Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate 351332 BT1804 electron transfer flavoprotein beta-subunit (NCBI ptt file)
Query= BRENDA::H6LBB0 (264 letters) >FitnessBrowser__Btheta:351332 Length = 290 Score = 147 bits (372), Expect = 2e-40 Identities = 93/255 (36%), Positives = 140/255 (54%), Gaps = 26/255 (10%) Query: 1 MKILVCIKQVPGTSNVEVDP--ETGVLIRDGVESKLNPYDLFGLETAFRLKE-QLGGTIT 57 +KI+V KQVP T NV D G + R + + NP DL LE A RLK+ G T+T Sbjct: 3 LKIVVLAKQVPDTRNVGKDAMKADGTINRAALPAIFNPEDLNALEQALRLKDAHPGSTVT 62 Query: 58 TLSMGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQGTKRLGDFDLIICG 117 L+MGP ++ +++ E + GAD G LL+DR F GAD +ATSY LA +++G+ D+II G Sbjct: 63 ILTMGPGRAADIIREGLFRGADNGYLLTDRAFAGADTLATSYALATAIRKIGECDIIIGG 122 Query: 118 KQTTDGDTAQVGPEMAEFLGIPHVTNVIKILAADEKGLTLQMNMEESLEIQRVPYPCLIT 177 +Q DGDTAQVGP++AE LG+ +T +IL + + ++ +++ +E P P +IT Sbjct: 123 RQAIDGDTAQVGPQVAEKLGLTQITYAEEILEVGDGKIKVKRHIDGGVETVEGPLPIVIT 182 Query: 178 VDKDIYTPR------LPSYKRKLDISKNPEIKILTLKDMYDTNE---------------- 215 V+ R + YK +++ + L D+YD + Sbjct: 183 VNGSAAPCRPRNAKLVQKYKHAKTVTEKQQGN-LDYTDLYDKRDYLNLPEWSVADVNGDL 241 Query: 216 KKYGLSGSPTQVERI 230 + GLSGSPT+V+ I Sbjct: 242 AQCGLSGSPTKVKAI 256 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: 208 Number of extensions: 11 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: 290 Length adjustment: 25 Effective length of query: 239 Effective length of database: 265 Effective search space: 63335 Effective search space used: 63335 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