Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate WP_051952964.1 Q392_RS05980 alpha-hydroxy-acid oxidizing protein
Query= reanno::WCS417:GFF3737 (376 letters) >NCBI__GCF_000745855.1:WP_051952964.1 Length = 387 Score = 268 bits (685), Expect = 2e-76 Identities = 148/360 (41%), Positives = 199/360 (55%), Gaps = 3/360 (0%) Query: 7 SDYRAAAKRKLPRFLFDYIDGGAYAEHTLRANSSDLAEISLRQRILRNVDNLSLKTTLFG 66 +D+R A+ +LPRF+FDY+DGGA E L N L E+ L ++R+ + L +FG Sbjct: 6 ADFRRRARARLPRFVFDYVDGGAEDEACLARNRQALDELRLVPHVMRDTREVDLSVEVFG 65 Query: 67 QELDMPVILSPVGLTGMYARRGEVQAAKAAANKGIPFCLSTVSVCPIEEVASQSAQAI-W 125 + MP ++PVG G+ G+V AKAAA +G+PF LST S +E V + + QA+ W Sbjct: 66 RRWSMPAGIAPVGFAGLVRPAGDVLLAKAAAAQGVPFVLSTASNARLEAVRAAAPQAVQW 125 Query: 126 FQLYVLKDRGFMRNALERAQAAGVTTLVFTVDMPTPGARYRDAHSGMSGPFA-AQRRMLQ 184 QLYV+ DR + RA+ A LV TVD+ G R RD +G PF R + Sbjct: 126 MQLYVMGDRSIAEQIVRRAREARFDALVLTVDVAVSGMRERDMRNGFRLPFRPGLRTAID 185 Query: 185 AVTKPQWAFDVGLMGRPHDLGNISKYLGKPTHLEDYIGWLANNFDASISWKDLEWIREFW 244 P W+ L G P N+ + P + LA D ++W+ L W+R W Sbjct: 186 LAAHPAWSIAAALAGTP-GFANLVEAPSTPASPQVQAALLARAMDRGLTWESLAWLRRLW 244 Query: 245 KGPMIIKGILDPQDAKDAVSFGADGIVVSNHGGRQLDGVLSTAKALPPIADAVGDDLTVL 304 GP+++KG+L P DA AV+ GADG+VVSNHGGRQLD V + ALP + DAV + V Sbjct: 245 DGPLLVKGVLGPGDAAAAVAHGADGLVVSNHGGRQLDVVPAAISALPGVIDAVRGRIPVF 304 Query: 305 VDSGIRSGLDVVRMLALGAKACLLGRATAYALAADGQHGVENLLDIFAKEMRVAMTLTGV 364 VDSG R G DV + LALGA A +GR + LAA GQ GVE L + E + L GV Sbjct: 305 VDSGFRRGSDVAKALALGATAAFMGRLPIWGLAAGGQAGVEQALALVKAEFERTLILLGV 364 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: 378 Number of extensions: 25 Number of successful extensions: 3 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: 387 Length adjustment: 30 Effective length of query: 346 Effective length of database: 357 Effective search space: 123522 Effective search space used: 123522 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 Sep 24 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