Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_052473864.1 SUTH_RS14665 L-lactate dehydrogenase
Query= reanno::WCS417:GFF3737 (376 letters) >NCBI__GCF_000828635.1:WP_052473864.1 Length = 396 Score = 392 bits (1007), Expect = e-114 Identities = 188/376 (50%), Positives = 262/376 (69%), Gaps = 3/376 (0%) Query: 4 SSASDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSLKTT 63 ++ASDYR A+R+LPR LFDY+DG AY E T N + LRQR++R+V L+L T Sbjct: 13 ATASDYREMARRRLPRHLFDYLDGAAYEERTAGENQQAFQRLQLRQRVMRDVSRLNLSTK 72 Query: 64 LFGQELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQSAQA 123 + GQ+L +P++L+P+G+ G A R EVQAA+AA G+PFC STVS+C IEEV + + Sbjct: 73 VLGQDLALPLVLAPLGIAGAMACRAEVQAARAAEAAGVPFCESTVSICSIEEVRAATTAP 132 Query: 124 IWFQLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFAAQRRML 183 W+QLYV++DRG+ ++ + RA AAG LV TVD+ GARYRD +GM+G + +M Sbjct: 133 FWYQLYVMRDRGYAKDLMARAHAAGCPVLVLTVDLAVMGARYRDVRNGMAGGLSLGGKMA 192 Query: 184 QA---VTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFDASISWKDLEWI 240 +A ++ PQW DVG+ G+P GN++ + L ++ W+ + FD +++WKDL W+ Sbjct: 193 KAWDLLSHPQWLLDVGVRGKPLTFGNLTAAVPDAGSLPEFKAWVDSQFDPAVTWKDLAWV 252 Query: 241 REFWKGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDD 300 RE W G +++KG+LD DA++A + GADGIVVSNHGGRQLD V ++ ALP I DAVGD Sbjct: 253 RENWPGKILLKGVLDIDDAREAAAAGADGIVVSNHGGRQLDSVAASIDALPRIVDAVGDK 312 Query: 301 LTVLVDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMT 360 L VL+D G+RSGLDVV+ LALGAKAC+LGRA YA+AA G+ GV ++L + EM VA+ Sbjct: 313 LDVLMDGGVRSGLDVVKALALGAKACMLGRAWGYAVAARGEAGVAHMLSVMRSEMNVALA 372 Query: 361 LTGVTSIAQIDRSTLV 376 L GV +A++DR L+ Sbjct: 373 LCGVADVAKLDRQALL 388 Lambda K H 0.321 0.136 0.401 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: 399 Number of extensions: 14 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: 376 Length of database: 396 Length adjustment: 30 Effective length of query: 346 Effective length of database: 366 Effective search space: 126636 Effective search space used: 126636 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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