Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_110806407.1 C8J30_RS13690 aldehyde dehydrogenase family protein
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_003217355.1:WP_110806407.1 Length = 503 Score = 746 bits (1927), Expect = 0.0 Identities = 376/498 (75%), Positives = 420/498 (84%) Query: 13 EAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLV 72 E LL ++GV + GG M SFSP+TG +I +L + A I +A AFR WRLV Sbjct: 6 ETRTLLCRLGVVPAAFEGGSMASFSPLTGAQIGALTPETPKSTAAAIARAAAAFRLWRLV 65 Query: 73 PAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLY 132 PAPKRGELVRL EELRA KADLGRLVSIEAGK SEGLGEVQEMIDICDFAVGLSRQLY Sbjct: 66 PAPKRGELVRLWAEELRAAKADLGRLVSIEAGKSASEGLGEVQEMIDICDFAVGLSRQLY 125 Query: 133 GLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPL 192 GLTIATERPGHRMMETWHPLGVVG+ISAFNFPVAVW+WN ALALVCG+ V+WKPSEKTPL Sbjct: 126 GLTIATERPGHRMMETWHPLGVVGVISAFNFPVAVWAWNTALALVCGNPVLWKPSEKTPL 185 Query: 193 TALACQAILERAIARFGDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGP 252 TALA QA+L RA+ARF APEGL+Q+LIG +G LV+ PKV L+SATGSTRMGR VGP Sbjct: 186 TALAAQAVLGRALARFDAAPEGLAQLLIGGPEVGAALVESPKVALISATGSTRMGRIVGP 245 Query: 253 RLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYD 312 ++A RF R+ILELGGNNAGIVC SADLDM LRA+AFGAMGTAGQRCTTLRRLFVH+SVYD Sbjct: 246 KVAARFGRSILELGGNNAGIVCASADLDMTLRAVAFGAMGTAGQRCTTLRRLFVHDSVYD 305 Query: 313 QLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELG 372 L+PRL +AY SVSVGNPLE+ ALVGPL+D+AAFD MQ A+ A GG V GG RV G Sbjct: 306 TLMPRLIRAYASVSVGNPLETQALVGPLIDRAAFDAMQSALDAALAAGGIVHGGTRVACG 365 Query: 373 HENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRD 432 ++ YYV+PALVEMP Q GPVLEETFAPILYVM++SD +AV+ EHNAVAAGLSS+IFT D Sbjct: 366 PDSAYYVRPALVEMPAQIGPVLEETFAPILYVMRFSDLEAVIEEHNAVAAGLSSAIFTLD 425 Query: 433 MQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNT 492 ++E E FL+A GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK YMRRATNT Sbjct: 426 LREMETFLSAAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRATNT 485 Query: 493 VNYSKALPLAQGVSFDIE 510 +N+S+ LPLAQGV FDIE Sbjct: 486 INFSRDLPLAQGVVFDIE 503 Lambda K H 0.317 0.134 0.390 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: 870 Number of extensions: 34 Number of successful extensions: 1 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: 510 Length of database: 503 Length adjustment: 34 Effective length of query: 476 Effective length of database: 469 Effective search space: 223244 Effective search space used: 223244 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 (21.7 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