Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Korea:Ga0059261_3677 Length = 503 Score = 652 bits (1681), Expect = 0.0 Identities = 320/496 (64%), Positives = 379/496 (76%), Gaps = 1/496 (0%) Query: 3 ELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNP 62 E+ HFI AGT R S++F+P TG VQ V L + ADL AA+ +A AQ WAATNP Sbjct: 7 EISHFIGNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAATNP 66 Query: 63 QRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSE 122 QRRARV F L+ NM ELA +LS EHGK I DAKGDI RGLEV EFV GIPH+ K E Sbjct: 67 QRRARVMFNFKALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLKGE 126 Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182 +T+GAGPGID+YS+RQP+G+ AGITPFNFP MIPMWMF AIACGNAFILKPSERDPSVP Sbjct: 127 YTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVP 186 Query: 183 IRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGK 242 +RLAELM+EAGLP G+L VV GDK VDAIL HP+I AVSFVGS+ IA YVY GK Sbjct: 187 VRLAELMLEAGLPEGVLQVVQGDKEMVDAILDHPEIKAVSFVGSSDIAHYVYRRGVAAGK 246 Query: 243 RAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDKL 302 R Q GGAKNH I+MPDADLDQ N L GA +GSAGERCMA+ V VPVG++TA+ L KL Sbjct: 247 RVQAMGGAKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRAKL 306 Query: 303 VPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENG 362 +P +E+LR+G TD A GPVVT + +I S I G+++GA+LVVDGR F LQG+E G Sbjct: 307 LPAIEALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHEQG 366 Query: 363 HFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDA 422 F+G LFD VTP M Y+ EIFGPVL +VRA ++E AL LP +H+YGNGVAI+TR+G A Sbjct: 367 FFVGPTLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNGHA 426 Query: 423 ARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRW 482 AR+FA+R+N+GMVG+NVPIPVP+AYH+FGGWK S+FGD NQHG + IKF+T+ KT+T RW Sbjct: 427 AREFAARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQRW 486 Query: 483 PSGIKDGAE-FSIPTM 497 P G DG F IPTM Sbjct: 487 PDGSPDGGNAFVIPTM 502 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: 806 Number of extensions: 24 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: 503 Length adjustment: 34 Effective length of query: 464 Effective length of database: 469 Effective search space: 217616 Effective search space used: 217616 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