Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS12240 AZOBR_RS12240 2-hydroxy-acid oxidase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__azobra:AZOBR_RS12240 Length = 467 Score = 229 bits (585), Expect = 1e-64 Identities = 156/460 (33%), Positives = 235/460 (51%), Gaps = 16/460 (3%) Query: 12 AAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPV 71 A K L+ +R + E DE + P+ + TSTEEVS I+ +H +P+ Sbjct: 19 AEFKALL-GDRFTTAAAVREHHGKDESYHPNFPPDGVAFATSTEEVSAIVTLCAKHKLPI 77 Query: 72 VVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDL 131 + G+GT L G L GG+ ++ + M +L + E+L VTV+ GV +L++ + + L Sbjct: 78 IPFGTGTSLEGGVAALAGGVCIDVSNMKEVLRVSPEDLDVTVQAGVTRKQLNEHLRDTGL 137 Query: 132 FYPPDPGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSS 191 F+P DPG A++ G ST A G AV+YG R+ V GLTVVLA+G II+ GG+ K+++ Sbjct: 138 FFPIDPGA-DASLGGMASTRASGTNAVRYGTMRENVLGLTVVLADGRIIKTGGRARKSAA 196 Query: 192 GYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPT 251 GY L L +G+EGTL +IT+ L+L +P+ S + PF +I A V + I+S Sbjct: 197 GYDLTRLFVGAEGTLGIITEVTLRLYGIPEAISSAVCPFNDIRGAVDTVIQTIQSGIPVA 256 Query: 252 AIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKD 311 IE ++ + D + K A L T V+ + E VA + G + Sbjct: 257 RIELLDEVQM----DAVNKYSKLDYKVAPTLFFEFHGTAAGVKEQAEMVAAIAAEFGGSE 312 Query: 312 VYIVDTVERKDSVWSAR--GAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369 E + +W AR G + ++ DV VP +R+A+ I T E Sbjct: 313 FTWATRPEDRSKLWQARHDGYYAALALRPGSKGWPTDVCVPISRLADCILETKKDIAESS 372 Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM---DRMYAKALTFEGLVSGEHGIG 426 + P GH GDGN H+ D D +LAEA DRM +AL G +GEHGIG Sbjct: 373 MLAPLVGHVGDGNFHLVYVID----PDKPEELAEAKRLNDRMVDRALAMGGTCTGEHGIG 428 Query: 427 YAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466 Y K ++L + G + A+M +K+ FDP+N +NP KV ++ Sbjct: 429 YGKMEFLEKEAG-DAFAVMGELKRAFDPENRMNPGKVVRI 467 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: 525 Number of extensions: 27 Number of successful extensions: 5 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: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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