Align Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial; SBCAD; 2-methyl branched chain acyl-CoA dehydrogenase; 2-MEBCAD; 2-methylbutyryl-coenzyme A dehydrogenase; 2-methylbutyryl-CoA dehydrogenase; EC 1.3.8.5 (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase
Query= SwissProt::P45954 (432 letters) >NCBI__GCF_000428045.1:WP_029134232.1 Length = 397 Score = 176 bits (446), Expect = 1e-48 Identities = 114/366 (31%), Positives = 191/366 (52%), Gaps = 7/366 (1%) Query: 55 QTFTDEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGT 114 Q T+EE M++ + +K+ QEQ+ P V + + ++ ++ + + GL+G+ +D Y Sbjct: 21 QQLTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTIDG-YDCA 79 Query: 115 GASFLSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGS 173 G +++S L+ E+ +VD+ +Q++L+ I +GTEEQ+ YLP+L T E VG Sbjct: 80 GLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGC 139 Query: 174 FCLSEAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGIT 233 F L+E GSD +KTRA Y L+GSKMWI+++ A +F+V A D + I Sbjct: 140 FGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDDEGV----IR 195 Query: 234 SFLVDRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEG 293 F++++ GL K E K LRAS T + + V VP N+L + G G LN Sbjct: 196 GFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNV-KGLAGPFGCLNRA 254 Query: 294 RIGIAAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNA 353 R GIA +LG A+ C+ + Y +R QFG+ L Q +Q ++A++ T++ Sbjct: 255 RYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCLQL 314 Query: 354 ARLLEAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIY 413 RL +AG+ + S+ K + A + GG G + ++ V ++ + + Y Sbjct: 315 GRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVNTY 374 Query: 414 EGASNI 419 EG ++ Sbjct: 375 EGTHDV 380 Lambda K H 0.318 0.134 0.385 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: 341 Number of extensions: 16 Number of successful extensions: 5 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: 432 Length of database: 397 Length adjustment: 31 Effective length of query: 401 Effective length of database: 366 Effective search space: 146766 Effective search space used: 146766 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: 50 (23.9 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