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_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase
Query= SwissProt::P45954 (432 letters) >NCBI__GCF_001046645.1:WP_066607952.1 Length = 381 Score = 259 bits (662), Expect = 1e-73 Identities = 143/371 (38%), Positives = 219/371 (59%), Gaps = 3/371 (0%) Query: 59 DEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGTGASF 118 D MI+ S +F+ ++IAPL + +D + + + + GL GI V E GG G + Sbjct: 10 DNADMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGGLGLGY 69 Query: 119 LSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGSFCLS 177 L V+ EE+A+ AS+ + + L IR+ G EQKA YLP+L + + VGS +S Sbjct: 70 LEHVVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHVGSLAMS 129 Query: 178 EAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITSFLV 237 EAGAGSD ++K +A+K+GD Y+LNG+K WI++A +A +V A G KGIT+FL+ Sbjct: 130 EAGAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTGE--GSKGITTFLI 187 Query: 238 DRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGRIGI 297 ++D G IG+ +K+G+R S T L F++ +VPE NI+G + G + L+ R + Sbjct: 188 EKDMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYERTVL 247 Query: 298 AAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAARLL 357 A LG+ Q C D +PY++ER QFG+ + FQ +Q +VA + L +AR Y AR Sbjct: 248 AGIQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVARAC 307 Query: 358 EAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYEGAS 417 ++GK +A+ A ASE A + + ++ +GG GYTKD+PVE+Y RDAK+ I G + Sbjct: 308 DSGKTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGAGTN 367 Query: 418 NIQLNTIAKHI 428 I+ I + + Sbjct: 368 EIRRMLIGREL 378 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: 361 Number of extensions: 12 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: 432 Length of database: 381 Length adjustment: 31 Effective length of query: 401 Effective length of database: 350 Effective search space: 140350 Effective search space used: 140350 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