Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate HSERO_RS07235 HSERO_RS07235 aldehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__HerbieS:HSERO_RS07235 Length = 477 Score = 194 bits (492), Expect = 8e-54 Identities = 134/462 (29%), Positives = 226/462 (48%), Gaps = 16/462 (3%) Query: 29 TGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEEL 88 +G + +P T E I + A+ +E A + F WR + A +R +++R + L Sbjct: 18 SGRTIDVINPATEEVIGKIAHADRADLDRALEAASKGFETWRNMSAFERSKIMRRAADLL 77 Query: 89 RAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMET 148 R ++ RL+++E GK +E E D D+ +R+ YG + PG M Sbjct: 78 RERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEARRTYGRLVPARVPGAYQMVI 137 Query: 149 WHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARF 208 P+G V + +NFP+ + AL G +++ K E+TP A A L RA A Sbjct: 138 KEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPEETP----ASPAELIRAYADA 193 Query: 209 GDAPEGLSQVLIGDRA-IGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGG 267 G P G+ ++ G A I E L+ HP + +S TGST +G+++ + RA +ELGG Sbjct: 194 G-VPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAALAGQHMKRATMELGG 252 Query: 268 NNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSV 327 + +V AD+D+A + +A AGQ C + R V + V++ V + + + V Sbjct: 253 HAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKGVFNAFVDKFVTYAEQLKV 312 Query: 328 GNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAV-TGGERVELGHENGYYVKP-ALVE 385 GN LE+ +GP+ +K ++ I +A + G + TGG+R+ GY+ +P L Sbjct: 313 GNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKRI---GNKGYFFQPTVLTN 369 Query: 386 MPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGS 445 +P Q + EE F P+ + + D V+ E N + GL++ F + A Sbjct: 370 LPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFAKSAHTKHALAAR--V 427 Query: 446 DCGIANVN-IGTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486 + G+ +N +G + E+ FGG K++G G E G++A +AY+ Sbjct: 428 ESGMLTINHLGLALPEL--PFGGIKDSGYGSEGGTEAIEAYI 467 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: 524 Number of extensions: 25 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: 477 Length adjustment: 34 Effective length of query: 476 Effective length of database: 443 Effective search space: 210868 Effective search space used: 210868 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