Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_023432895.1 N177_RS13385 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >NCBI__GCF_000496075.1:WP_023432895.1 Length = 499 Score = 662 bits (1709), Expect = 0.0 Identities = 314/496 (63%), Positives = 397/496 (80%) Query: 3 ELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNP 62 E+GHFI G+ V G SGR + +++P+TGE G VALAS+AD+ +AV +A+ A P WAAT P Sbjct: 4 EIGHFIGGRNVGGGSGRTAPVYDPSTGEEAGRVALASEADVRSAVAAARDAFPDWAATTP 63 Query: 63 QRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSE 122 RRAR+ +F+++L + +++LA +++ EHGKT+ DAKG+I RG+EV EF P L K E Sbjct: 64 LRRARILNRFLRILEERIDDLAAVITAEHGKTLSDAKGEIERGMEVVEFATAAPQLLKGE 123 Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182 TE G ID +S+RQP+G+ AGITPFNFP M+PMWMF A+ACGN F+LKPSERDPS Sbjct: 124 VTENVGTRIDSHSLRQPLGVVAGITPFNFPAMVPMWMFPVALACGNTFVLKPSERDPSAS 183 Query: 183 IRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGK 242 I +AE + EAG+P G+ NVV+GDK AVDAILT PD+ AVSFVGSTPIARY+Y TAA GK Sbjct: 184 IVIAEWLKEAGVPDGVFNVVHGDKEAVDAILTDPDVQAVSFVGSTPIARYIYETAAKTGK 243 Query: 243 RAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302 R Q GGAKNHMI+MPDADLDQAA+AL+GA YGSAGERCMA+SVAVPVGE+TA+ L+ KL Sbjct: 244 RCQALGGAKNHMIVMPDADLDQAADALMGAAYGSAGERCMAVSVAVPVGEKTADALVAKL 303 Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENG 362 P VE+L++GP TD +++MGP+VTK+ R+ S IDSG+E GA+LVVDGR KLQGY+NG Sbjct: 304 KPRVEALKVGPGTDPQSEMGPLVTKQHRDRVLSYIDSGVEAGAELVVDGRGLKLQGYDNG 363 Query: 363 HFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDA 422 +++GG LFD VT DM IY+ EIFGPVL V RA ++E A +HE+GNG AI+TRDGDA Sbjct: 364 YYVGGTLFDRVTTDMKIYREEIFGPVLCVARAGDFETAAKWINEHEFGNGTAIFTRDGDA 423 Query: 423 ARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRW 482 AR+FA RI +GMVG+NVPIPVP+A+HSFGGWKSS FGD + HG + ++F+TR KTITSRW Sbjct: 424 AREFAHRIQVGMVGINVPIPVPMAFHSFGGWKSSLFGDHHMHGPEGVRFYTRLKTITSRW 483 Query: 483 PSGIKDGAEFSIPTMR 498 P+GI+ GA+F +PTMR Sbjct: 484 PTGIRAGADFVMPTMR 499 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: 785 Number of extensions: 22 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: 499 Length adjustment: 34 Effective length of query: 464 Effective length of database: 465 Effective search space: 215760 Effective search space used: 215760 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