Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate PP_3745 PP_3745 glycolate oxidase, putative FAD-linked subunit
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Putida:PP_3745 Length = 499 Score = 230 bits (586), Expect = 9e-65 Identities = 139/457 (30%), Positives = 239/457 (52%), Gaps = 7/457 (1%) Query: 8 ASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEH 67 A+ + A+++ +P + E + + D L + + P ++ E+V ++K ++ Sbjct: 19 AALLQALRDALPDLEILHRDEDLKPYECDGLSAYRTVPLLVALPERLEQVQTLLKLCHQR 78 Query: 68 NIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVE 127 +PVV RG+GTGL G +PL GI+L N ILE++ + V+PGV + +S+ Sbjct: 79 GVPVVARGAGTGLSGGALPLAKGILLVMARFNRILEVNPQGRYARVQPGVRNLAISQAAA 138 Query: 128 ENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKI 186 + ++Y PDP + A +I GN++ NAGG+ +KYG+T V + ++ GE + LG Sbjct: 139 PHGMYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNVLKVDILTVEGERLSLGSDA 198 Query: 187 VKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS 246 + +S G+ L L IGSEG L ++T+ +KLLP P++ +L F+++ DA V II + Sbjct: 199 L-DSPGFDLLALFIGSEGMLGIVTEVTVKLLPKPQVARVILASFDSVEDAGRAVADIIAA 257 Query: 247 KAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLA 306 IP +E M+ I AEDF+ +P ++ A +L DG + V + E VA + Sbjct: 258 GIIPGGLEMMDNLAIRAAEDFIHAGYPVDAA-AILLCELDG-VEADVYDDCERVAAVLTQ 315 Query: 307 EGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAK 366 GA++V++ + W+ R A+ + + D +PR + ++ DL+ Sbjct: 316 AGAREVHLACDEAERARFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPRVLKGISDLSA 375 Query: 367 EMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM-DRMYAKALTFEGLVSGEHGI 425 E +R+ + HAGDGN+H + D E + AEA+ ++ + G ++GEHG+ Sbjct: 376 EYGLRVANVFHAGDGNMHPLILFD--ANLPGELERAEAIGGKILELCVKVGGSITGEHGV 433 Query: 426 GYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKK 462 G K + F ++ + L +K FDP+ LLNP K Sbjct: 434 GREKINQMCAQFNSDEITLFHAVKAAFDPQGLLNPGK 470 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: 523 Number of extensions: 29 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: 499 Length adjustment: 34 Effective length of query: 432 Effective length of database: 465 Effective search space: 200880 Effective search space used: 200880 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: 52 (24.6 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