Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Putida:PP_3492 Length = 383 Score = 441 bits (1133), Expect = e-128 Identities = 215/373 (57%), Positives = 285/373 (76%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 +++EQ I D R FA+ + P A+ W+K + +M ELGL GM+VPE +GGS T Sbjct: 6 LSEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSYT 65 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 YVAYA+A+EEI+AG GA +MS+HNSVGC P+L +G +Q++Q+L LA+G ++G F Sbjct: 66 DYVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQWLPRLASGEVIGCFC 125 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182 LTEPQAGS+A +L+TRA L +V+NG+KQF+++ + AG+ IVFAVTDPE GK+G+SAF Sbjct: 126 LTEPQAGSEAHNLRTRAELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKGLSAF 185 Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242 +VPTD+PG++V R E K+G ASDTC + FDN ++P AN LG G+G IAL+NLEGGRI Sbjct: 186 LVPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLEGGRI 245 Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302 GIA+QA+G+ARAAFE A Y+ +R FGKP+ EHQ++A LADM +++ AR ++LHAA Sbjct: 246 GIAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLILHAAR 305 Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 LR AG+P L EAS AKLFASEMAE+VCS A+Q GGYGYL D+P+ER YRD R+ QIYEG Sbjct: 306 LRSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQIYEG 365 Query: 363 TSDIQRMVIARNL 375 +S+IQRM+IAR L Sbjct: 366 SSEIQRMLIAREL 378 Lambda K H 0.319 0.134 0.382 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: 430 Number of extensions: 14 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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