Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 209 bits (533), Expect = 1e-58 Identities = 152/468 (32%), Positives = 231/468 (49%), Gaps = 22/468 (4%) Query: 4 WINGDWITGQGASRVK-RNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 +I +W+ V NP +G++L A + ++A AA + W + ER Sbjct: 15 FIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERS 74 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVT---AMINKIAISIKAYHVRTGEQ 119 A++ ++ LL N+ +L I+ E GKP E+ E+ A A K + Sbjct: 75 AILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVY------ 128 Query: 120 RSEMPDGAASLR----HRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPW 175 +P AS R +P GV+A P+NFP + AL AG T++ KP+ TP+ Sbjct: 129 GDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPF 188 Query: 176 SGEAVMRLWQQAGLPPGVLNLVQGGRET-GQALSALEDLDGLLFTGSANTGYQLHRQLSG 234 S A+ +L QQAG+P GV N+V G G L+A + L FTGS G +L R +G Sbjct: 189 SALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAG 248 Query: 235 QPEKILALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAF 294 ++ L++E+GGN P I+ + ADIDAAV + + +GQ C CA R+ +++G D F Sbjct: 249 TMKR-LSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVY-DEF 306 Query: 295 LARLVAVSQRLTPGN-WDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQA 353 +L A Q L GN +DD Q G LI A + V + + GG+ L Sbjct: 307 CRKLTAAVQELKVGNGFDDGVQQ--GPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHAL 364 Query: 354 GTSLLTPGII-EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPER 412 G + P II ++T V EE FGPL V+++DT +E +R AN+T FGL+ + + Sbjct: 365 GRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDM 424 Query: 413 EKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460 + ++ + G+V N + + APFGG+ SGN R + Y D Sbjct: 425 ARSWRIGEKLEYGLVGINSGII-SNPVAPFGGVKESGNGREGSKYGLD 471 Lambda K H 0.318 0.134 0.412 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: 562 Number of extensions: 23 Number of successful extensions: 5 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: 492 Length of database: 484 Length adjustment: 34 Effective length of query: 458 Effective length of database: 450 Effective search space: 206100 Effective search space used: 206100 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 (21.7 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