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_011427241.1 RHE_RS20725 aldehyde dehydrogenase family protein
Query= SwissProt::Q9ZPB7 (508 letters) >NCBI__GCF_000092045.1:WP_011427241.1 Length = 512 Score = 478 bits (1231), Expect = e-139 Identities = 240/483 (49%), Positives = 325/483 (67%), Gaps = 9/483 (1%) Query: 33 GPVISTVSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDALR 92 G +S SP +EI K+ E ++ E + + + A W+ +PAPKRGE+VR +G+ LR Sbjct: 28 GGTLSVTSPVTGKEIGKLREHTVSETKAAIEEAHKAFLEWRDVPAPKRGELVRLLGEELR 87 Query: 93 EKLQHLGKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEVW 152 LG+LVS+E+GKI +EG+GEVQE+I +CDFAVGLSRQL G I +ER +H M E W Sbjct: 88 AAKTALGRLVSIEVGKITSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERSEHRMMESW 147 Query: 153 NPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVL---- 208 +PLG +G+I+AFNFP AV WNA +A+VCGN VWK + TPL +AV L + L Sbjct: 148 HPLGAIGIISAFNFPVAVWSWNAALAMVCGNSTVWKPSEKTPLTALAVQALFEKALKRFV 207 Query: 209 -EKNNLPAAIFTAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLEL 267 E PA + T GG E+GE + +IPLVS TGS+ +G V +++RF + +LEL Sbjct: 208 AEGGKAPANLSTLIIGGREVGEVLVDHPKIPLVSATGSTAMGRAVGPRLSQRFARAILEL 267 Query: 268 SGNNALIVMDDADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQV 327 GNNA IV AD+ L +R + F+A+GTAGQRCTT RRL++H+S+Y ++ +L Y V Sbjct: 268 GGNNAAIVCPSADLDLTLRGVAFSAMGTAGQRCTTLRRLFVHDSVYDQLVPRLQKAYGSV 327 Query: 328 KIGDPLEEGTLVGPVHTKASRENFEKGISTIKSQGGKILTGGSVIE---SDGNFVQPTIV 384 IG+PLE GTLVGP+ + E + + KS GGK+ TGG ++ +D +V+P +V Sbjct: 328 TIGNPLEAGTLVGPLIDGQAFEKMQAALGEAKSAGGKV-TGGERVDNGSADAFYVRPALV 386 Query: 385 EIASNASVVKEELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHG 444 E+ + V+ E F P+LYVMK+ + +AL+N+VPQGLSSSIFT+ ++ G Sbjct: 387 EMPAQTGPVEHETFAPILYVMKYSDFDAVLALHNAVPQGLSSSIFTNDMREAETFVSARG 446 Query: 445 SDCGIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQG 504 SDCGI NVN+ +GAEIGGAFGGEK TGGGRE+GSD+WK YMRR+T TINYG+ LPLAQG Sbjct: 447 SDCGIANVNLGPSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTINYGSTLPLAQG 506 Query: 505 INF 507 + F Sbjct: 507 VKF 509 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: 733 Number of extensions: 29 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: 508 Length of database: 512 Length adjustment: 34 Effective length of query: 474 Effective length of database: 478 Effective search space: 226572 Effective search space used: 226572 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 Apr 09 2024. 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