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_029132530.1 A3GO_RS0105360 aldehyde dehydrogenase family protein
Query= SwissProt::Q9ZPB7 (508 letters) >NCBI__GCF_000428045.1:WP_029132530.1 Length = 514 Score = 466 bits (1200), Expect = e-136 Identities = 239/481 (49%), Positives = 316/481 (65%), Gaps = 5/481 (1%) Query: 33 GPVISTVSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDALR 92 G I +P + + + S + + + A +S+PAP RG+ VRQ+G+ R Sbjct: 34 GEAIRLSTPIDGATLGSIRMASASQVADVIERAKAAFLELRSIPAPVRGDFVRQLGNVFR 93 Query: 93 EKLQHLGKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFEVW 152 E Q L +L++LE GKIL E +GEVQEVI +CDFAVGLSRQL+G I SERPDH M E W Sbjct: 94 EHKQPLAELITLECGKILQESLGEVQEVIDICDFAVGLSRQLHGLTIASERPDHRMMEQW 153 Query: 153 NPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLEK-N 211 +PLG V +I+AFNFP AV WNA ++ VCG+ ++WK + TPL +A KLI + LE Sbjct: 154 HPLGPVAIISAFNFPMAVWAWNAMLSFVCGDTILWKPSEKTPLCALACQKLITQTLEGFP 213 Query: 212 NLPAAIFTAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLELSGNN 271 P I G +++G+ + I LVS TGS +G KV V R G+ LLEL GNN Sbjct: 214 RFPRGISQVVIGDSQVGQQLVGSPDIALVSATGSVAMGKKVATTVAARLGRSLLELGGNN 273 Query: 272 ALIVMDDADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQVKIGD 331 A+IV AD+ +A+R+I F+AVGT GQRCT+ RRL +H+SI +L +L Y + IGD Sbjct: 274 AMIVTASADLEMALRAIVFSAVGTCGQRCTSLRRLIVHDSIVDELLQRLQAAYGSLSIGD 333 Query: 332 PLEEGTLVGPVHTKASRENFEKGISTIKSQGGKILTGGSVI----ESDGNFVQPTIVEIA 387 P TLVGP+ + E ++ I T +S+GG+++ GG + + +G +V P I+ I Sbjct: 334 PFSASTLVGPLIDIQAYEQMQQAIQTAESEGGELICGGDRVVVTGKEEGVYVDPAIIRIP 393 Query: 388 SNASVVKEELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHGSDC 447 S+A VV++E F P+LYVM + + EAIA+ NSVPQGLSS+IFT ++ GSDC Sbjct: 394 SHAEVVRQETFAPILYVMNYTEIIEAIAIQNSVPQGLSSAIFTQDVREAELFLSARGSDC 453 Query: 448 GIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQGINF 507 G+ NVNI T+GAEIGGAFGGEK TGGGRE+GSD+WK YMRRST TINYGT+LPLAQGI F Sbjct: 454 GLANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKNYMRRSTNTINYGTDLPLAQGIRF 513 Query: 508 G 508 G Sbjct: 514 G 514 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: 715 Number of extensions: 35 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: 514 Length adjustment: 35 Effective length of query: 473 Effective length of database: 479 Effective search space: 226567 Effective search space used: 226567 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