Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_02215 CCNA_02215 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Caulo:CCNA_02215 Length = 403 Score = 358 bits (920), Expect = e-103 Identities = 192/407 (47%), Positives = 262/407 (64%), Gaps = 15/407 (3%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHN--TKEEMVEWYRILNKKGWAVT 58 MDL FS E++AF+ EVR + R+++ + ++ K V+W + L ++GWA Sbjct: 1 MDLAFSAEDLAFQQEVRDWIATAYDDDLRRQMSQSKNGYLDKAGQVKWQKKLAERGWAAP 60 Query: 59 HWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIA 118 WP E GG G++ Q YIFN E+ A P G+ MV PVI FGS+ QK + LP I Sbjct: 61 DWPVELGGAGFTPSQRYIFNMEMSLAGVPTSSPMGLKMVAPVIMAFGSDAQKAQHLPPIL 120 Query: 119 NVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178 N D WWCQG+SEPGSGSDLASL+ +A + GD +++NG K WTT AQ ADW+FCL RT Sbjct: 121 NSDIWWCQGYSEPGSGSDLASLQMRAVRDGDDYVLNGSKIWTTHAQWADWMFCLVRTSTE 180 Query: 179 AKKQEGISFILVDMKTKGITVRPIQTIDG----GHEVNEVFFDDVEVPLENLVGQENKGW 234 K QEGISF+L+ M T GI ++P+ T+DG E+N+VFFD+V VP+ N +G+ENKGW Sbjct: 181 GKPQEGISFLLLRMDTPGIQIKPLPTLDGPPDNEQEINQVFFDNVRVPVANRIGEENKGW 240 Query: 235 DYAKFLLGNERTGIARVGMSKERIRRIKQLAA--QVESGGKPVIEDPKFRDKLAAVEIEL 292 YAK+LL ER G+ ++++K++AA + + GG+ +I+DP FR K+A +EI++ Sbjct: 241 TYAKYLLEFERGNAYAPGL-MNMLKKVKRIAALERADDGGR-LIDDPDFRSKIANLEIQV 298 Query: 293 KALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY--DVH 350 +AL ++LR+ + G GK PASS+LK GSE QQA TEL +E +G +A P+ D Sbjct: 299 EALNASELRIFSGRGA-GK-NIGPASSMLKCVGSEHQQAITELTLEAVGNYATPFVRDTW 356 Query: 351 GD-DDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 +D D+ AP YFN RK SIY GSNEIQRNI+ K VLGL Sbjct: 357 SPANDGRAGPDYAGPAAPAYFNYRKASIYAGSNEIQRNIMAKMVLGL 403 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: 466 Number of extensions: 18 Number of successful extensions: 5 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: 403 Length adjustment: 31 Effective length of query: 365 Effective length of database: 372 Effective search space: 135780 Effective search space used: 135780 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