Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate BWI76_RS13425 BWI76_RS13425 1-pyrroline dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Koxy:BWI76_RS13425 Length = 475 Score = 212 bits (539), Expect = 3e-59 Identities = 145/453 (32%), Positives = 219/453 (48%), Gaps = 19/453 (4%) Query: 30 GGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELR 89 G +P F+P TGE+I S+ +AA+ +E AD+AF +W R E + L + Sbjct: 16 GEAVPVFNPATGEEIVSIAEATAAQVEAAVEAADQAFISWSQTTPRSRAECLLALANVID 75 Query: 90 AFKADLGRLVSIEAGKIPSEGL--GEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMME 147 L +L S+ GK P + E+ + D+ F G +R L G+ GH M Sbjct: 76 EHAQTLAKLESLNCGK-PLHCVINDELPAVADVFRFFAGAARCLPGMAAGEYLEGHTSMI 134 Query: 148 TWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIAR 207 P+GVV I+ +N+P+ + +W A AL G+ VV KPSE TPLTAL + + Sbjct: 135 RRDPVGVVASIAPWNYPLMMAAWKLAPALAAGNCVVIKPSEITPLTALKLGELAKEIF-- 192 Query: 208 FGDAPEGLSQVLIGDRA-IGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELG 266 P G+ VL G A +G+ L H KV +VS TGS G + A R +ELG Sbjct: 193 ----PAGVLNVLFGRGATVGDPLTAHAKVRMVSLTGSIATGAHIIGHTASSIKRTHMELG 248 Query: 267 GNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVS 326 G IV AD+D + + AGQ CT R++ +YDQLV +L A S+ Sbjct: 249 GKAPVIVFDDADIDAVVEGVRTFGFYNAGQDCTAACRIYAQAGIYDQLVEKLGAAVASLK 308 Query: 327 VGNPLESAALVGPLVDKAAFDGMQKAI--AEAKNHGGAVTGGERVELGHENGYYVKPALV 384 +G P + +GPL +A D + A+ A A H + GG + NGYY +P L+ Sbjct: 309 MGPPEDETTELGPLSSQAHLDRVSAAVDAARALPHIQVIAGGSKAP---GNGYYYQPTLL 365 Query: 385 EMPKQEGPVLE-ETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAAD 443 +QE +++ E F P++ + ++D + L+ N GL+SS++TRD+ + R A Sbjct: 366 AGARQEDAIVQREVFGPVVSITSFTDEEQALSWANDSQYGLASSVWTRDVGRAHRLSARL 425 Query: 444 GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE 476 C N + GG+K +G G++ Sbjct: 426 QYGCTWVNTHFMLVSEM---PHGGQKLSGYGKD 455 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: 525 Number of extensions: 22 Number of successful extensions: 5 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: 475 Length adjustment: 34 Effective length of query: 476 Effective length of database: 441 Effective search space: 209916 Effective search space used: 209916 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