Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate AO356_21850 AO356_21850 electron transfer flavoprotein subunit beta
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21850 Length = 311 Score = 121 bits (304), Expect = 3e-32 Identities = 91/315 (28%), Positives = 159/315 (50%), Gaps = 14/315 (4%) Query: 76 VYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKYGVDKVFVYD 135 V +H GQ+ T+ + A L V + + ++A L G+ +V + Sbjct: 5 VIAEHSAGQLTAGTWSAVTAAMALGTETDLLVMGGTAASAVAQQA--ALTQGLARVLLAQ 62 Query: 136 KPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTILEM 195 ++ + E ++ + + + ++ A+++GR++ PR+AA G+ +D T + Sbjct: 63 GAMFENALAENVQPLVTSLVAEGY-THVVADASSMGRNVLPRIAASLDVGMLSDVTQIV- 120 Query: 196 KENTDLVQIRPAFGGNIMAQIVTENTRP-QFCTVRYKVFTAPERVNEPWGDVEMMDIEKA 254 +TD Q RP + GN +A + ++ P + TVR F E++ +E Sbjct: 121 --STDTFQ-RPIYAGNAIATV--QSLDPIKLLTVRASAFAQALSHEHR---CEVVVVEGG 172 Query: 255 KLVSAIE-VMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACTRPG 313 + S + V E + + DLS A +V+ GRG++ ++ +I A+K+G V +R Sbjct: 173 QSASNVRFVSEQLTASERPDLSSARVVVSGGRGMQGKEHFALIERVADKLGGAVGASRAA 232 Query: 314 IEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIFNIA 373 +++G+ LQ+G +G+ V P+L IA GISGA+Q AGM S+ I+AIN D +API +A Sbjct: 233 VDSGFAPNDLQVGQTGKIVAPELYIAAGISGAIQHLAGMSGSKVIVAINQDAEAPIAQVA 292 Query: 374 HCGMVGDLYEILPEL 388 V DL+E LP L Sbjct: 293 DYMWVADLFEALPAL 307 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: 269 Number of extensions: 14 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: 311 Length adjustment: 29 Effective length of query: 389 Effective length of database: 282 Effective search space: 109698 Effective search space used: 109698 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