Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 3608345 Dshi_1747 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Dino:3608345 Length = 499 Score = 762 bits (1968), Expect = 0.0 Identities = 370/498 (74%), Positives = 423/498 (84%), Gaps = 1/498 (0%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M EL HFI+GKRVAGTSGR +++ NPATGEVQ V LAS +L AAV +A AAQP WAAT Sbjct: 1 MEELSHFINGKRVAGTSGRFADVMNPATGEVQARVPLASPEELDAAVAAAAAAQPAWAAT 60 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120 NPQRRARV M+FV+LLN +M++LAE LSREHGKT+ DAKGD+VRGLEV EF IG PHL K Sbjct: 61 NPQRRARVLMEFVRLLNRDMDKLAEALSREHGKTLPDAKGDVVRGLEVVEFCIGAPHLLK 120 Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 EFT+ AGPGIDMYS+RQ +G+ AGITPFNFP MIPMW APA+ACGNAFILKPSERDPS Sbjct: 121 GEFTDSAGPGIDMYSMRQALGVVAGITPFNFPAMIPMWKMAPALACGNAFILKPSERDPS 180 Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240 VP+ LAELM EAGLP G+L V+NGDKGAVDAIL + I A+ FVGSTPIA Y+Y N Sbjct: 181 VPLMLAELMTEAGLPDGLLQVINGDKGAVDAILDNDTIQAIGFVGSTPIAEYIYSRGCAN 240 Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300 GKR QCFGGAKNHMIIMPDADLDQAA+AL+GAGYG+AGERCMAISVAVPVGEETA+RLI+ Sbjct: 241 GKRVQCFGGAKNHMIIMPDADLDQAADALVGAGYGAAGERCMAISVAVPVGEETADRLIE 300 Query: 301 KLVPMVESLRIGPYTD-EKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGY 359 KLVP VE+L++GPYT D GPVVT A+ I L+ SG++QGAKLVVDGRDF LQGY Sbjct: 301 KLVPRVEALKVGPYTSGTDVDYGPVVTAAAKANIERLVQSGVDQGAKLVVDGRDFSLQGY 360 Query: 360 ENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRD 419 ENG F+G LFD+V+ +MDIY+TEIFGPVL VRA++YEEAL L M HEYGNG AI+TRD Sbjct: 361 ENGFFVGPHLFDNVSKEMDIYRTEIFGPVLCTVRAKSYEEALGLAMDHEYGNGTAIFTRD 420 Query: 420 GDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTIT 479 GDAARDFA+RINIGMVG+NVPIPVPLAYH+FGGWK S FGDLNQHG D+ +F+TRTKT+T Sbjct: 421 GDAARDFANRINIGMVGINVPIPVPLAYHTFGGWKKSGFGDLNQHGPDAFRFYTRTKTVT 480 Query: 480 SRWPSGIKDGAEFSIPTM 497 +RWPSGIK+G EFSIP M Sbjct: 481 ARWPSGIKEGGEFSIPVM 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: 876 Number of extensions: 21 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