Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_090445639.1 BLS63_RS14235 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15203 (503 letters) >NCBI__GCF_900100495.1:WP_090445639.1 Length = 476 Score = 251 bits (642), Expect = 3e-71 Identities = 154/457 (33%), Positives = 239/457 (52%), Gaps = 12/457 (2%) Query: 30 TGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVM-FKFLELLNAHKDELAEA 88 T + G A AS D SA+AAA+ A P W+ PP +RA + F E+L ++EL Sbjct: 25 TNDLVGLYAQASADDTQSAIAAAEHAQPLWAAKPPQQRADALDFIGAEIL-LRREELGTL 83 Query: 89 ITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVAGI 148 + RE GK +A EV R I +F G + G++ + V GI+ RQP+GV+ I Sbjct: 84 LAREEGKTLPEAIAEVVRAGQIFKFFAGEALRIPGEHLDSVRPGIEVDVLRQPVGVIGII 143 Query: 149 TPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLKQAGLPDGVFNVVQGDK 208 P+NFP+ +P W A+A GN+ V KP+ L P ++ +++++ +AGLPDG FN+V G Sbjct: 144 APWNFPIAIPAWKIAPALAYGNAVVFKPADLVPGSAWALSEIIHRAGLPDGTFNLVMGRG 203 Query: 209 DSV-EALIDHPDVKALSFVGSTPIA-NLIYERGARSGKRIQALGGAKNHMVVMPDANLDK 266 V + L++ P VKALSF GS+ +++ GAR K +Q G KN +VV+ DA+L++ Sbjct: 204 SVVGQTLVESPRVKALSFTGSSDTGRRILHSAGARFAK-LQLEMGGKNPLVVLNDADLEQ 262 Query: 267 AVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARDLKIKNGLELDAEMGPIV 326 A++ + AY S G+RC A S ++ + + + R + L++ + L D ++GP+ Sbjct: 263 AIECAVQGAYFSTGQRCTASSRFIVEKGIYRRFSEGVQARLQALQVGHALHADTQIGPVA 322 Query: 327 TSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADGFWMGGTLFDHVTPEMTIYR 386 +++ Y++ G++EGA + GR G++M LF +M I + Sbjct: 323 EQGQYEQNLAYVDIGLSEGAVLACGGRPLQRD------TQGYYMSPALFVDAEAQMRIAQ 376 Query: 387 EEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGINVPI 446 EEIFGP+ + D A+QL N +G T S A F R + GMV IN P Sbjct: 377 EEIFGPIACAIPADDYEHALQLANASPYGLSAGICTTSLKYAAHFKRHMHSGMVMINTPT 436 Query: 447 PVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSI 483 FGG K S +G + G F+T K++ Sbjct: 437 AGVDYHVPFGGTKGSSYG-SREQGRYAAEFFTTVKTV 472 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: 596 Number of extensions: 26 Number of successful extensions: 4 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: 476 Length adjustment: 34 Effective length of query: 469 Effective length of database: 442 Effective search space: 207298 Effective search space used: 207298 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 24 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