Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate WP_092482220.1 BM299_RS04215 electron transfer flavoprotein subunit beta/FixA family protein
Query= BRENDA::H6LBB0 (264 letters) >NCBI__GCF_900115975.1:WP_092482220.1 Length = 269 Score = 183 bits (464), Expect = 4e-51 Identities = 103/263 (39%), Positives = 161/263 (61%), Gaps = 5/263 (1%) Query: 1 MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGT-ITTL 59 M I+ +KQVPGT NV+++PETG ++R G ++ +NP D L A R+K+Q GT +T + Sbjct: 1 MNIVALVKQVPGTDNVKMNPETGTMVRTGKDNVINPLDENALTEALRIKQQTTGTTVTAV 60 Query: 60 SMGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQGTKRLGDFDLIICGKQ 119 SMGP +++ L E+ +GADEG LLS R F GAD +AT+ LA K+L + +I+CG++ Sbjct: 61 SMGPQTAEKALKEAIALGADEGILLSSRAFAGADTIATARVLAAAVKKLENVSMILCGER 120 Query: 120 TTDGDTAQVGPEMAEFLGIPHVTNVIKILAADEKGLTLQMNMEESLEIQRVPYPCLITVD 179 TDG+T Q GP +A LGIP VT V +I + + +++ +E E +PYP + TV Sbjct: 121 ATDGETGQTGPMVAAMLGIPVVTFVKEINVGENTAIVIRI-VENGYEKVEIPYPFMATVV 179 Query: 180 KDIYTPRLPSYKRKLDISKNPEIKILTLKDMYDTNEKKYGLSGSPTQVERIFPPESNVEK 239 KDI P P+ K+ ++ +K+ + +++ + + GL+GSPT+V +IF P+ + Sbjct: 180 KDINEPGFPTLSGKVQ-ARETLVKVWSEEEL-GLPKNELGLTGSPTRVVKIFSPKLARDT 237 Query: 240 TSFEGDGKVLAKALL-GILTEKK 261 + DG A +L +L EKK Sbjct: 238 RILKHDGSGNAVGILVKLLQEKK 260 Lambda K H 0.316 0.137 0.386 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: 192 Number of extensions: 6 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: 264 Length of database: 269 Length adjustment: 25 Effective length of query: 239 Effective length of database: 244 Effective search space: 58316 Effective search space used: 58316 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: 42 (22.0 bits) S2: 47 (22.7 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