Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Pf1N1B4_5862 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5862 Length = 499 Score = 226 bits (575), Expect = 2e-63 Identities = 145/458 (31%), Positives = 233/458 (50%), Gaps = 7/458 (1%) Query: 7 EASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYE 66 +A+ + A+++ +P + E + + D L + + P ++ E+V ++K + Sbjct: 18 KAALLKALQQEVPDLDILWREEELKPYECDGLSAYRTTPMLVALPRQLEQVQALLKLCHA 77 Query: 67 HNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFV 126 N+PVV RG+GTGL G +PL G++L NNIL +D T V+PGV + +S+ Sbjct: 78 RNVPVVARGAGTGLSGGALPLDKGVLLVMVRFNNILHIDPAARTARVQPGVRNLAISQAA 137 Query: 127 EENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGK 185 L+Y PDP + A +I GN++ NAGG+ +KYG+T + L V+ GE + LG Sbjct: 138 APFGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKLEVLTLEGEHLTLGAD 197 Query: 186 IVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIK 245 + ++ G+ L L GSEG L +IT+ +KLLP P++ LL F+++ A V +II Sbjct: 198 SL-DAPGFDLLALFTGSEGLLGIITEVTVKLLPKPQVAKVLLASFDSVEKAGRTVAEIIA 256 Query: 246 SKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCL 305 + IP +E M+ I AEDF+ +P + A +L DG + V + E V + Sbjct: 257 AGIIPGGLEMMDNLAIRAAEDFIHAGYP-VDAEAILLCELDG-VEADVHDDCERVREVLQ 314 Query: 306 AEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLA 365 GA DV + W+ R AI + + D +PR + ++ LA Sbjct: 315 QAGASDVRQARDEAERVRFWAGRKNAFPAIGRLSPDYYCMDGTIPRRELPGVLKGIASLA 374 Query: 366 KEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM-DRMYAKALTFEGLVSGEHG 424 +E +R+ + HAGDGN+H + D E + AEA+ ++ + G ++GEHG Sbjct: 375 QEYGLRVANVFHAGDGNMHPLILFD--ANQPGELERAEALGGKILELCVKVGGSITGEHG 432 Query: 425 IGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKK 462 +G K + F ++ L L +K FDPK LLNP K Sbjct: 433 VGREKINQMCAQFNSDELTLFHAVKAAFDPKGLLNPGK 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: 528 Number of extensions: 22 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