Align L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 (characterized)
to candidate Ga0059261_2629 Ga0059261_2629 L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases
Query= CharProtDB::CH_000618 (396 letters) >FitnessBrowser__Korea:Ga0059261_2629 Length = 379 Score = 513 bits (1322), Expect = e-150 Identities = 252/379 (66%), Positives = 303/379 (79%), Gaps = 1/379 (0%) Query: 1 MIISAASDYRAAAQRILPPFLFHYMDGGAYSEYTLRRNVEDLSEVALRQRILKNMSDLSL 60 MII+++ D+ AA+R +P FLF Y +GGAY E TL RNV DL+ +ALRQR+LK+++++ L Sbjct: 1 MIIASSHDFEKAARRRVPRFLFDYAEGGAYDEVTLGRNVSDLAAIALRQRVLKDVANVDL 60 Query: 61 ETTLFNEKLSMPVALAPVGLCGMYARRGEVQAAKAADAHGIPFTLSTVSVCPIEEVAPAI 120 +TTLF ++++PVAL PVG+ GMYARRGEVQAA+AA A GIP LSTVS+C +EEVA A Sbjct: 61 KTTLFGREVALPVALGPVGISGMYARRGEVQAARAAKAAGIPTCLSTVSICALEEVAAAA 120 Query: 121 KRPMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPTPGARYRDAHSGMSGPNAAMR 180 P WFQLYV+RDRGFMR+ + RAKAAG +VFTVDMP PGARYR HSGM+GPNA +R Sbjct: 121 D-PFWFQLYVIRDRGFMRDLIARAKAAGAEAMVFTVDMPIPGARYRSEHSGMAGPNARLR 179 Query: 181 RYLQAVTHPQWAWDVGLNGRPHDLGNISAYLGKPTGLEDYIGWLGNNFDPSISWKDLEWI 240 + LQA+ P WAWDVGL GRPH LGN++ LGK +GL DY+GWLG NFDPSI WKDL+WI Sbjct: 180 QILQAIGKPHWAWDVGLMGRPHTLGNLAPVLGKDSGLSDYMGWLGKNFDPSIQWKDLDWI 239 Query: 241 RDFWDGPMVIKGILDPEDARDAVRFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGD 300 R WD P++IKGILDPEDAR+A GA+GIVVSNHGGRQLDGVLSSARALP IADAV G Sbjct: 240 RAEWDRPLIIKGILDPEDAREAAAIGANGIVVSNHGGRQLDGVLSSARALPPIADAVGGQ 299 Query: 301 IAILADSGIRNGLDVVRMIALGADTVLLGRAFLYALATAGQAGVANLLNLIEKEMKVAMT 360 + +LAD GIR GLDVVRM+ALGAD VLLGRA++YALA G+AGV LL LI +EMKVAMT Sbjct: 300 LTVLADGGIRTGLDVVRMLALGADGVLLGRAWVYALAAQGEAGVTKLLALIAREMKVAMT 359 Query: 361 LTGAKSISEITQDSLVQGL 379 LTG I I + L +G+ Sbjct: 360 LTGVNRIGAIDRSILAEGV 378 Lambda K H 0.320 0.136 0.407 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: 549 Number of extensions: 21 Number of successful extensions: 2 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: 396 Length of database: 379 Length adjustment: 30 Effective length of query: 366 Effective length of database: 349 Effective search space: 127734 Effective search space used: 127734 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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