Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 183 bits (464), Expect = 1e-50 Identities = 140/466 (30%), Positives = 224/466 (48%), Gaps = 15/466 (3%) Query: 6 HFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRR 65 +FI G+ VA G + +P TG VA AD+ A+++A A+ W T R Sbjct: 21 NFIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKAKDAWGKTPAAER 80 Query: 66 ARVFMKFVQLLNDNMNELAEMLSREHGKTI-DDAKGDIVRGLEVCEFVIGIPHLQKSEFT 124 A + K Q L+DN++ LA + + ++GK I + DI ++ + G Q+ + Sbjct: 81 ANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSLS 140 Query: 125 EGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIR 184 E + Y +P+G+ I P+NFP ++ W +PA+A GN +LKP+E+ P + Sbjct: 141 EIDHDTV-AYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMSILA 199 Query: 185 LAELMIEAGLPAGILNVVNG-DKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKR 243 +AEL+ + LP G+LN+VNG A + ++ IA ++F G T R + AA N Sbjct: 200 VAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAENLIP 258 Query: 244 AQCFGGAKNHMIIM------PDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANR 297 G K+ I DA LD+A + GE C S A+ V ++ Sbjct: 259 VTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFAL-NQGEVCTCPSRAL-VQRSIYDK 316 Query: 298 LIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQ 357 ++K + V +R G D +G + + ++I S +D G ++GAK+++ G L+ Sbjct: 317 FMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSVLE 376 Query: 358 G-YENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIY 416 G + G+++ + M +++ EIFGPV+SV EEAL + YG G ++ Sbjct: 377 GELKEGYYMQPTALEGHN-RMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGLW 435 Query: 417 TRDGDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLN 462 TRDG A I G V N P A+ +FGG+K S G N Sbjct: 436 TRDGSRAYRCGRAIRAGRVWTNCYHAYP-AHAAFGGYKQSGIGREN 480 Lambda K H 0.319 0.137 0.409 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: 544 Number of extensions: 30 Number of successful extensions: 6 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: 498 Length of database: 506 Length adjustment: 34 Effective length of query: 464 Effective length of database: 472 Effective search space: 219008 Effective search space used: 219008 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