Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_004109547.1 RHSP_RS04195 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_000359745.1:WP_004109547.1 Length = 498 Score = 893 bits (2307), Expect = 0.0 Identities = 431/498 (86%), Positives = 466/498 (93%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M E+GHFI GKRVAGTSGR SN++NPATGEVQ TVALAS +L AAV +AKAAQPKW AT Sbjct: 1 MREIGHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGAT 60 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120 NPQRRARVF +FV+LLN NM+ELA +LS EHGKT++D+KGDI+RGLEVCEFV GIPHLQK Sbjct: 61 NPQRRARVFFRFVELLNQNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQK 120 Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 EFTEGAGP IDMYSIRQPVG+GAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS Sbjct: 121 GEFTEGAGPAIDMYSIRQPVGVGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240 +PIRLAELMIEAGLPAGILNVVNGDK AVDAILT PDIAAVSFVGSTPIARYVYGTAAMN Sbjct: 181 LPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSFVGSTPIARYVYGTAAMN 240 Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300 GKRAQCFGGAKNHMIIMPDAD+DQA NAL+GAGYGSAGERCMA+SVAVPVGE+TANRL++ Sbjct: 241 GKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDTANRLVE 300 Query: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360 KLVP +ESLRIGPYTD+KADMGP+VTKEA R+ LID G+E+GAKLVVDGR FKLQGYE Sbjct: 301 KLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYE 360 Query: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420 G+F+GG LFD V PDMDIYKTEIFGPVLSVVRA+NYEEAL LPMKHEYGNGVAIYTRDG Sbjct: 361 EGYFVGGTLFDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDG 420 Query: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480 DAARDFASRINIGM+GVNVPIPVPLAYHSFGGWK+SSFGDLNQHGTDSIKFWTRTKTIT+ Sbjct: 421 DAARDFASRINIGMIGVNVPIPVPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITA 480 Query: 481 RWPSGIKDGAEFSIPTMR 498 RWPSGIKDGAEF +PTM+ Sbjct: 481 RWPSGIKDGAEFVMPTMK 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: 921 Number of extensions: 21 Number of successful extensions: 1 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 Sep 24 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