Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109) (characterized)
to candidate SMa0822 SMa0822 FixA electron transfer flavoprotein beta chain
Query= BRENDA::Q18AQ6 (260 letters) >FitnessBrowser__Smeli:SMa0822 Length = 292 Score = 191 bits (485), Expect = 1e-53 Identities = 109/239 (45%), Positives = 151/239 (63%), Gaps = 14/239 (5%) Query: 1 MNIVVCIKQVPDTTEVKLDPNTGTLIRDGVPSIINPDDKAGLEEAIKLKEEMGAHVTVIT 60 M++VVCIKQVPD+ ++++ P T T++R GVP+IINP D A LEEA+KL + G VTV+T Sbjct: 1 MHLVVCIKQVPDSAQIRVHPVTNTIMRQGVPTIINPHDLAALEEALKLCDTYGGEVTVVT 60 Query: 61 MGPPQADMALKEALAMGADRGILLTDRAFAGADTWATSSALAGALKNIDF-----DIIIA 115 MGP A+ AL++AL GA R +LLTDR FAG+DT ATS ALA A+ I D++ Sbjct: 61 MGPKMAEDALRKALTFGAHRAVLLTDRHFAGSDTLATSFALAQAIAEIGETFGTPDVVFT 120 Query: 116 GRQAIDGDTAQVGPQIAEHLNLPSITYAEE---IKTEGEYVLVKRQFEDCCHDLKVKMPC 172 G+Q IDGDTAQVGP IA+ L+L +TY + I + V+R+ E L+ +PC Sbjct: 121 GKQTIDGDTAQVGPGIAKRLDLQQLTYVAKILSIDAASREITVERRAEGGSQILRTGLPC 180 Query: 173 LITTLKDMNTPRYMKVGRIYDAFE--NDVVETWTVKDIEV-DPSNLGLKGSPTSVFKSF 228 L+T L + ++ GR+ DA V W+ D + +P+N GL+GSPT V + F Sbjct: 181 LVTMLDGADA---IRRGRLDDALRAARTKVVKWSAADAGIAEPANCGLRGSPTVVKRVF 236 Lambda K H 0.316 0.135 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: 204 Number of extensions: 8 Number of successful extensions: 3 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: 260 Length of database: 292 Length adjustment: 25 Effective length of query: 235 Effective length of database: 267 Effective search space: 62745 Effective search space used: 62745 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: 41 (21.6 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