Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate CCNA_02357 CCNA_02357 methylmalonic acid semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Caulo:CCNA_02357 Length = 498 Score = 640 bits (1651), Expect = 0.0 Identities = 307/498 (61%), Positives = 384/498 (77%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M ++ HF+ G+ + G SGR ++FNP TGEVQ V A+DA+L AAV+ A AQ WA T Sbjct: 1 MRDIAHFVKGQTLVGASGRFGDVFNPNTGEVQARVQFATDAELDAAVQVAAKAQVGWAQT 60 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120 NPQRRARV +F +L+ +MN LAE+LS EHGK I D+KGDI RGLEV EF GIPH+ K Sbjct: 61 NPQRRARVMFEFKRLIERDMNTLAEILSSEHGKVIADSKGDIQRGLEVIEFACGIPHILK 120 Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 E+TEGAGPGID+YS+RQP+G+ AGITPFNFP MIPMWMF +IA GN+FILKPSE+DP+ Sbjct: 121 GEYTEGAGPGIDVYSMRQPLGVCAGITPFNFPAMIPMWMFGISIAVGNSFILKPSEKDPT 180 Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240 VP++LAELM+EAG PAG+LNVV+GDK AVDAILTHP I AVSFVGS+ IA YVY T + Sbjct: 181 VPVKLAELMMEAGAPAGVLNVVHGDKSAVDAILTHPLIRAVSFVGSSDIAHYVYQTGTAH 240 Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300 GKR Q GGAKNH I++PDAD+DQ L GA +GSAGERCMA+ V VPVG++TA+ L + Sbjct: 241 GKRVQAMGGAKNHGIVLPDADMDQVVKDLSGAAFGSAGERCMALPVVVPVGQKTADELRE 300 Query: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360 ++V + SL++G TD A GPVV+ + +I I G E+GA+LVVDGRDF+LQG+E Sbjct: 301 RMVAEIASLKVGVSTDPDAHYGPVVSAQHRDKIADYIRIGQEEGAELVVDGRDFQLQGFE 360 Query: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420 G FIG LFD V M Y EIFGPVL +VRA EEA++LP +H+YGNGVAI+TR+G Sbjct: 361 KGFFIGPSLFDGVKKGMKTYHEEIFGPVLQIVRAETLEEAIALPSEHQYGNGVAIFTRNG 420 Query: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480 AAR+FA+ +N+GMVG+NVPIPVP+AYH+FGGWK S+FGD NQHG + +KF+T+ KT+T+ Sbjct: 421 RAAREFAANVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGVEGVKFYTKVKTVTA 480 Query: 481 RWPSGIKDGAEFSIPTMR 498 RWP G + F IPTM+ Sbjct: 481 RWPEGEVADSSFVIPTMK 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: 812 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: 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 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