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 Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase
Query= SwissProt::P70584 (432 letters) >FitnessBrowser__PS:Dsui_0975 Length = 390 Score = 246 bits (629), Expect = 7e-70 Identities = 132/373 (35%), Positives = 218/373 (58%), Gaps = 4/373 (1%) Query: 63 MMQKAVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGMMGIEVEAKYGGTEASFLCSV 122 M++ V+ FA ++IAP + +D +++ + Q G++G+ E +YGGT +L + Sbjct: 16 MLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTAEEEYGGTAMGYLAHI 75 Query: 123 LVIEELAKVDASVALLCDIQNTVINKLFRKHGTEEQKATYLPKLVT-EKLGSFCLSEAGA 181 + +EE+++ ASV L + + R++GT QKA YLP L++ ++G+ +SE A Sbjct: 76 VAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGLISGTQVGALAMSEPNA 135 Query: 182 GSDSFALKTRADKSGNYYVINGSKMWISNAEHAELFLVFANVDPPSGYRGITCFLVDRDT 241 GSD ++K +A+K G+ YV+NGSKMWI+N A+ +V+A D +G +G+T F+V++ Sbjct: 136 GSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLNAGAKGMTAFIVEKGF 195 Query: 242 EGFQIGRRENKMGIRASSTCQLTFENVKVPETSVLGKIGHGYKYAIGSLNEGRIGIAAQM 301 +GF G +K+G+R S+T L F++ +VPE +VLG +G+G K + L+ R + Sbjct: 196 KGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVLMSGLDYERAVLCGGP 255 Query: 302 LGLAQGCFDYTIPYIKERMQFGKRIFDFQGLQHQVAHVATQLEAARLLTY---NAARLVE 358 LG+ C D +PY+ ER QFG I +FQ +Q ++A + + +A R Y A + Sbjct: 256 LGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQATRAYVYAVGQACDRAD 315 Query: 359 AGRPFIKEASMAKYYASEVAGLTTSKCIEWMGGVGYTKDYPVEKFFRDAKIGTIYEGTSN 418 R K+A+ A Y++E A I+ +GGVGYT +YP + +RDAK+ I GTS Sbjct: 316 HARSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRLWRDAKLYEIGAGTSE 375 Query: 419 IQLNTIAKHIDAE 431 I+ I + + AE Sbjct: 376 IRRMLIGRELFAE 388 Lambda K H 0.319 0.134 0.389 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: 403 Number of extensions: 19 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: 390 Length adjustment: 31 Effective length of query: 401 Effective length of database: 359 Effective search space: 143959 Effective search space used: 143959 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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