Align Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Matured fruit 60 kDa protein; MF-60; EC 1.2.1.3 (characterized)
to candidate WP_009763131.1 MICLODRAFT_RS17515 aldehyde dehydrogenase family protein
Query= SwissProt::Q9ZPB7 (508 letters) >NCBI__GCF_000262405.1:WP_009763131.1 Length = 516 Score = 482 bits (1241), Expect = e-140 Identities = 241/472 (51%), Positives = 325/472 (68%), Gaps = 3/472 (0%) Query: 39 VSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDALREKLQHL 98 +SP + IA V E + +E + + + A K W+ +PAPKRGE +R +G+ LR L Sbjct: 41 LSPITGEVIAHVRETTPDEAKAAIGRADAAFKAWRKVPAPKRGEFIRLLGEELRAAKDDL 100 Query: 99 GKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEVWNPLGIV 158 G+LV+LE GKI++EG+GEVQE+I +CDFAVGLSRQL G I +ER DH M E W+PLG+ Sbjct: 101 GRLVTLEAGKIVSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERADHRMMETWHPLGVC 160 Query: 159 GVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLEK-NNLPAAI 217 GVI+AFNFP AV WNA +ALVCG+ VVWK + T L +A ++ ++ +P + Sbjct: 161 GVISAFNFPVAVWSWNAALALVCGDSVVWKPSEKTLLTALATHAIVERAAKRFGGVPEGL 220 Query: 218 FTAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLELSGNNALIVMD 277 GG EIGE + +D R+P++S TGS+ +G +V + ERF + +LEL GNNA IV Sbjct: 221 CEVLLGGREIGEILVEDHRVPVLSATGSTAMGRQVGPKLAERFARAILELGGNNAAIVAP 280 Query: 278 DADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQVKIGDPLEEGT 337 AD+ LA+R I FAA+GTAGQRCTT RRL++HES+Y ++ +LV +Y VKIGDP EGT Sbjct: 281 SADLDLALRGIAFAAMGTAGQRCTTLRRLFVHESVYDQLVPRLVKVYGSVKIGDPRAEGT 340 Query: 338 LVGPVHTKASRENFEKGISTIKSQGGKILTGG--SVIESDGNFVQPTIVEIASNASVVKE 395 LVGP+ KA+ +N E+ + ++ GGK+ GG + + ++G + +P +VE+ S V Sbjct: 341 LVGPLIDKAAFDNMERALDEARAAGGKVHGGGRYTDVANEGVYARPALVEMPSQTGPVTR 400 Query: 396 ELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHGSDCGIVNVNIP 455 E F P+LYVM++ +E IAL+N+V GLSSSIFT ++ GSDCGI NVNI Sbjct: 401 ETFAPILYVMRYSDFDEVIALHNAVGAGLSSSIFTLNLREAEAFVSAAGSDCGIANVNIG 460 Query: 456 TNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQGINF 507 +GAEIGGAFGGEK TGGGRE+GSD+WK YMRR+T TINYG+ LPLAQG+ F Sbjct: 461 PSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTINYGSTLPLAQGVKF 512 Lambda K H 0.317 0.136 0.404 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: 708 Number of extensions: 27 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: 508 Length of database: 516 Length adjustment: 35 Effective length of query: 473 Effective length of database: 481 Effective search space: 227513 Effective search space used: 227513 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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