Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate WP_086509769.1 BZY95_RS09885 pimeloyl-CoA dehydrogenase large subunit
Query= metacyc::MONOMER-20676 (396 letters) >NCBI__GCF_002151265.1:WP_086509769.1 Length = 397 Score = 414 bits (1064), Expect = e-120 Identities = 200/399 (50%), Positives = 279/399 (69%), Gaps = 5/399 (1%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M+L+F+ EE AFR EVR+F +P R+++ GR + ++ + W +L+++GW W Sbjct: 1 MNLDFTPEEQAFRREVREFLAAELPDDIRERVRLGRRLSADDHLRWQNVLSRRGWLAAGW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P+E+GG GW V+ +IF+EE AA AP + FGVSMV PVI FGSE Q++ +LPRI Sbjct: 61 PREHGGPGWGPVERHIFDEECAAAHAPTIVPFGVSMVAPVIMKFGSEAQQRHYLPRILAN 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180 DWWCQG+SEPG+GSDLASL+T+A + GD ++++GQKTWTTL QHA+ +FCL RTDP A+ Sbjct: 121 RDWWCQGYSEPGAGSDLASLRTRAVRDGDDYVVSGQKTWTTLGQHANMMFCLVRTDPEAR 180 Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240 KQ GISF+L+DM + GI+VRPI T+DG HEVNEVF D+V VP+ N +G+E +GW AKFL Sbjct: 181 KQAGISFLLIDMHSPGISVRPIVTLDGAHEVNEVFLDEVRVPVTNRIGEEGQGWTCAKFL 240 Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300 L +ERTGIA +G +K+ +R +K LA +V G+P++E FR ++ E+EL ALE+T L Sbjct: 241 LTHERTGIAGIGHAKQALRHLKVLAGRVRHRGRPLLELASFRQRVVKAEVELMALEVTHL 300 Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY---DVHGDDDSNE 357 RV+A G P SS+LK++GSE++Q +EL +GP A P+ ++GD + Sbjct: 301 RVLA--AARDGGAPGAESSLLKVRGSELRQELSELTRRALGPAALPFFPDFLYGDAELEP 358 Query: 358 TMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 A I Y N RK+SIYGGSNEIQ++I+ K +LG+ Sbjct: 359 DRAERAAIGAQYLNRRKLSIYGGSNEIQKSIVAKTLLGM 397 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: 438 Number of extensions: 14 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: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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