Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_011427241.1 RHE_RS20725 aldehyde dehydrogenase family protein
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_000092045.1:WP_011427241.1 Length = 512 Score = 750 bits (1936), Expect = 0.0 Identities = 376/507 (74%), Positives = 425/507 (83%), Gaps = 4/507 (0%) Query: 8 IDVASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFR 67 +D+A+E A LL ++GV Y GG + SPVTG++I L+ + +E IE+A +AF Sbjct: 6 LDLATETAKLLAELGVDAGRYHGGTLSVTSPVTGKEIGKLREHTVSETKAAIEEAHKAFL 65 Query: 68 AWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGL 127 WR VPAPKRGELVRLLGEELRA K LGRLVSIE GKI SEGLGEVQEMIDICDFAVGL Sbjct: 66 EWRDVPAPKRGELVRLLGEELRAAKTALGRLVSIEVGKITSEGLGEVQEMIDICDFAVGL 125 Query: 128 SRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPS 187 SRQLYGLTIATER HRMME+WHPLG +GIISAFNFPVAVWSWNAALA+VCG++ VWKPS Sbjct: 126 SRQLYGLTIATERSEHRMMESWHPLGAIGIISAFNFPVAVWSWNAALAMVCGNSTVWKPS 185 Query: 188 EKTPLTALACQAILERAIARF----GDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGS 243 EKTPLTALA QA+ E+A+ RF G AP LS ++IG R +GEVLVDHPK+PLVSATGS Sbjct: 186 EKTPLTALAVQALFEKALKRFVAEGGKAPANLSTLIIGGREVGEVLVDHPKIPLVSATGS 245 Query: 244 TRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRR 303 T MGR VGPRL++RFARAILELGGNNA IVCPSADLD+ LR +AF AMGTAGQRCTTLRR Sbjct: 246 TAMGRAVGPRLSQRFARAILELGGNNAAIVCPSADLDLTLRGVAFSAMGTAGQRCTTLRR 305 Query: 304 LFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAV 363 LFVH+SVYDQLVPRL+KAY SV++GNPLE+ LVGPL+D AF+ MQ A+ EAK+ GG V Sbjct: 306 LFVHDSVYDQLVPRLQKAYGSVTIGNPLEAGTLVGPLIDGQAFEKMQAALGEAKSAGGKV 365 Query: 364 TGGERVELGHENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAG 423 TGGERV+ G + +YV+PALVEMP Q GPV ETFAPILYVMKYSDFDAVLA HNAV G Sbjct: 366 TGGERVDNGSADAFYVRPALVEMPAQTGPVEHETFAPILYVMKYSDFDAVLALHNAVPQG 425 Query: 424 LSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK 483 LSSSIFT DM+E+E F++A GSDCGIANVN+G SGAEIGGAFGGEKETGGGRESGSDAWK Sbjct: 426 LSSSIFTNDMREAETFVSARGSDCGIANVNLGPSGAEIGGAFGGEKETGGGRESGSDAWK 485 Query: 484 AYMRRATNTVNYSKALPLAQGVSFDIE 510 AYMRRATNT+NY LPLAQGV FD+E Sbjct: 486 AYMRRATNTINYGSTLPLAQGVKFDVE 512 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: 856 Number of extensions: 41 Number of successful extensions: 2 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: 512 Length adjustment: 35 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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 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