Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Putida:PP_0213 Length = 480 Score = 224 bits (572), Expect = 4e-63 Identities = 149/462 (32%), Positives = 225/462 (48%), Gaps = 12/462 (2%) Query: 26 DLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLG 85 D G + +P TGE I ++ + AE IE AD+A AWR + A +R +R Sbjct: 21 DADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWF 80 Query: 86 EELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRM 145 E + + DL RL++ E GK +E GE+ ++ ++++YG TI +P R+ Sbjct: 81 ELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRL 140 Query: 146 METWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAI 205 + P+GV I+ +NFP A+ + A AL G +V KP+ +TP +ALA + RA Sbjct: 141 IVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRA- 199 Query: 206 ARFGDAPEGLSQVLIGDRA-IGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILE 264 P G+ V+ G +G L + V +S TGST +GR++ AK + LE Sbjct: 200 ----GIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLE 255 Query: 265 LGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQS 324 LGGN IV ADLD A+ GQ C R++V + VYD +L A Sbjct: 256 LGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAK 315 Query: 325 VSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALV 384 + +GN LE GPL+D A +Q+ I +A + G V G ++ E ++ LV Sbjct: 316 LKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKL---IEGNFFEPTILV 372 Query: 385 EMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADG 444 ++PK EETF P+ + ++ D V+A N GL+S + RDM S F A+ Sbjct: 373 DVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDM--SRVFRVAEA 430 Query: 445 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486 + G+ +N G E+ FGG K +G GRE + Y+ Sbjct: 431 LEYGMVGINTGLISNEV-APFGGIKASGLGREGSKYGIEDYL 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: 547 Number of extensions: 29 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