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_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase
Query= SwissProt::P45954 (432 letters) >NCBI__GCF_000775615.1:WP_036834050.1 Length = 400 Score = 260 bits (664), Expect = 6e-74 Identities = 137/374 (36%), Positives = 215/374 (57%), Gaps = 1/374 (0%) Query: 56 TFTDEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGTG 115 TF++E+ M++ +V++F ++I P + DE + +++ L GLMG+ + +YGG+G Sbjct: 4 TFSEEQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYGGSG 63 Query: 116 ASFLSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYL-PQLTTEKVGSF 174 + + +V EEL + D + + L + + + GTEEQK YL PQ EK+G+F Sbjct: 64 MDYNALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKIGAF 123 Query: 175 CLSEAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGITS 234 L+E GAGSD +++T A ++GDYY LNG K WIS + A FLV A D ++GI++ Sbjct: 124 GLTEPGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQGISA 183 Query: 235 FLVDRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEGR 294 F+V+R G + KLG+RA +T L E+V VP N LG+ G G+K A+ SL+ GR Sbjct: 184 FIVERTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLDNGR 243 Query: 295 IGIAAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNAA 354 +AA GL C + ++ Y ER FGK + Q +Q +A++ L+ +RLL Y A Sbjct: 244 FTVAAGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVYRAG 303 Query: 355 RLLEAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIYE 414 L +GK +E S+AK+ A + A + ++ G GY+ +Y VE+Y R++K IYE Sbjct: 304 ELKNSGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPVIYE 363 Query: 415 GASNIQLNTIAKHI 428 G I A+++ Sbjct: 364 GTREIHTIMQAEYV 377 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: 400 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 401 Effective length of database: 369 Effective search space: 147969 Effective search space used: 147969 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