Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ac3H11_1711 Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor (EC 1.3.99.13)
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1711 Length = 393 Score = 404 bits (1039), Expect = e-117 Identities = 211/400 (52%), Positives = 275/400 (68%), Gaps = 12/400 (3%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDL F+ EE AFRDEVR + N+P K+ T+ +M W +IL KKGW W Sbjct: 1 MDLAFTPEEQAFRDEVRAWVHANLPQDISHKVHNALRLTRADMQGWAKILGKKGWLGFGW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 PKE+GG GW++VQ ++F EE A AP+ + FG MV PVI FG+ EQ+KRFLP IA+ Sbjct: 61 PKEFGGPGWTAVQKHLFEEECALAGAPRIIPFGPVMVAPVIMAFGNAEQQKRFLPGIASG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 + WW QG+SEPGSGSDLAS+KT+AE+ GDK+I+NGQKTWTTL QH DW+F L RT K Sbjct: 121 EVWWSQGYSEPGSGSDLASVKTRAERVGDKYIVNGQKTWTTLGQHGDWMFNLVRTSNEGK 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 Q GISF+L+DMK+KG+TVRPI+ +DG EVNEVFFD+VEVP ENL+G+ENKGW YAK L Sbjct: 181 PQTGISFLLLDMKSKGVTVRPIKLLDGECEVNEVFFDNVEVPAENLIGEENKGWTYAKHL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ERT IA V SK + R+K++A + V +D +FRD++A +E+++ ALE+ L Sbjct: 241 LSHERTNIADVNRSKRELERLKRIAKT-----EGVWDDQRFRDQIALLEVDIVALEMLVL 295 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY-----DVHGDDDS 355 RV++ E K GK + A +LKIKGSEIQQ EL+M GPF+ P+ + + Sbjct: 296 RVLSAE-KSGKNSLDIA-GLLKIKGSEIQQRYAELMMLAAGPFSLPFIEEAMEAGWQGNF 353 Query: 356 NETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLG 395 + A +A YFN RK +IYGGSNE+QRNI+ + VLG Sbjct: 354 PGGVTANAPLASTYFNLRKTTIYGGSNEVQRNIVAQTVLG 393 Lambda K H 0.317 0.135 0.411 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: 504 Number of extensions: 23 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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 (21.6 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