Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_035391821.1 BA79_RS18270 glycolate oxidase subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >NCBI__GCF_000691145.1:WP_035391821.1 Length = 469 Score = 328 bits (842), Expect = 2e-94 Identities = 181/452 (40%), Positives = 270/452 (59%), Gaps = 6/452 (1%) Query: 14 IKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVV 73 +KE++ A V +S+D + P+ +++ + EEV +I+K + +P+V Sbjct: 10 LKEIVGAPNVQDSKADRLAYSYDATPNFQQMPDAIVRPHTAEEVQQIVKLCASYKVPIVP 69 Query: 74 RGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFY 133 RGSGT L P GG+++ T MN +LE+D ENLT TV+PG++ EL VEE LFY Sbjct: 70 RGSGTNLCAGTCPTQGGLVILFTRMNQLLEIDEENLTATVQPGLITQELIHQVEEKGLFY 129 Query: 134 PPDPGE-KSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSG 192 PPDP K +T+ GNI+ N+GG+R +KYGVTRDYV GL VVL NG+II+ GGK+ K+ +G Sbjct: 130 PPDPSSMKISTLGGNINENSGGLRGLKYGVTRDYVLGLEVVLPNGDIIKTGGKLAKDVAG 189 Query: 193 YSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTA 252 Y + L +GSEGTL ++T+A+LKLLPLP+ ++L +E++ +AA V II + IP Sbjct: 190 YDMTRLFVGSEGTLGIVTEAVLKLLPLPETKQTMLCLYESLEEAATSVSAIIAERIIPAT 249 Query: 253 IEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDV 312 +EFM++ T+ EDF P + A +L+ DGN E V + + +A +C GA V Sbjct: 250 LEFMDQPTLEVVEDFANIGLP-TDVQAVLLIEQDGN-PEAVSRDIQKIAEVCEQHGATSV 307 Query: 313 YIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVR 371 I + E ++ +AR + L A+ + S T + E D VPR+ IA + D+A++ +V Sbjct: 308 KIAHSEEEASALLTARRSALSALARLSPTTILE-DATVPRSEIANMVRAIEDIARKYEVN 366 Query: 372 IPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRK 431 I +FGHAGDGNLH C + + ++ A ++ KA+ G ++GEHG+G K Sbjct: 367 ICTFGHAGDGNLH-PTCATDARNEEEMKRVEAAFQAIFEKAVALGGTITGEHGVGLMKAP 425 Query: 432 YLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 YL E +A M IKQ DP +++NP KV Sbjct: 426 YLELKVKKEGIAAMKAIKQALDPAHIMNPDKV 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: 492 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: 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 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