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_011654325.1 RL_RS28880 isovaleryl-CoA dehydrogenase
Query= SwissProt::P45954 (432 letters) >NCBI__GCF_000009265.1:WP_011654325.1 Length = 381 Score = 273 bits (697), Expect = 9e-78 Identities = 140/368 (38%), Positives = 226/368 (61%), Gaps = 1/368 (0%) Query: 64 IKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGTGASFLSTVL 123 I+ + +FA + IAPL + +DE++ + + + GL GI V+ E+GG G +L V+ Sbjct: 13 IRETTARFAADHIAPLAAEIDESNTFPRQLWPEMGALGLHGITVEEEFGGAGLGYLDHVV 72 Query: 124 VIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGSFCLSEAGAG 182 +EE+++ ASV + + L IR+ + EQK +LP+L + E VGS +SE GAG Sbjct: 73 AMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRHLPKLISGEHVGSLAMSEVGAG 132 Query: 183 SDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITSFLVDRDTP 242 SD +++ RA+K+GD Y+LNG+K WI++A HA + +V A DP G KGI++F++++ P Sbjct: 133 SDVVSMRLRAEKKGDRYILNGTKFWITNAPHADVLVVYAKTDPAAGPKGISAFIIEKGLP 192 Query: 243 GLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGRIGIAAQML 302 G + K +KLG+R S T L FE+ +VP ++G+ G G K + L+ R +A L Sbjct: 193 GFSVSKKLSKLGMRGSDTAELVFEDCEVPAEALMGREGEGVKILMSGLDYERAVLAGGPL 252 Query: 303 GLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAARLLEAGKP 362 G+ Q C D +PY+++R QFGK + DFQ +Q ++A + L +AR Y+ AR +AG+ Sbjct: 253 GIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYSVARACDAGRA 312 Query: 363 FIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYEGASNIQLN 422 +A+ A +ASE A + + + I+ +GG GYTK++PVE++ RDAK+ I G + I+ Sbjct: 313 TRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDIGAGTNEIRRY 372 Query: 423 TIAKHIDA 430 I + + A Sbjct: 373 LIGRELIA 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: 363 Number of extensions: 12 Number of successful extensions: 2 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