Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate WP_057508390.1 ABB28_RS09465 electron transfer flavoprotein subunit alpha/FixB family protein
Query= BRENDA::H6LBB1 (418 letters) >NCBI__GCF_001431535.1:WP_057508390.1 Length = 312 Score = 141 bits (355), Expect = 3e-38 Identities = 99/318 (31%), Positives = 155/318 (48%), Gaps = 16/318 (5%) Query: 74 ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132 I V +H +G+++ T + + A A+ G V+ L++ + T A E K GV KV Sbjct: 4 ILVIAEHHDGKLNAATAKTVSAA---TAISGAEVHVLVLAADPTAVAAEAAKINGVSKVL 60 Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKP--SSILVGATNVGRSLAPRVAARYRTGLTADC 190 + P A VL I K S + +T G+ L P VAA +D Sbjct: 61 TVANAANAN----PIAQVLAPQIAKAAAGYSHVFGPSTTFGKDLMPCVAALLGVAQVSDL 116 Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250 +E RP + GN + + + TVR + PE VE + Sbjct: 117 MTVEGSHTFK----RPIYAGNAIITVEAPADQTVVATVRSASW--PEAAQGGSASVEALS 170 Query: 251 IEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVACT 310 +E V DL A+ +V+ GRGV E++ +I++ A+K+GA V + Sbjct: 171 VEATLPTHTRFVGLAAASSDRPDLQSAKRVVSGGRGVGSEENFKVIYQLADKLGAAVGAS 230 Query: 311 RPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPIF 370 R ++AG+ LQ+G +G+ + P+L +A+GISGA+Q G++++ I+AIN DP +PIF Sbjct: 231 RAAVDAGYVPNELQVGQTGKIIAPELYLAIGISGAIQHLTGIKDAGTIVAINKDPDSPIF 290 Query: 371 NIAHCGMVGDLYEILPEL 388 IA G+VGDL+ +LPEL Sbjct: 291 EIADIGLVGDLFTLLPEL 308 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: 261 Number of extensions: 8 Number of successful extensions: 1 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: 312 Length adjustment: 29 Effective length of query: 389 Effective length of database: 283 Effective search space: 110087 Effective search space used: 110087 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 24 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