Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109) (characterized)
to candidate WP_092482220.1 BM299_RS04215 electron transfer flavoprotein subunit beta/FixA family protein
Query= BRENDA::Q18AQ6 (260 letters) >NCBI__GCF_900115975.1:WP_092482220.1 Length = 269 Score = 191 bits (485), Expect = 1e-53 Identities = 105/260 (40%), Positives = 161/260 (61%), Gaps = 4/260 (1%) Query: 1 MNIVVCIKQVPDTTEVKLDPNTGTLIRDGVPSIINPDDKAGLEEAIKLKEEM-GAHVTVI 59 MNIV +KQVP T VK++P TGT++R G ++INP D+ L EA+++K++ G VT + Sbjct: 1 MNIVALVKQVPGTDNVKMNPETGTMVRTGKDNVINPLDENALTEALRIKQQTTGTTVTAV 60 Query: 60 TMGPPQADMALKEALAMGADRGILLTDRAFAGADTWATSSALAGALKNID-FDIIIAGRQ 118 +MGP A+ ALKEA+A+GAD GILL+ RAFAGADT AT+ LA A+K ++ +I+ G + Sbjct: 61 SMGPQTAEKALKEAIALGADEGILLSSRAFAGADTIATARVLAAAVKKLENVSMILCGER 120 Query: 119 AIDGDTAQVGPQIAEHLNLPSITYAEEIKTEGEYVLVKRQFEDCCHDLKVKMPCLITTLK 178 A DG+T Q GP +A L +P +T+ +EI +V R E+ +++ P + T +K Sbjct: 121 ATDGETGQTGPMVAAMLGIPVVTFVKEINVGENTAIVIRIVENGYEKVEIPYPFMATVVK 180 Query: 179 DMNTPRYMKVGRIYDAFENDVVETWTVKDIEVDPSNLGLKGSPTSVFKSFTKSVKPAGTI 238 D+N P + + A E +V+ W+ +++ + + LGL GSPT V K F+ + I Sbjct: 181 DINEPGFPTLSGKVQARET-LVKVWSEEELGLPKNELGLTGSPTRVVKIFSPKLARDTRI 239 Query: 239 YNEDAKTSA-GIIIDKLKEK 257 D +A GI++ L+EK Sbjct: 240 LKHDGSGNAVGILVKLLQEK 259 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: 180 Number of extensions: 10 Number of successful extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 235 Effective length of database: 244 Effective search space: 57340 Effective search space used: 57340 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 Apr 09 2024. 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