Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 293 bits (750), Expect = 9e-84 Identities = 172/471 (36%), Positives = 259/471 (54%), Gaps = 20/471 (4%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YIDGQ+V+ G I+V +P A+++ +P G A DA KA+ AA A W PA ERA Sbjct: 8 YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPAAERA 67 Query: 70 SWLRKISAGIRERASEISALIVEEGG---KIQQLAEV--EVAFTADYIDYMAEWARRYEG 124 ++L+KI ++ RA EI+ I E G K Q +V A Y +A++ +E Sbjct: 68 AYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFP--FEE 125 Query: 125 EIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNN 184 ++ N + + A+GV I PWN+P IA K+A AL G T+V+KPSE P N Sbjct: 126 KV-------GNSKVVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLN 178 Query: 185 AIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKN 244 A A+I+ G+P GVFNL+ G G VG+ + + +V MVS TGS AG ++ A+ Sbjct: 179 AFLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASAT 238 Query: 245 ITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNR 304 + +V LELGGK+ AI++DDAD +AVK +V + +NSGQ C R+ V Y + Sbjct: 239 VKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKL 298 Query: 305 LGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG----KAVEG 360 EA QA + G+P + +GPL + +RV + + + EG + GG + V Sbjct: 299 AVEAAQAYRVGDPMAEG-VTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNP 357 Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420 GYY PT+ V+ + SI EE FGPVL ++++ EDA+S+AN + YGL +++ Sbjct: 358 DGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATD 417 Query: 421 NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 A + + ++ G+ IN F F G+++SG G GK+GL ++L+ Sbjct: 418 EHAEQVARRMRTGQVEINGGTFNMYAPF-GGYKQSGNGRELGKYGLEDFLE 467 Lambda K H 0.318 0.135 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: 555 Number of extensions: 16 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: 479 Length of database: 479 Length adjustment: 34 Effective length of query: 445 Effective length of database: 445 Effective search space: 198025 Effective search space used: 198025 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: 51 (24.3 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