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_011655127.1 RL_RS31715 acyl-CoA dehydrogenase
Query= SwissProt::P45954 (432 letters) >NCBI__GCF_000009265.1:WP_011655127.1 Length = 395 Score = 186 bits (473), Expect = 9e-52 Identities = 118/379 (31%), Positives = 193/379 (50%), Gaps = 6/379 (1%) Query: 51 FAPLQTFTDEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPE 110 F ++ T EE M++ + +AQE++AP V N K + + + + + GL+G + P+ Sbjct: 14 FRLVEQLTSEERMVQDTAHAYAQEKLAPRVLDAFRNEKTDPEIFREMGELGLLGPTISPD 73 Query: 111 YGGTGASFLSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-E 169 YGG G +++ L+ E+ KVD+ +Q++L+ I G++ QK YLP+L T E Sbjct: 74 YGGAGLGYVAYGLIAREVEKVDSGYRSMMSVQSSLVMVPIETFGSQAQKLKYLPKLATGE 133 Query: 170 KVGSFCLSEAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGY 229 +G F L+E GSD ++ TRA K Y L GSK WIS+A A +F+V A + + Sbjct: 134 WIGCFGLTEPDHGSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADVFVVWAKTEDGL-- 191 Query: 230 KGITSFLVDRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGS 289 I F++++ GL K+GLRAS T + + V VPE N+L + G K Sbjct: 192 --IRGFILEKGWKGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLLPDV-TGLKGPFTC 248 Query: 290 LNEGRIGIAAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLL 349 LN R GIA LG A+ C+ Y ER QFG+ L Q +Q ++A +A ++ Sbjct: 249 LNSARFGIAWGALGAAEDCYARARQYTLERKQFGRPLAANQLIQKKLADMAAEISLGLQG 308 Query: 350 TYNAARLLEAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKI 409 R+ E G P ++ S+ K + A + + +GG G + ++ + ++ + ++ Sbjct: 309 CLRLGRMKEEGHPPVELTSILKRNSCGKALEIARAARDMLGGNGISDEFGIARHLVNLEV 368 Query: 410 GTIYEGASNIQLNTIAKHI 428 YEG +I I + I Sbjct: 369 VNTYEGTHDIHALIIGRAI 387 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: 357 Number of extensions: 22 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: 432 Length of database: 395 Length adjustment: 31 Effective length of query: 401 Effective length of database: 364 Effective search space: 145964 Effective search space used: 145964 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 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