Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS05595 RR42_RS05595 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS05595 Length = 400 Score = 461 bits (1187), Expect = e-134 Identities = 232/402 (57%), Positives = 298/402 (74%), Gaps = 8/402 (1%) Query: 1 MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60 MDLN+S + AFR EVR + + N+PA+ K++ R ++++V W+++L +GW+ HW Sbjct: 1 MDLNYSASDDAFRAEVRGWLEANLPAEISSKILNHRRPNRDDLVRWHKLLAGRGWSAPHW 60 Query: 61 PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120 P +YGGTGW++ Q +I++EE AP L FGV+MV PVI +GSE QK +LPRI + Sbjct: 61 PVQYGGTGWNATQRHIWDEENARVGAPGVLPFGVAMVAPVIMKYGSEAQKSYYLPRILDC 120 Query: 121 DDWWCQGFSEPGSGSDLASLKTKAE--KKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178 DWWCQG+SEPGSGSDLASLKT+AE G +I+NGQKTWTTL QHAD IFCL RTD Sbjct: 121 TDWWCQGYSEPGSGSDLASLKTRAELTSDGKHYIVNGQKTWTTLGQHADMIFCLVRTDFE 180 Query: 179 AKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAK 238 AKKQEGISF+L+DMKT GITVRPI +D HEVNEVFFD+V+VP+EN VG+EN+GW YAK Sbjct: 181 AKKQEGISFLLIDMKTPGITVRPIIMLDEEHEVNEVFFDNVQVPVENRVGEENRGWTYAK 240 Query: 239 FLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELT 298 +LLG+ERTGIARVG SK + +K++A Q + G+P++EDP F K+AA+EIEL ALELT Sbjct: 241 YLLGHERTGIARVGNSKRELGFLKRVAKQQQKNGRPLLEDPLFGAKVAALEIELMALELT 300 Query: 299 QLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNE- 357 LRVV+ E GKG P P +S+LKIKG+EIQQ TEL++E +GP+A P+D + +E Sbjct: 301 VLRVVSSESA-GKG-PGPEASMLKIKGTEIQQMLTELMVEAVGPYAQPFDTAYLECEHEH 358 Query: 358 ---TMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 D A +A YFN RK SIYGGSNEIQ+NII + +LGL Sbjct: 359 AVTGYDDAAPLAAYYFNYRKTSIYGGSNEIQKNIISQMILGL 400 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: 463 Number of extensions: 15 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: 400 Length adjustment: 31 Effective length of query: 365 Effective length of database: 369 Effective search space: 134685 Effective search space used: 134685 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