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) >FitnessBrowser__Phaeo:GFF1706 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:
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