Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__BFirm:BPHYT_RS28770 Length = 480 Score = 226 bits (576), Expect = 1e-63 Identities = 152/456 (33%), Positives = 236/456 (51%), Gaps = 12/456 (2%) Query: 34 PSFSPV-TGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFK 92 P+ +P T + I SA + I A AFR W L +R +L+ G + A K Sbjct: 20 PNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQQRFDLLDQAGSTILARK 79 Query: 93 ADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPL 152 +LG+L++ E GK +E +GEV I F G + ++ G + + RPG + T P+ Sbjct: 80 NELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRVGGEILPSVRPGLTVEVTREPV 139 Query: 153 GVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAP 212 GV+G+I+ +NFP+A+ +W A AL G+ VV KP+E P + I+ A AP Sbjct: 140 GVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGSVWELVKIIAEA-----GAP 194 Query: 213 EGLSQVLIGDRAI-GEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAG 271 G+ +++G +I GE+LV V VS TGS G+ + + + LE+GG N Sbjct: 195 AGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAIAAKCVATGKKFQLEMGGKNPM 254 Query: 272 IVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPL 331 +V ADLD+A+ A GA + GQRCT RL V ++D+ V + +S+ +GN L Sbjct: 255 VVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHDRFVEAMLARMRSLKIGNAL 314 Query: 332 ESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQEG 391 +++ +GP+VD + ++ I A+N GG+V GGERV E G+++ PALV Sbjct: 315 DASTQIGPVVDAKQLEQDERYIELARNEGGSVFGGERVTSATE-GFFLAPALVTNTTPAM 373 Query: 392 PV-LEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIA 450 + EE F P+ V+K ++++ LA N GLS+ I T + + F G+ Sbjct: 374 TINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMSLAHASHF--KRHVQAGMV 431 Query: 451 NVNIGTSGAEIGGAFGGEKETG-GGRESGSDAWKAY 485 +N T+G + FGG K + G RE G+ A + Y Sbjct: 432 MINTATAGVDYHVPFGGRKGSSLGPREQGTYAREFY 467 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: 596 Number of extensions: 32 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: 510 Length of database: 480 Length adjustment: 34 Effective length of query: 476 Effective length of database: 446 Effective search space: 212296 Effective search space used: 212296 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 17 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