Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate H281DRAFT_01833 H281DRAFT_01833 aldehyde dehydrogenase (NAD+)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Burk376:H281DRAFT_01833 Length = 499 Score = 659 bits (1700), Expect = 0.0 Identities = 329/498 (66%), Positives = 395/498 (79%), Gaps = 2/498 (0%) Query: 13 EAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLV 72 +A+A+L ++G++ L GD+ SP+ GE I + + + AE + A +A+ +WR V Sbjct: 2 KASAILSELGISH-LAEAGDIAVHSPINGELIGRVASRTVAEVDAALASAQKAYASWRNV 60 Query: 73 PAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLY 132 PAP+RGELVRLLG +LR K LG ++++E GKI EGLGEVQEMIDICDFAVGLSRQLY Sbjct: 61 PAPRRGELVRLLGNKLREQKHALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLY 120 Query: 133 GLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPL 192 GLTIA+ERPGHRM ETWHPLGV +ISAFNFP AVWSWNAALALVCG+AVVWKPSEKTPL Sbjct: 121 GLTIASERPGHRMAETWHPLGVCTVISAFNFPAAVWSWNAALALVCGNAVVWKPSEKTPL 180 Query: 193 TALACQAILERAIARFGDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGP 252 TALA IL+ A+ FGDAPEGL+ V+ G R +G LV P+ +VSATGST MGR VG Sbjct: 181 TALAVDKILQDALKEFGDAPEGLTSVVNGGREVGAKLVADPRSNIVSATGSTEMGRAVGV 240 Query: 253 RLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYD 312 +A+RF R+ILELGGNNAGIV SAD+++ALR I F A+GTAGQRCT+LRRLFVHESVYD Sbjct: 241 EVARRFGRSILELGGNNAGIVSGSADMELALRGIVFSAVGTAGQRCTSLRRLFVHESVYD 300 Query: 313 QLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGER-VEL 371 + V RLK Y V +GNPLE L+GPL+D+ +F+ MQ A+ +AK+ GG V GGER Sbjct: 301 KAVERLKALYSKVVIGNPLEQGVLMGPLIDEQSFNRMQAALEQAKSEGGKVFGGERHAVA 360 Query: 372 GHENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTR 431 G+E G+YV+PA+VEMP Q VL+ETFAPILYV+KYSDFD + +NA GLSS +FT Sbjct: 361 GNEKGFYVRPAIVEMPSQTSVVLKETFAPILYVLKYSDFDDAIGGNNAAVHGLSSCVFTT 420 Query: 432 DMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATN 491 D++E+ERFL+A GSDCGIANVNIG SGAEIGGAFGGEKETGGGRESGSD+WKAYMRRATN Sbjct: 421 DLREAERFLSASGSDCGIANVNIGPSGAEIGGAFGGEKETGGGRESGSDSWKAYMRRATN 480 Query: 492 TVNYSKALPLAQGVSFDI 509 TVNYS ALPLAQG+ F+I Sbjct: 481 TVNYSSALPLAQGIDFNI 498 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: 778 Number of extensions: 33 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: 499 Length adjustment: 34 Effective length of query: 476 Effective length of database: 465 Effective search space: 221340 Effective search space used: 221340 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