Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_085123792.1 B9O00_RS16490 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_900177295.1:WP_085123792.1 Length = 498 Score = 672 bits (1733), Expect = 0.0 Identities = 317/495 (64%), Positives = 396/495 (80%), Gaps = 1/495 (0%) Query: 4 LGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQ 63 L HFI G+ VAGTSGR S +FNPATGEV+ V LAS A+L +AV++AKAA P WAAT P Sbjct: 5 LHHFIGGRIVAGTSGRTSEVFNPATGEVKAKVDLASAAELDSAVQTAKAAFPGWAATAPL 64 Query: 64 RRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSEF 123 +RAR+ +F +LL N +LAE++ EHGK + DA G++ RG+EV EF GIP L K EF Sbjct: 65 QRARIMFRFKELLEANKAKLAELIGSEHGKVLGDAAGEVTRGIEVVEFACGIPQLLKGEF 124 Query: 124 TEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVPI 183 E G G+D YS+RQP+G+ AGITPFNFP M+PMWMF A+ACGNAFILKPSERDPS P+ Sbjct: 125 NENVGTGVDAYSVRQPLGVVAGITPFNFPAMVPMWMFPVALACGNAFILKPSERDPSAPL 184 Query: 184 RLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKR 243 LAEL+ +AGLP G+ NVVNGDK AVDAIL HPDI AVSFVGSTPIA YVY T KR Sbjct: 185 YLAELLKQAGLPDGVFNVVNGDKEAVDAILAHPDIEAVSFVGSTPIAEYVYRTGTSTNKR 244 Query: 244 AQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKLV 303 Q GGAKNHMI+MPDAD+DQA +AL+GA YGSAGERCMAISVAV VG + ++L+++L Sbjct: 245 VQALGGAKNHMIVMPDADMDQATDALMGAAYGSAGERCMAISVAVAVG-DAGDKLMERLE 303 Query: 304 PMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENGH 363 P V L+IG YTD +A+MGP+VT++ ++++ +D G+++GAKLVVDGRDF++QGYENG+ Sbjct: 304 PRVRGLKIGAYTDAEAEMGPLVTRQHYEKVKGYVDLGVQEGAKLVVDGRDFRMQGYENGY 363 Query: 364 FIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDAA 423 FIGGCLFD+V P+M IYK EIFGPVL+V+R+ +YE+AL L HE+GNG AI+TRDGDAA Sbjct: 364 FIGGCLFDEVKPEMRIYKEEIFGPVLAVMRSGSYEDALDLVNAHEFGNGTAIFTRDGDAA 423 Query: 424 RDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRWP 483 R+FA R IGMVG+NVPIPVP+A+HSFGGWK S FGD + HG + ++F+TR K +T+RWP Sbjct: 424 RNFAQRARIGMVGINVPIPVPMAFHSFGGWKRSLFGDHHMHGPEGVRFYTRLKAVTTRWP 483 Query: 484 SGIKDGAEFSIPTMR 498 +GI+ GAEF +PTM+ Sbjct: 484 TGIRSGAEFVMPTMK 498 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: 782 Number of extensions: 31 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: 498 Length of database: 498 Length adjustment: 34 Effective length of query: 464 Effective length of database: 464 Effective search space: 215296 Effective search space used: 215296 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