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_011841984.1 RSPH17029_RS14890 aldehyde dehydrogenase family protein
Query= SwissProt::Q9ZPB7 (508 letters) >NCBI__GCF_000015985.1:WP_011841984.1 Length = 494 Score = 465 bits (1196), Expect = e-135 Identities = 240/480 (50%), Positives = 317/480 (66%), Gaps = 4/480 (0%) Query: 31 ASGPVISTVSPSNNQEIAKVTEVSMEEYEEGLRSCNDAAKTWKSLPAPKRGEIVRQIGDA 90 A+G +S +SP + EI +V + +A + W+ +PAP+RGE+VR G+ Sbjct: 14 ATGGTLSVLSPIDGAEIGRVHPTDSAAMPGLIARAQEAFRHWREVPAPRRGELVRLFGEE 73 Query: 91 LREKLQHLGKLVSLEMGKILAEGIGEVQEVIYMCDFAVGLSRQLNGSIIPSERPDHMMFE 150 LR LG LV+LE GKI +EG+GEVQE+I +CDFAVGLSRQL G I SERP H M E Sbjct: 74 LRAAKAELGALVTLEAGKITSEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMME 133 Query: 151 VWNPLGIVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLVTIAVTKLIAEVLEK 210 W+P+G VI+AFNFP AV WNA +ALVCGN V+WK + TPL +A + L + Sbjct: 134 TWHPMGPCAVISAFNFPVAVWSWNAALALVCGNPVIWKPSEKTPLTALASMAIFGRALAR 193 Query: 211 -NNLPAAIFTAFCGGAEIGEAIAKDTRIPLVSFTGSSKVGAKVQQIVTERFGKCLLELSG 269 + P + GG EIGEA+ +P+VS TGS+++G V V RFG+ +LEL G Sbjct: 194 FGDAPEGLAQLVMGGPEIGEALVLSPEVPIVSATGSTRMGRIVGPKVAARFGRPILELGG 253 Query: 270 NNALIVMDDADVGLAVRSIFFAAVGTAGQRCTTCRRLYLHESIYQNVLDKLVGLYNQVKI 329 NNA+IV AD+ +AVR+I F+AVGTAGQRCT+ RRL +H S+ + ++ +LV Y +KI Sbjct: 254 NNAMIVAPSADLDMAVRAIVFSAVGTAGQRCTSLRRLIVHHSVREELVGRLVKAYASLKI 313 Query: 330 GDPLEEGTLVGPVHTKASRENFEKGISTIKSQGGKILTGGSVIES--DGNFVQPTIVEIA 387 GDP +GTLVGP+ ASR+ + +++GG + GG +E G ++QP +VE+ Sbjct: 314 GDPRADGTLVGPLIDAASRDRMVAALDRARAEGGTV-HGGKPVEGVPGGAYIQPALVEMP 372 Query: 388 SNASVVKEELFGPVLYVMKFKTLEEAIALNNSVPQGLSSSIFTSKPNTIFKWIGPHGSDC 447 + VV EE F P+LYVM ++TL+EAIAL N+VPQGLSS IFT ++ GSDC Sbjct: 373 AQTGVVCEETFAPILYVMGYETLDEAIALQNAVPQGLSSCIFTLNLREAEAFVSAAGSDC 432 Query: 448 GIVNVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRSTCTINYGTELPLAQGINF 507 GI NVNI +GAEIGGAFGGEK TGGGRE+GSD+W+ YMRR T TIN+ LPLAQG+ F Sbjct: 433 GIANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWRGYMRRQTNTINWSAALPLAQGVKF 492 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: 736 Number of extensions: 33 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: 494 Length adjustment: 34 Effective length of query: 474 Effective length of database: 460 Effective search space: 218040 Effective search space used: 218040 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 10 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