Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate 6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__SB2B:6938906 Length = 486 Score = 159 bits (403), Expect = 2e-43 Identities = 137/453 (30%), Positives = 207/453 (45%), Gaps = 17/453 (3%) Query: 30 GGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELR 89 G +M S +P GE I K A+ + A +A W ++ R +V EL Sbjct: 14 GKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQAIVEAYRNELE 73 Query: 90 AFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETW 149 A KA+L +++ E GK E E MI +V + G T E R + Sbjct: 74 ANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTG-TEVNEGAAGRAVLRH 132 Query: 150 HPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFG 209 P GVV + +NFP + + + AL+ G+ VV+KPSE TP A + E+A Sbjct: 133 KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMLKLWEKA----- 187 Query: 210 DAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAI-LELGGN 268 P G+ ++ G+ G+ L HP++ + TGS+R G + + A + + LE+GGN Sbjct: 188 GLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALEMGGN 247 Query: 269 NAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVY-DQLVPRLKKAYQSVSV 327 N IV +D A+ I A ++GQRCT RRL+V + D+L+ L +A +++ V Sbjct: 248 NPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVEAVKAIKV 307 Query: 328 GN-PLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGH--ENGYYVKPALV 384 G + +G ++ + A GM A N G VE+ H V P L+ Sbjct: 308 GPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAK----SLVEMTHLQAGTGLVSPGLI 363 Query: 385 EMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADG 444 ++ + EE F P+L V++Y+ FD + N GLS+ I D + E FLA Sbjct: 364 DVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLAR-- 421 Query: 445 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRES 477 GI N N +GA FGG +G R S Sbjct: 422 IRAGIVNWNKQITGASGAAPFGGVGASGNHRAS 454 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: 533 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 510 Length of database: 486 Length adjustment: 34 Effective length of query: 476 Effective length of database: 452 Effective search space: 215152 Effective search space used: 215152 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