Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Pf6N2E2_137 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_137 Length = 511 Score = 213 bits (541), Expect = 2e-59 Identities = 139/454 (30%), Positives = 225/454 (49%), Gaps = 7/454 (1%) Query: 11 IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70 + A++ IP + E + + D L + + P ++ E+V ++K + ++P Sbjct: 34 LQALQAQIPDLDILHQEEDLKPYECDGLSAYRTTPLLVALPRRVEQVQALLKLCHGLDVP 93 Query: 71 VVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130 VV RG+GTGL G +PL G++L N IL +D + T ++PGV + +S+ Sbjct: 94 VVARGAGTGLSGGALPLESGVLLVMARFNQILHIDPDARTARLQPGVRNLAISQAAAPFG 153 Query: 131 LFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189 L+Y PDP + A +I GN++ NAGG+ +KYG+T + L ++ GE + LG + + + Sbjct: 154 LYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKLEILTIEGERLTLGSEAL-D 212 Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAI 249 S G L L GSEG L VIT+ +KLLP P++ LL F+++ A V II + I Sbjct: 213 SPGLDLLALFTGSEGLLGVITEVTVKLLPRPQVAKVLLASFDSVDKAGRAVADIIAAGII 272 Query: 250 PTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGA 309 P +E M+ I AEDF+ +P + A +L DG + V + E V + GA Sbjct: 273 PGGLEMMDNLAIRAAEDFIHAGYP-VEAEAILLCELDG-VEADVHDDCERVRQVLEQAGA 330 Query: 310 KDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369 +V + W+ R A+ + D +PR + E ++ L E Sbjct: 331 TEVRQARDEAERLRFWAGRKNAFPAVGRLAPDYYCMDGTIPRRALPEVLQRIASLGAEHG 390 Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM-DRMYAKALTFEGLVSGEHGIGYA 428 +R+ + HAGDGN+H + D E + AE + ++ + G ++GEHG+G Sbjct: 391 LRVANVFHAGDGNMHPLILFD--ANQPGELERAETLGGKILELCVQVGGSITGEHGVGRE 448 Query: 429 KRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKK 462 K + F ++ L L +K FDP+ LLNP K Sbjct: 449 KINQMCTQFNSDELNLFHAVKAAFDPQGLLNPGK 482 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: 558 Number of extensions: 24 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: 511 Length adjustment: 34 Effective length of query: 432 Effective length of database: 477 Effective search space: 206064 Effective search space used: 206064 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