Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Ac3H11_1605 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1605 Length = 511 Score = 726 bits (1873), Expect = 0.0 Identities = 365/502 (72%), Positives = 421/502 (83%), Gaps = 2/502 (0%) Query: 10 VASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAW 69 + SE LL ++GV + YTGG + + SP+TGE +A + SAA+A I +A AF AW Sbjct: 10 LVSEVDQLLQRLGVPRAAYTGGTLAARSPITGEVLAQVPQQSAADATAAIGRAHAAFLAW 69 Query: 70 RLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSR 129 R VPAP+RGELVRLLGEELRA K DLG LV+IEAGKIPSEGLGEVQEMIDICDFAVGLSR Sbjct: 70 RNVPAPRRGELVRLLGEELRAAKGDLGLLVTIEAGKIPSEGLGEVQEMIDICDFAVGLSR 129 Query: 130 QLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEK 189 QLYGLTIATERPGHRMMETWHPLGV G+ISAFNFPVAVWSWNAALALVCGD+VVWKPSEK Sbjct: 130 QLYGLTIATERPGHRMMETWHPLGVCGVISAFNFPVAVWSWNAALALVCGDSVVWKPSEK 189 Query: 190 TPLTALACQAILERAIARFG-DAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGR 248 TPLTALA AI +RAIARFG DAPEGL ++++G R IGEVLVD +VP++SATGST MGR Sbjct: 190 TPLTALATHAIAQRAIARFGTDAPEGLLELIVGQRDIGEVLVDDARVPVLSATGSTAMGR 249 Query: 249 EVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHE 308 VGPRLA RFAR ILELGGNNA IV P+ADL++ALR IAF AMGTAGQRCTTLRRLFVH Sbjct: 250 AVGPRLAARFARGILELGGNNAAIVAPTADLNLALRGIAFAAMGTAGQRCTTLRRLFVHA 309 Query: 309 SVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGER 368 S+YDQLVP+L K Y +V VG+P LVGPL+D+ AFDGMQKA+ +++ G V GG R Sbjct: 310 SIYDQLVPQLAKVYANVQVGDPRTPGTLVGPLIDRMAFDGMQKALEQSRALGATVHGGGR 369 Query: 369 VE-LGHENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSS 427 VE +G + YYV+PALVE+ K EGP L ETFAPILYV++YS D +A +NAV AGLSSS Sbjct: 370 VEGVGGADAYYVRPALVELQKHEGPALHETFAPILYVVRYSAIDEAIAMNNAVGAGLSSS 429 Query: 428 IFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMR 487 IFT +++E+E+F++A GSDCGIANVNIG SGAEIGGAFGGEKETGGGRE+GSD+WKAYMR Sbjct: 430 IFTLNVREAEQFMSAAGSDCGIANVNIGPSGAEIGGAFGGEKETGGGREAGSDSWKAYMR 489 Query: 488 RATNTVNYSKALPLAQGVSFDI 509 RATNT+NYS ALPLAQGV+FD+ Sbjct: 490 RATNTINYSTALPLAQGVTFDV 511 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: 811 Number of extensions: 31 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: 511 Length adjustment: 35 Effective length of query: 475 Effective length of database: 476 Effective search space: 226100 Effective search space used: 226100 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