Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate GFF2925 PGA1_c29720 glycolate oxidase subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Phaeo:GFF2925 Length = 482 Score = 212 bits (540), Expect = 2e-59 Identities = 132/430 (30%), Positives = 222/430 (51%), Gaps = 9/430 (2%) Query: 36 DELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLET 95 D L + P +++ +T+EVS +++ + +PVV RG+GT L G +P ++L Sbjct: 43 DALTAYKCPPMLVVLPRTTKEVSDVLRICHAAGVPVVPRGAGTSLAGGALPTADCVILGV 102 Query: 96 TLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEKSA-TIAGNISTNAGG 154 MN +LE D +N + V+ G + +S VEE + FY PDP + A IAGNI+ N+GG Sbjct: 103 ARMNAVLETDYDNRIIRVQTGRTNLSVSGAVEEEEFFYAPDPSSQLACAIAGNIAMNSGG 162 Query: 155 MRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAIL 214 +KYGVT + + G+T+V+ +G ++E+GG + ++ G L ++ GSEG L V+T+A L Sbjct: 163 AHCLKYGVTTNNLMGVTMVMMDGTVVEIGGAHL-DAGGLDLLGVICGSEGQLGVVTEATL 221 Query: 215 KLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAEDFLGKKFPD 274 ++L P+ +LI +++ A V IIK+ +P AIEFM+R I E F +P Sbjct: 222 RILRKPEGARPVLIGYDSNEVAGACVSDIIKAGVLPVAIEFMDRPCIEACEAFAKAGYP- 280 Query: 275 SSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEA 334 A +++ +G+ E ++ + + + + ++ + +W R + A Sbjct: 281 -MCEALLIVEVEGSDAE-IDHQLRLITEIARSHNPVELREARDSDEAARIWLGRKSAFGA 338 Query: 335 IKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNLHIYVCRDELCQ 394 + M D +P + + +++KE + + + HAGDGN+H + D Sbjct: 339 MGQINDYMC-LDGTIPVTSLPHVLRRIGEMSKEFGLDVANVFHAGDGNMHPLILFDANKP 397 Query: 395 ADWEAKLAEAMDRMYAK-ALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFD 453 D E EA K + G ++GEHG+G KR +L+ +G + +K FD Sbjct: 398 GDLET--CEAFGAEILKLCVEVGGCLTGEHGVGIEKRDLMLDQYGVADIEAQLRVKDVFD 455 Query: 454 PKNLLNPKKV 463 PK LLNP KV Sbjct: 456 PKWLLNPAKV 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: 514 Number of extensions: 32 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: 482 Length adjustment: 33 Effective length of query: 433 Effective length of database: 449 Effective search space: 194417 Effective search space used: 194417 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