Align aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)
to candidate Ac3H11_1605 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::Q69P84 (509 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1605 Length = 511 Score = 454 bits (1169), Expect = e-132 Identities = 238/482 (49%), Positives = 314/482 (65%), Gaps = 7/482 (1%) Query: 33 SGPVVTSTNPTNNQVIAEVVEASAREYEEGMRACYDAAKTWMAIPAPKRGEIVRQIGDAL 92 +G + + +P +V+A+V + SA + + + A W +PAP+RGE+VR +G+ L Sbjct: 29 TGGTLAARSPITGEVLAQVPQQSAADATAAIGRAHAAFLAWRNVPAPRRGELVRLLGEEL 88 Query: 93 RAKLHHLGRLVSLEMGKILPEGIGEVQEIIDMCDYAVGLSRQLNGSIIPSERPNHMMMEV 152 RA LG LV++E GKI EG+GEVQE+ID+CD+AVGLSRQL G I +ERP H MME Sbjct: 89 RAAKGDLGLLVTIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMET 148 Query: 153 WNPLGVVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLITIAMTKIVASVLER- 211 W+PLGV GVI+AFNFP AV WNA +ALVCG+ VVWK + TPL +A I + R Sbjct: 149 WHPLGVCGVISAFNFPVAVWSWNAALALVCGDSVVWKPSEKTPLTALATHAIAQRAIARF 208 Query: 212 -NNLPGSIFTAFCGGADIGQAISLDTRIPLVSFTGSTKVGLMVQQQVNARFGKCLLELSG 270 + P + G DIG+ + D R+P++S TGST +G V ++ ARF + +LEL G Sbjct: 209 GTDAPEGLLELIVGQRDIGEVLVDDARVPVLSATGSTAMGRAVGPRLAARFARGILELGG 268 Query: 271 NNAIIVMDDADIQLAVRSVLFAAVGTAGQRCTTCRRLLLHESIYRTFLDQLVEVYKQVRI 330 NNA IV AD+ LA+R + FAA+GTAGQRCTT RRL +H SIY + QL +VY V++ Sbjct: 269 NNAAIVAPTADLNLALRGIAFAAMGTAGQRCTTLRRLFVHASIYDQLVPQLAKVYANVQV 328 Query: 331 GDPLENGTLLGPLHTPASRDAFLKGIQTIRSQGGKILYGGSAIESEGN----FVQPTIVE 386 GDP GTL+GPL + D K ++ R+ G + +GG +E G +V+P +VE Sbjct: 329 GDPRTPGTLVGPLIDRMAFDGMQKALEQSRALGATV-HGGGRVEGVGGADAYYVRPALVE 387 Query: 387 ISPSAPVVREELFGPVLYVMKVQNLKEAVEINNSVPQGLSSSIFTKRPDIIFKWIGPHGS 446 + E F P+LYV++ + EA+ +NN+V GLSSSIFT +++ GS Sbjct: 388 LQKHEGPALHETFAPILYVVRYSAIDEAIAMNNAVGAGLSSSIFTLNVREAEQFMSAAGS 447 Query: 447 DCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRATCTINYGSELPLAQGI 506 DCGI NVNI +GAEIGGAFGGEK TGGGREAGSDSWK YMRRAT TINY + LPLAQG+ Sbjct: 448 DCGIANVNIGPSGAEIGGAFGGEKETGGGREAGSDSWKAYMRRATNTINYSTALPLAQGV 507 Query: 507 NF 508 F Sbjct: 508 TF 509 Lambda K H 0.320 0.137 0.416 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: 714 Number of extensions: 24 Number of successful extensions: 3 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: 509 Length of database: 511 Length adjustment: 34 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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: 52 (24.6 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