Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >FitnessBrowser__Putida:PP_3492 Length = 383 Score = 672 bits (1733), Expect = 0.0 Identities = 333/381 (87%), Positives = 356/381 (93%) Query: 1 MHDIELTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEW 60 M D+EL+EEQ+MIRDMARDFARGEIAPHAQAWEKAGWIDD +V KMGELGLLGMVVPE++ Sbjct: 1 MQDLELSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDF 60 Query: 61 GGTYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQA 120 GG+Y DYVAYALAVEEISAG GATGA+MSIHNSVGCGP+L YGT EQ+Q WL LASG+ Sbjct: 61 GGSYTDYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQWLPRLASGEV 120 Query: 121 IGCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKK 180 IGCFCLTEPQAGSEAHNLRTRAEL DGQWVINGAKQFVSN RRA LAIVFAVTDP+LGKK Sbjct: 121 IGCFCLTEPQAGSEAHNLRTRAELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKK 180 Query: 181 GLSAFLVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNL 240 GLSAFLVPTD PGF VDRSEHKMGIRASDTCAVT +NC IP AN+LGERGKGLAIALSNL Sbjct: 181 GLSAFLVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNL 240 Query: 241 EGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLI 300 EGGRIGIAAQALGIARAAFEAAL Y+RDR+QF KPI EHQS+AN+LADM ++NAARLLI Sbjct: 241 EGGRIGIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLI 300 Query: 301 LHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARIT 360 LHAARLRSAGKPCLSEASQAKLFASEMAE+VCS AIQ+HGGYGYLEDYPVERYYRDARIT Sbjct: 301 LHAARLRSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARIT 360 Query: 361 QIYEGSSEIQRMVIARELKNY 381 QIYEGSSEIQRM+IARELKNY Sbjct: 361 QIYEGSSEIQRMLIARELKNY 381 Lambda K H 0.319 0.134 0.394 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: 499 Number of extensions: 8 Number of successful extensions: 1 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: 383 Length of database: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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