Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 332 bits (851), Expect = 2e-95 Identities = 182/450 (40%), Positives = 265/450 (58%), Gaps = 3/450 (0%) Query: 11 SVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEE 70 ++NP TGE V + P A++ EV A+ A A + W+ +A R L++ LR + Sbjct: 5 TINPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQ 64 Query: 71 VAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVEN---NQAVIEYRPL 127 A+++TLEMGK I +A GEV A + ++YA+H +LA E + Q+ +E+ P Sbjct: 65 YAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHVPQ 124 Query: 128 GAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFG 187 G +LAV PWNFP +Q++R A P L AGN +LKHA NV A +F AGLP G F Sbjct: 125 GILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGFT 184 Query: 188 WVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDA 247 + AT D + II D R+ V +TGS AG + AQAG ALKK +ELGG+D F+VL DA Sbjct: 185 NLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLADA 244 Query: 248 DLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYV 307 DLD+AV+ AVTGR+ N+GQVC +SKR I+ I +AF K+ VA L+ GDP + + Sbjct: 245 DLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPSTTL 304 Query: 308 GPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELF 367 PM+ D+L +Q+ + GA + + ++ G ++ P +L +V+ E F Sbjct: 305 APMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYWEFF 364 Query: 368 GPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCASDA 427 GPV+ + ARD A+ +ANDS FGL +V+TTD A+++ G V++N A Sbjct: 365 GPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTGVAA 424 Query: 428 RVAFGGVKKSGFGRELSHFGLHEFCNAQTV 457 + FGGV++SG+GREL+ G+ EF N + + Sbjct: 425 DLPFGGVRRSGYGRELTGLGIKEFVNHKLI 454 Lambda K H 0.319 0.133 0.392 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: 518 Number of extensions: 20 Number of successful extensions: 2 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: 462 Length of database: 463 Length adjustment: 33 Effective length of query: 429 Effective length of database: 430 Effective search space: 184470 Effective search space used: 184470 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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