Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_086511948.1 BZY95_RS21585 pimeloyl-CoA dehydrogenase large subunit
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_002151265.1:WP_086511948.1 Length = 398 Score = 432 bits (1112), Expect = e-126 Identities = 213/400 (53%), Positives = 288/400 (72%), Gaps = 6/400 (1%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M+++FS++E+AFRDEVR F +PA K+ G+ TK++ W IL+++GW +W Sbjct: 1 MNIHFSEQELAFRDEVRAFLAAELPADIAAKVRLGKKLTKQDHQRWQAILHRRGWYAANW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P E+GGTGWS V+ +IF EE AA AP+ ++FGV+MV PVI FG+ EQK +LPRI + Sbjct: 61 PVEHGGTGWSVVEKHIFEEECAAAGAPRLISFGVNMVAPVIIRFGTPEQKAHYLPRILDG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 DWWCQG+SEPG+GSDLA++KT+A ++GD +I+NGQKTWTTL QHA+WIFCL RTDP AK Sbjct: 121 TDWWCQGYSEPGAGSDLAAVKTRAVREGDHYIVNGQKTWTTLGQHANWIFCLVRTDPEAK 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 Q GISF+L+DM++ GI+VRPI T+DG HEVNEVFFD+V VP+ NLVGQEN GW AK+L Sbjct: 181 PQAGISFLLIDMESPGISVRPIITLDGAHEVNEVFFDNVRVPVANLVGQENDGWTCAKYL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ERTG A +G+SK + +K++A Q G+P +EDP R ++A VE+ L A+E++ L Sbjct: 241 LTHERTGQAGIGISKAALAHLKEVARQEVIDGRPALEDPLLRQRIAEVEMRLMAVEMSTL 300 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY---DVHGDDDSNE 357 R++A G P SS+LKI GSEI+QA ++L V+GP A P+ ++ + D Sbjct: 301 RILA--RAQAGGVPGAESSILKITGSEIRQAISDLARRVLGPHALPFLAEEMQLEHDGEP 358 Query: 358 T-MDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 D++ A Y N RK+SIYGGSNEIQ+NI+ KA LGL Sbjct: 359 LHADYSVAPAAQYLNLRKLSIYGGSNEIQKNILAKAQLGL 398 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: 467 Number of extensions: 16 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: 396 Length of database: 398 Length adjustment: 31 Effective length of query: 365 Effective length of database: 367 Effective search space: 133955 Effective search space used: 133955 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 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