Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_013258753.1 DEBA_RS09720 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000143965.1:WP_013258753.1 Length = 383 Score = 352 bits (902), Expect = e-101 Identities = 190/385 (49%), Positives = 252/385 (65%), Gaps = 2/385 (0%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 MD +L+ E + LR++V +FA +AP+ EF E R MG +GLFG+ E YG Sbjct: 1 MDFQLSMEQDILRKSVRDFAEKEIAPQAQRLDADEEFSMETFRAMGELGLFGMIVDEAYG 60 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G G DY++ IA+EE+AR+D S A T+ AG SLG PI +G++ QK ++LP LC+G L Sbjct: 61 GQGMDYISYIIAVEEIARIDGSHAATVAAGNSLGIGPIFYYGSEEQKHKYLPELCAGRAL 120 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 FGLTEP+ GSDAG RTTA LD + W+ING+K FITN+ T + VTV A TG P Sbjct: 121 WGFGLTEPNAGSDAGGARTTAVLDGDS--WLINGSKIFITNASTPASLGVTVMARTGVFP 178 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 DG+P +S I+V +GTPGF + K+ W AS+T EL F D RVPA N+LG++G+G+ Q Sbjct: 179 DGRPELSCILVENGTPGFEARPMHGKMMWRASNTSELYFEDCRVPATNILGQRGKGFHQM 238 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L LD GR++I A+ G AQG + ++KYA +R FGR I A+Q FK+ADM M+ A Sbjct: 239 LATLDAGRLSIGAMGVGGAQGAYELALKYAKQREQFGRPIAAFQVNAFKLADMAMEIEAA 298 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R+ A + + F K AA+AKLY+S V A EA Q+HGGYG M EY V R +RD Sbjct: 299 RLLLYKACWQKDNHQSFSKLAAMAKLYASEVMGRVATEAVQLHGGYGLMREYDVERFFRD 358 Query: 361 SKILEIGEGTSEVQRMLIARELGLV 385 K+L IGEGTSEVQR++IAR +G + Sbjct: 359 QKLLTIGEGTSEVQRLVIARLIGAI 383 Lambda K H 0.318 0.136 0.402 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: 447 Number of extensions: 18 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: 386 Length of database: 383 Length adjustment: 30 Effective length of query: 356 Effective length of database: 353 Effective search space: 125668 Effective search space used: 125668 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