Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__Smeli:SMc04397 Length = 504 Score = 253 bits (646), Expect = 1e-71 Identities = 155/477 (32%), Positives = 250/477 (52%), Gaps = 13/477 (2%) Query: 10 INGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPA--WSDTPPIRR 67 I+G +G E P G V + A++AD + A+AAA+ AF W R Sbjct: 24 IDGQWVDGAEGRTIERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPRMTASER 83 Query: 68 ARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTE 127 + ++ + +++ A DELA E GK + A+GE+A DI +A + + L G+ Sbjct: 84 SLILLRAADMIAARADELAFLDAVESGKPISQAKGELAGAADIWRYAAALARELSGESYN 143 Query: 128 QVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMM 187 + G R+P+GVV+ ITP+NFP ++ P A+AAG + V+KPS L +++L++ Sbjct: 144 TLGEGTLGVVLREPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTSASTLVL 203 Query: 188 ADLLKQAGLPDGVFNVVQGDKDSVEA-LIDHPDVKALSFVGSTPIANLIYERGARSGKRI 246 ++L+ AG+P GV N++ G A L HP V +SF GST I L A++ K++ Sbjct: 204 GEILEAAGVPQGVVNIIVGTGPEAGAPLTTHPHVDMVSFTGSTGIGQLTMANAAQTLKKV 263 Query: 247 QALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAER 306 G KN +V PDANLD+ +DA + AY +AGE C A S +L D+A+++ R+A Sbjct: 264 SLELGGKNPQIVFPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRDIAEEVTARIASL 323 Query: 307 ARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCAD 366 + +K+ + L+ + ++G I+T Q Q+I GY+ EGA + G D + Sbjct: 324 SAKVKVGDPLDPETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTTLDLGM------- 376 Query: 367 GFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGS 426 G +M T+ V PEM + REE+FGPVL+ + AI++ N ++G ++ Sbjct: 377 GQFMAPTILSAVRPEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVWSRDFD 436 Query: 427 VAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSI 483 GRR++ G V +N + + FGG+++S G G V YT+ K++ Sbjct: 437 TCLTIGRRVRAGTVWMNTFMD-GASELPFGGYRQSGLG--RELGRHAVEDYTETKTL 490 Lambda K H 0.319 0.136 0.406 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: 568 Number of extensions: 20 Number of successful extensions: 3 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: 503 Length of database: 504 Length adjustment: 34 Effective length of query: 469 Effective length of database: 470 Effective search space: 220430 Effective search space used: 220430 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 (21.8 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