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 CCNA_02254 CCNA_02254 isovaleryl-CoA dehydrogenase
Query= SwissProt::P70584 (432 letters) >FitnessBrowser__Caulo:CCNA_02254 Length = 386 Score = 261 bits (668), Expect = 2e-74 Identities = 140/384 (36%), Positives = 231/384 (60%), Gaps = 5/384 (1%) Query: 48 ALCFAPLQTFT--DEDIMMQKAVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGMMGI 105 ++ FAP F + +++ +FA ++IAP+ + +DE + + + + G+ GI Sbjct: 2 SMTFAPSMDFALGETADAIRETTARFAADKIAPIAAKIDETNSFPRELWVPMGDLGLHGI 61 Query: 106 EVEAKYGGTEASFLCSVLVIEELAKVDASVALLCDIQNTVINKLFRKHGTEEQKATYLPK 165 VE ++GG +L V+ +EE+++ ASV L + + R+ T EQKA YLPK Sbjct: 62 TVEEEFGGLGLGYLEHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWATPEQKARYLPK 121 Query: 166 LVT-EKLGSFCLSEAGAGSDSFALKTRADKSGNYYVINGSKMWISNAEHAELFLVFANVD 224 L++ E +GS +SEAGAGSD ++K RA++ G+ Y++NG+K WI+NA HA+ +V+A Sbjct: 122 LISGEHVGSLAMSEAGAGSDVVSMKLRAEQVGDRYILNGTKFWITNAPHADTLVVYAKTG 181 Query: 225 PPSGYRGITCFLVDRDTEGFQIGRRENKMGIRASSTCQLTFENVKVPETSVLGKIGHGYK 284 G RGIT F+V++ +GF + ++ +KMG+R S T +L FE+ ++PE +V+G +G G Sbjct: 182 --EGSRGITAFIVEKGMKGFSVSKKLDKMGMRGSDTAELVFEDCEIPEENVMGPVGGGVG 239 Query: 285 YAIGSLNEGRIGIAAQMLGLAQGCFDYTIPYIKERMQFGKRIFDFQGLQHQVAHVATQLE 344 + L+ R +AA LG+ Q C D +PY+++R QFG+ I FQ +Q ++A + L Sbjct: 240 VLMSGLDYERAVLAAGPLGIMQACLDVVLPYVRDRKQFGQPIGSFQLMQGKIADMYVALN 299 Query: 345 AARLLTYNAARLVEAGRPFIKEASMAKYYASEVAGLTTSKCIEWMGGVGYTKDYPVEKFF 404 +AR Y A+ +AG+ +A+ A ASE A + + I+ +GG GYTK++PVE+ Sbjct: 300 SARAYVYAVAKACDAGKTTRFDAAGAILMASENAVKVSLEAIQALGGAGYTKEWPVERLL 359 Query: 405 RDAKIGTIYEGTSNIQLNTIAKHI 428 RDAK+ I GT+ I+ I + + Sbjct: 360 RDAKLYDIGAGTNEIRRFLIGREL 383 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: 377 Number of extensions: 13 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: 386 Length adjustment: 31 Effective length of query: 401 Effective length of database: 355 Effective search space: 142355 Effective search space used: 142355 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