Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 529 bits (1363), Expect = e-155 Identities = 278/504 (55%), Positives = 344/504 (68%), Gaps = 7/504 (1%) Query: 42 LKELGLREENEGVY--NGSWGGRGEV--ITTYCPANNEPIARVRQASVADYEETVKKARE 97 LK LG+ E+ G Y G W + + PA E I V +S ADYE VK+A+E Sbjct: 6 LKALGIGAEHSGTYLGQGEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQE 65 Query: 98 AWKIWADIPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYA 157 A+K W PAP+RGE VR G+ALR+ LGSLV+LEMGKI EG GEVQE +DI D+A Sbjct: 66 AFKTWRTTPAPRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIADFA 125 Query: 158 VGLSRMIGGPILPSERSGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLW 217 VG SRM+ G + SER GH + EQ++P+GLVGII+AFNFPVAV+ WN +A ICG++C+W Sbjct: 126 VGQSRMLYGYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIW 185 Query: 218 KGAPTTSLISVAVTKIIAKVLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQ 277 K +P T L ++A KI + L+ P G D+ D+R+ L+SFTGST+ Sbjct: 186 KPSPKTPLSAIATMKICNEALKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTGSTK 245 Query: 278 VGKQVGLMVQERFGRSLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLF 337 VG+ VG V R GRSLLELGGNNAII ADL L +P+ +F AVGTAGQRCTT RRLF Sbjct: 246 VGRMVGERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLF 305 Query: 338 IHESIHDEVVNRLKKAYAQI--RVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTV 395 +HESI EV ++L AY Q+ ++G+P L GPL+++ AV +LGAVE+AK GG V Sbjct: 306 VHESIVGEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKV 365 Query: 396 VYGGKVM-DRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQG 454 + GG + DR GN+V PTIVTG+ + + TETFAPILY+ FK+ +E N+V QG Sbjct: 366 LTGGAALSDRKGNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQG 425 Query: 455 LSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWK 514 LSS+IFT+DL ++L GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK Sbjct: 426 LSSAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK 485 Query: 515 QYMRRSTCTINYSKDLPLAQGIKF 538 YMRR T T NYS LPLAQGIKF Sbjct: 486 VYMRRQTNTSNYSDSLPLAQGIKF 509 Lambda K H 0.318 0.136 0.417 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: 846 Number of extensions: 34 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: 539 Length of database: 511 Length adjustment: 35 Effective length of query: 504 Effective length of database: 476 Effective search space: 239904 Effective search space used: 239904 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