Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Dsui_3415 Dsui_3415 FAD/FMN-dependent dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__PS:Dsui_3415 Length = 486 Score = 216 bits (551), Expect = 1e-60 Identities = 143/460 (31%), Positives = 232/460 (50%), Gaps = 11/460 (2%) Query: 7 EASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYE 66 +A+ +AA+ ++P RV+ E + D L + + P + + EV I++ + Sbjct: 15 QAALLAALGRILPPGRVYGEPEDLRPYECDGLTAYRNLPLAVALPETEAEVQAILQLCHR 74 Query: 67 HNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFV 126 +PVV RG+ TGL G +P G++L IL++D T V+PGV + +S+ Sbjct: 75 LQVPVVPRGAATGLSGGAMPHHQGLLLSLAKFKKILKVDPVARTALVQPGVRNLAVSEAA 134 Query: 127 EENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRD---YVRGLTVVLANGEIIEL 182 +L+Y PDP + A TI GN+S N+GG+ +KYG+T VRG T+ GE + Sbjct: 135 APYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLQVRGYTMA---GEAVTF 191 Query: 183 GGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPK 242 G + ++ G+ L L+ GSEG L VIT+ ++KL P P++ +L F++++ A V + Sbjct: 192 GSAAL-DAPGFDLLALLNGSEGMLAVITEVLVKLTPKPQVAKVVLAYFDSVTKAGNAVAE 250 Query: 243 IIKSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVAN 302 +I + IP +E M++ E ++ K D + A +L DG T E+VE E + Sbjct: 251 VIAAGIIPAGLEMMDKPATHAVEPYV-KAGYDLDAEAVLLCESDG-TPEEVEEEIAAMRA 308 Query: 303 LCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTH 362 + GA + + + W+ R A A+ T + D +PR R+AE + Sbjct: 309 VLEKSGATSLRVSANEAERLRFWAGRKAAFPAVGRITPDYLCMDGTIPRKRVAEMLTAIA 368 Query: 363 DLAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGE 422 + K+ +R + HAGDGNLH + D + E A + + ++ G ++GE Sbjct: 369 AMEKKYGLRCANVFHAGDGNLHPLIMYDANQPGELEQATAFGAE-ILELSVALGGSITGE 427 Query: 423 HGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKK 462 HG+G K + F E LA G+KQ+FDP LLNP K Sbjct: 428 HGVGVEKITQMCAQFTPEELARFEGVKQSFDPAGLLNPGK 467 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: 524 Number of extensions: 32 Number of successful extensions: 6 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: 486 Length adjustment: 33 Effective length of query: 433 Effective length of database: 453 Effective search space: 196149 Effective search space used: 196149 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