Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF1706 PGA1_c17300 methylmalonate-semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >lcl|FitnessBrowser__Phaeo:GFF1706 PGA1_c17300 methylmalonate-semialdehyde dehydrogenase Length = 499 Score = 725 bits (1872), Expect = 0.0 Identities = 347/498 (69%), Positives = 408/498 (81%), Gaps = 1/498 (0%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M ELGHFI+GK V+GTSGR ++FNPATG+VQ +AS A+ +E A AAQP W AT Sbjct: 1 MKELGHFINGKLVSGTSGRFDDVFNPATGDVQYQCPMASAAETTDIIEKAAAAQPAWGAT 60 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120 NPQ+RARV MK V L+N +M++LAE LSREHGKTI DAKGD+ RGLEV E+ +G P + K Sbjct: 61 NPQKRARVMMKMVALMNRDMDKLAEALSREHGKTIPDAKGDLQRGLEVIEYCVGAPQMLK 120 Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 EFT+ AGPGIDMYS+RQP+G+ I PFNFP M+P+W PA+ACGNA +LKPSERDPS Sbjct: 121 GEFTDSAGPGIDMYSMRQPLGVVGSIMPFNFPAMMPLWHVGPALACGNAVVLKPSERDPS 180 Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240 VP+ LAEL +EAGLP G+ VVNGDK AVD IL I VSFVGSTPIA+Y+Y A N Sbjct: 181 VPLMLAELFVEAGLPEGVFQVVNGDKEAVDTILDSEIIQGVSFVGSTPIAQYIYSRATAN 240 Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300 GKRAQCFGGAKNHMI+MPDADLD AA+AL+GAG+G+AGERCMAISVAVPVGEETA++LI+ Sbjct: 241 GKRAQCFGGAKNHMIVMPDADLDLAADALVGAGFGAAGERCMAISVAVPVGEETADKLIE 300 Query: 301 KLVPMVESLRIGPYT-DEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGY 359 KL+P +E L++GPYT + D+GPVVT +++RI LI SG++QGAKLVVD RDFKLQGY Sbjct: 301 KLIPRIEKLKVGPYTAGDDVDLGPVVTAASKERILGLIQSGVDQGAKLVVDNRDFKLQGY 360 Query: 360 ENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRD 419 E+G F+G LFD VTPDMDIYK EIFGPVLS VRA +YE+AL L M HEYGNG AI+TRD Sbjct: 361 EDGFFVGAHLFDHVTPDMDIYKQEIFGPVLSTVRANSYEDALKLAMDHEYGNGTAIFTRD 420 Query: 420 GDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTIT 479 GD ARDFASR+NIGMVG+NVPIPVPLAYH+FGGWK S FGDLNQHG DS KF+TRTKT+T Sbjct: 421 GDTARDFASRVNIGMVGINVPIPVPLAYHTFGGWKKSMFGDLNQHGPDSFKFYTRTKTVT 480 Query: 480 SRWPSGIKDGAEFSIPTM 497 SRWPSGIK+G EF+ M Sbjct: 481 SRWPSGIKEGGEFNFKAM 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: 838 Number of extensions: 28 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: 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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