Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate N515DRAFT_4319 N515DRAFT_4319 electron transfer flavoprotein alpha subunit apoprotein
Query= BRENDA::H6LBB1 (418 letters) >FitnessBrowser__Dyella79:N515DRAFT_4319 Length = 314 Score = 140 bits (353), Expect = 5e-38 Identities = 98/318 (30%), Positives = 160/318 (50%), Gaps = 15/318 (4%) Query: 74 ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132 I V +H+ G+++ T + A AAV G + L++ ++ A E K GV KV Sbjct: 4 ILVVAEHLNGKLNSSTARAVSAA---AAVKGDSIDVLVLADSVDAIAAEAAKIDGVGKVL 60 Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKP--SSILVGATNVGRSLAPRVAARYRTGLTADC 190 + E H P A VL + K S + +T G+ +APRVAA +D Sbjct: 61 TIARAENAH----PLAAVLAPQVAKAAAGYSHVFFPSTTFGKDVAPRVAALLGVSQVSDV 116 Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250 +E + RP + GN + + T+R + A + VE + Sbjct: 117 MSVEGAHSFK----RPIYAGNAIVTVEANPAHAVVATIRTASWPAAGSRGDS-AAVEALA 171 Query: 251 IEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACT 310 ++ A V K DL A +V+ GRGV +++ ++I++ A+KIGA V + Sbjct: 172 VDAALPAHTRFVELQQGKSDRPDLQGAGKVVSGGRGVGSKENFEVIYKLADKIGAAVGAS 231 Query: 311 RPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIF 370 R ++AG+ LQ+G +G+ + P+L +A GISGA+Q G++++ I+AIN D +APIF Sbjct: 232 RAAVDAGYVPNELQVGQTGKIIAPELYMAFGISGAIQHLTGIKDAGTIVAINKDGEAPIF 291 Query: 371 NIAHCGMVGDLYEILPEL 388 IA G+VGDL++++PE+ Sbjct: 292 EIADIGLVGDLFKLIPEI 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: 266 Number of extensions: 10 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