Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_092483748.1 BM299_RS10480 electron transfer flavoprotein subunit alpha/FixB family protein
Query= BRENDA::D2RIQ3 (340 letters) >NCBI__GCF_900115975.1:WP_092483748.1 Length = 325 Score = 261 bits (668), Expect = 1e-74 Identities = 142/324 (43%), Positives = 200/324 (61%), Gaps = 7/324 (2%) Query: 13 KDLWVYVEHYKGEPVHVVYELLGECRKLADKCNQKLAAVLITDDAKDVPSKLIARGADLV 72 K +WV+ E G+ V +ELL E RK+AD+ ++L AVL+ + D+ + L GAD V Sbjct: 3 KGIWVFAEQRDGQIKKVTFELLSEGRKIADQLGEELGAVLLGNGVADLAASLGEYGADKV 62 Query: 73 YVCQDPAFKYYSTDEYTNAFCEMIDEYQPSSVFIGATNDGRDLGPRIAARVNTGLCADCT 132 YV A + Y+TD YTN +++ +Y PS + +G T GRDL ++A R+ TGL DCT Sbjct: 63 YVADSDALENYTTDGYTNVIADLVKQYAPSVLLMGCTVTGRDLAAQVAQRLETGLMTDCT 122 Query: 133 ILDAEEDGLIEWTRPAAGGNIMATILCKEHRPQMGTVRPKTFKAMEPDASRTGEVINYTL 192 ++ DG + +TRP G + C E RP M T+RP TF ++ E+IN T Sbjct: 123 GMEIA-DGQLVFTRPIYAGKAIVKAACPEARPVMATIRPNTFAVQA--GAKEAEIINVTP 179 Query: 193 KN-HVDDRVTCIRREEVVSEGEMAIDDAPFVCSGGRGMKAKENFSLLYDLAHALGGAVGG 251 ++ + I R+ VSE + +A + SGGRGMK ENF LL +LA LG AVG Sbjct: 180 NTGNIRQVIKDIVRQ--VSE-RPELTEADIIVSGGRGMKGPENFKLLEELADVLGAAVGA 236 Query: 252 SRAAVDEGFIEHPRQVGQSGKTVTPKIYFACGISGSVQHKAGMSKSDTIVCINKDPDAPM 311 SRAAVD G+I QVGQ+GKTV+P +Y ACGISG++QH AGMS + IV INKD +A + Sbjct: 237 SRAAVDAGWIPQSFQVGQTGKTVSPVLYIACGISGAIQHLAGMSSAKCIVAINKDEEANI 296 Query: 312 FEISKYGIVGDALKILPLLTAKIK 335 F+++ YGIVGD +++P+L ++K Sbjct: 297 FKVADYGIVGDLFEVVPILKEELK 320 Lambda K H 0.318 0.136 0.406 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: 313 Number of extensions: 16 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: 340 Length of database: 325 Length adjustment: 28 Effective length of query: 312 Effective length of database: 297 Effective search space: 92664 Effective search space used: 92664 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 (21.7 bits) S2: 49 (23.5 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