K Sbjct: 278 WMLLLELSSSRPGGLREALEEMLGQAFEDGLAVDAVIAESDAQRADFWRIREAIPEAQKK 337 Query: 338 STTEMDECDVVVPRNRIAEFI-EFTHDLAKEM-DVRIPSFGHAGDGNLHIYVCRDELCQA 395 + DV V +R+ E I T + M VR+ FGH GDGN H + + E A Sbjct: 338 EGGSIKH-DVAVATSRVPEMIRRCTRAVEAAMPGVRVVPFGHLGDGNTHFNLTQPE--GA 394 Query: 396 DWEAKLA--EAMDR-MYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTF 452 D A LA E M+R ++ + EG +S EHGIG K L + L LMA IK Sbjct: 395 DKAAFLARWEEMNRIVHDIVVEMEGSISAEHGIGRLKVDELAHYKPGVDLDLMARIKGAL 454 Query: 453 DPKNLLNPKKV 463 DP +NP K+ Sbjct: 455 DPLGQMNPGKI 465 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: 20 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: 469 Length adjustment: 33 Effective length of query: 433 Effective length of database: 436 Effective search space: 188788 Effective search space used: 188788 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 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