Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 8500826 DvMF_1567 D-lactate dehydrogenase (cytochrome) (RefSeq)
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Miya:8500826 Length = 474 Score = 269 bits (687), Expect = 2e-76 Identities = 157/435 (36%), Positives = 232/435 (53%), Gaps = 7/435 (1%) Query: 30 GEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFG 89 GE + D + + ++++ + E+V +++ A H IPV+ RG GTGL G C+ + G Sbjct: 43 GEPYDRDA-SELRAPADLVVLPETVEQVQALLRCASAHAIPVIPRGGGTGLAGGCLAVRG 101 Query: 90 GIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDP-GEKSATIAGNI 148 G++L MN I +DT NL VE GV+ + E L+YPPDP G +TI GN+ Sbjct: 102 GVVLSLERMNRIRAIDTRNLVAEVEAGVISQRVRDAAAEQGLYYPPDPAGMDRSTIGGNV 161 Query: 149 STNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCV 208 +TNAGG VKYGVTRDYV G+ VL +GE++ G + K GY + L+ GSEGTL V Sbjct: 162 ATNAGGPACVKYGVTRDYVLGVEAVLPDGELLRAGVRTRKGVVGYDMAHLLCGSEGTLGV 221 Query: 209 ITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAEDFL 268 IT LKL+PLP T+S+ + F +++ A V ++ +P+AIEF++ + I + L Sbjct: 222 ITALTLKLVPLPPATVSMAVAFPDMAAAMRGVAAVLGGGHLPSAIEFLDHRCIRLLGELL 281 Query: 269 GKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVWSAR 328 P + +++ DG +EQ+ E + VA +C +GA V E + VW AR Sbjct: 282 PIPVP-GDKPSLLIIELDG-AREQIVPELDLVAAICRQQGATHVLPAADEETRVRVWGAR 339 Query: 329 GAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNLHIYVC 388 I DV VP IAE + + + + I +FGHAGDGN+H+ V Sbjct: 340 RQVSLRIHDYAALYMSEDVAVPLGAIAELVAALPEFEQRYGMEIFAFGHAGDGNIHLNVT 399 Query: 389 RDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGI 448 D + + + + K L G +SGEHGIG AK+ L + + L GI Sbjct: 400 AP---TRDTRDVVEQGIVELVGKVLELGGTISGEHGIGEAKKHLLPLELSPASIRLQRGI 456 Query: 449 KQTFDPKNLLNPKKV 463 +Q FDP+ ++NP KV Sbjct: 457 RQVFDPRGIMNPGKV 471 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: 519 Number of extensions: 23 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: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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