Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01368 CCNA_01368 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Caulo:CCNA_01368 Length = 404 Score = 447 bits (1151), Expect = e-130 Identities = 232/406 (57%), Positives = 291/406 (71%), Gaps = 12/406 (2%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 M+L+FS E++AFRDEVR F +N PA R K EG KE+ + W+R+L KGW W Sbjct: 1 MNLDFSPEDLAFRDEVRAFIAENYPAGLRDKQEEGEEMAKEDFLSWHRVLANKGWVAPAW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P +YGG GW+SVQ YI++EE A L FG++MVGPVIYTFG+ EQK+RFLP + Sbjct: 61 PTQYGGPGWTSVQRYIWSEETARADCVPILPFGINMVGPVIYTFGTPEQKERFLPGTLSG 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEK-KGDK----WIINGQKTWTTLAQHADWIFCLCRT 175 D WW QG+SEPG+GSDLASLKTKAE+ GD +++NGQKTWTT+AQH DWIFCL RT Sbjct: 121 DIWWSQGYSEPGAGSDLASLKTKAERFTGDDGKEYYLVNGQKTWTTMAQHGDWIFCLVRT 180 Query: 176 DPAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWD 235 DP AK QEGISF+L+DMK+ G+TVRPI T+ G HEVNEV+F++V+VP+EN + ENKGW Sbjct: 181 DPNAKIQEGISFLLIDMKSPGVTVRPIITLGGEHEVNEVWFENVKVPVENRIYDENKGWT 240 Query: 236 YAKFLLGNERTGIARVGMSKERIRRIKQLAA-QVESGGKPVIEDPKFRDKLAAVEIELKA 294 AKFLL +ER+GIA V SK I RI+Q+A+ ++ G +I+DP F+ K+A +EI+L A Sbjct: 241 CAKFLLAHERSGIAGVARSKRGIERIRQIASTELSDDGDALIKDPMFKRKVAELEIDLTA 300 Query: 295 LELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY----DVH 350 LE T+LR +A E G+G P P SSVLKIKG+EIQQ TEL +E G + APY Sbjct: 301 LEYTELRTLAGEAA-GRG-PGPESSVLKIKGTEIQQRLTELALEAAGHYGAPYFRGFPKD 358 Query: 351 GDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 GD+ ++ + AP YFN RK SIYGGSNEIQRNII K VLGL Sbjct: 359 GDNAHPIGPEFAHRAAPTYFNVRKTSIYGGSNEIQRNIIAKMVLGL 404 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: 538 Number of extensions: 21 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: 404 Length adjustment: 31 Effective length of query: 365 Effective length of database: 373 Effective search space: 136145 Effective search space used: 136145 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