Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate CCNA_01360 CCNA_01360 malonate-semialdehyde dehydrogenase IolA
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Caulo:CCNA_01360 Length = 500 Score = 644 bits (1662), Expect = 0.0 Identities = 318/500 (63%), Positives = 384/500 (76%), Gaps = 3/500 (0%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M ++ HFI G++V G SGR +F+P TG+VQ VALAS +L A+ +AK AQ WAAT Sbjct: 2 MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120 NPQRRARV +F +LL +M+ELA +LS EHGK I D+KGDI RGLEV EF G+PHL K Sbjct: 62 NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121 Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180 E+T+GAGPGID+YS+RQP+G+ AGITPFNFP MIPMWMF PAIA GNAFILKPSERDPS Sbjct: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181 Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240 VP+RLAELMIEAGLP G+LNVV+GDK V+AIL HPDI AVSFVGS+ IA+ V+ A Sbjct: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241 Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300 GKR Q GGAKNH ++MPDADLDQA +IGA YGSAGERCMA+ V VPVGE+TA L + Sbjct: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301 Query: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360 KLV + LR+G TD A GPVV+ + RI S I G+++GA+LVVDGR F LQG+E Sbjct: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361 Query: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420 G F+G LFD V P Y EIFGPVL +VRA + EE ++L +H+YGNGVAI+TR+G Sbjct: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421 Query: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480 DAAR+FA ++ +GMVG+NVPIPVP+AYHSFGGWK S FGDLNQ+G D ++F+TRTKT+T Sbjct: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481 Query: 481 RWPSG--IKDGAEFSIPTMR 498 RWP G + D F IPTMR Sbjct: 482 RWPKGGAVLD-QSFVIPTMR 500 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: 825 Number of extensions: 30 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: 500 Length adjustment: 34 Effective length of query: 464 Effective length of database: 466 Effective search space: 216224 Effective search space used: 216224 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