Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate 5210234 Shew_2677 putative electron transfer flavoprotein FixA (RefSeq)
Query= BRENDA::H6LBB0 (264 letters) >FitnessBrowser__PV4:5210234 Length = 257 Score = 102 bits (255), Expect = 6e-27 Identities = 66/207 (31%), Positives = 111/207 (53%), Gaps = 13/207 (6%) Query: 1 MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGT-ITTL 59 MKI+ C K VP ++ V+ + G L + K+NP+DL +E +LK + G+ +T L Sbjct: 1 MKIITCYKLVPEEQDISVNGD-GSLDTNKAAPKINPFDLNAVEAGVQLKAMVEGSQLTAL 59 Query: 60 SMG------PMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQGTKRLGDFDL 113 S+G P K++L G D+ L+ D +FG T+ LA ++ +FDL Sbjct: 60 SVGGKALDNPKARKDILSR----GPDDLTLVIDEQFGALLPHQTARVLASAARQC-EFDL 114 Query: 114 IICGKQTTDGDTAQVGPEMAEFLGIPHVTNVIKILAADEKGLTLQMNMEESLEIQRVPYP 173 I+CG + D QVG ++ E L + + V KI++A + LT++ +++ +E+ + P Sbjct: 115 ILCGDGSGDLFAQQVGMQLGELLNVSCINAVSKIVSATDSTLTVERALDDEVEVLEIDLP 174 Query: 174 CLITVDKDIYTPRLPSYKRKLDISKNP 200 +I+V DI P++PS K L +K P Sbjct: 175 AVISVSADINEPQIPSMKTILAAAKKP 201 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: 154 Number of extensions: 13 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: 264 Length of database: 257 Length adjustment: 25 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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 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