Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__psRCH2:GFF374 Length = 480 Score = 227 bits (578), Expect = 8e-64 Identities = 160/473 (33%), Positives = 236/473 (49%), Gaps = 17/473 (3%) Query: 18 LDKMGVAKDLYTGGDMPS-FSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPK 76 +D V D Y PS S V GE + AA+ I A AF AW Sbjct: 11 IDGQWVGSDRYQANTNPSDLSDVIGEYAQA----DAAQVEQAIAAARRAFPAWATFGIQA 66 Query: 77 RGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTI 136 R + + +G E+ A + +LG L++ E GK E +GEV +I + G + G T+ Sbjct: 67 RADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLRQAGETL 126 Query: 137 ATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALA 196 + RPG + T PLGV+G+I+ +NFP+A+ +W A AL G+ VV KP++ P A A Sbjct: 127 QSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLVPGCAWA 186 Query: 197 CQAILERAIARFGDAPEGLSQVLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLA 255 I+ RA P G+ +++G R +GE +V+ V VS TGS +GR + Sbjct: 187 IAEIISRA-----GFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTCV 241 Query: 256 KRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLV 315 R A+ LE+GG N IV ADL++A+ A + GQRCT R+ V E +YD+ V Sbjct: 242 ARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRFV 301 Query: 316 PRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVT-GGERVELGHE 374 + + + + VG+ LE VGP+V +A + + I K G + GGERV+ G E Sbjct: 302 EAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGTE 361 Query: 375 NGYYVKPAL-VEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDM 433 GY++ P L V+ EE F P+ V+K D+D LA N GLS+ I T + Sbjct: 362 -GYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420 Query: 434 QESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETG-GGRESGSDAWKAY 485 + + F + G+ +N+ T+G + FGG K + G RE G A + Y Sbjct: 421 KYANHF--KRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEFY 471 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: 527 Number of extensions: 25 Number of successful extensions: 4 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 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