Align L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 (characterized)
to candidate 3609095 Dshi_2484 FMN-dependent alpha-hydroxy acid dehydrogenase (RefSeq)
Query= CharProtDB::CH_000618 (396 letters) >FitnessBrowser__Dino:3609095 Length = 389 Score = 216 bits (551), Expect = 7e-61 Identities = 137/379 (36%), Positives = 196/379 (51%), Gaps = 6/379 (1%) Query: 5 AASDYRAAAQRILPPFLFHYMDGGAYS-EYTLRRNVEDLSEVALRQRILKNMSDLSLETT 63 A SD R AA+R +P F+F Y+D E ++ L + L IL LET Sbjct: 9 AISDLRRAARRRIPGFVFEYLDSATGDREIGVQTTRAALDAIHLLPGILHGQITPELETP 68 Query: 64 LFNEKLSMPVALAPVGLCGMYARRGE-VQAAKAADAHGIPFTLSTVSVCPIEEVAPAIKR 122 L + + P +APVG+ G+ E + AA+AA A IP+ LSTV+ E V P Sbjct: 69 LLGQTYARPFGIAPVGMSGLIWPDAERLLAAEAATAR-IPYGLSTVATQTPERVGPVAGE 127 Query: 123 PMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPTPGARYRDAHSGMS-GPNAAMRR 181 WFQLY D G + + RA+A+G TLV TVD+P R R + ++ P R Sbjct: 128 MGWFQLYPPADPGIRDDIMARARASGFGTLVLTVDVPADSRRERQRRANLTIPPKITPRM 187 Query: 182 YLQAVTHPQWAWDVGLNGRPHDLGNISAYLGKPTGLEDYIGWLGNNFDPSISWKDLEWIR 241 Q + HP WA + +G P L +Y+ K TG Y+ G + W L+ +R Sbjct: 188 IFQMILHPTWALGMARHGTP-SLKLAESYVEK-TGAASYMAHAGKAIRGAPDWAYLDAVR 245 Query: 242 DFWDGPMVIKGILDPEDARDAVRFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGDI 301 WDGP+V+KG+L PEDA G D I VS+H RQ +G + LPAI AV D Sbjct: 246 AGWDGPLVVKGVLRPEDAVRLRAAGVDAIWVSDHSARQFEGGPGAITQLPAIRRAVGPDC 305 Query: 302 AILADSGIRNGLDVVRMIALGADTVLLGRAFLYALATAGQAGVANLLNLIEKEMKVAMTL 361 ++ DSGI GLD++R + LGAD V+LGRA+ +ALA G AGV +L++++ +++ M + Sbjct: 306 PVIYDSGIEGGLDILRAVGLGADFVMLGRAWHFALAGLGPAGVRHLIHILTQDLVTNMQI 365 Query: 362 TGAKSISEITQDSLVQGLG 380 G +++ G Sbjct: 366 CGIAKLADFRDQLATHSYG 384 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: 422 Number of extensions: 24 Number of successful extensions: 4 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: 389 Length adjustment: 31 Effective length of query: 365 Effective length of database: 358 Effective search space: 130670 Effective search space used: 130670 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