Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate H281DRAFT_03367 H281DRAFT_03367 electron transfer flavoprotein alpha subunit apoprotein
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Burk376:H281DRAFT_03367 Length = 314 Score = 144 bits (363), Expect = 4e-39 Identities = 104/321 (32%), Positives = 170/321 (52%), Gaps = 27/321 (8%) Query: 76 VYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVFVY 134 V +H I T I A++ +G ++ L+ G N AD K GV KV + Sbjct: 8 VIAEHDNTSIKGATLNTIAAAQK----VGGDIHVLVAGQNAQAAADAAAKIAGVSKVLLA 63 Query: 135 DKPELKHFVIE----PYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADC 190 D P+L + E N+ +D+ S I AT G+++APR+AA+ +D Sbjct: 64 DAPQLAEGLAENVEATVLNIAKDY------SHIFAPATAYGKNIAPRIAAKLDVAQISDI 117 Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250 T ++ + + RP + GN +A + + + + TVR F A V G+ + Sbjct: 118 TAVDSPDTFE----RPIYAGNAIATVQSADPI-KVITVRTTGFDA---VAAEGGNATVEK 169 Query: 251 IEKAKL--VSAIEVMEVIKKEKGIDLSEAETIVAVGRGV-KCEKDLDMIHEFAEKIGATV 307 IE A +S EV K ++ +L+ A+ IV+ GRG+ E ++ A+K+ A + Sbjct: 170 IEAAADAGISQFVSREVTKLDRP-ELTSAKIIVSGGRGLGNGENYTKVLEPLADKLNAAL 228 Query: 308 ACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKA 367 +R ++AG+ Q+G +G+ V P+L +A+GISGA+Q AGM++S+ I+AIN DP+A Sbjct: 229 GASRAAVDAGFVPNDYQVGQTGKIVAPQLYVAVGISGAIQHLAGMKDSKVIVAINKDPEA 288 Query: 368 PIFNIAHCGMVGDLYEILPEL 388 PIF++A G+VGDL+ ++PEL Sbjct: 289 PIFSVADYGLVGDLFTLVPEL 309 Lambda K H 0.319 0.137 0.395 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: 308 Number of extensions: 16 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: 418 Length of database: 314 Length adjustment: 29 Effective length of query: 389 Effective length of database: 285 Effective search space: 110865 Effective search space used: 110865 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 (21.7 bits) S2: 49 (23.5 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