Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090439664.1 BLS63_RS03170 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_900100495.1:WP_090439664.1 Length = 478 Score = 283 bits (723), Expect = 1e-80 Identities = 162/474 (34%), Positives = 258/474 (54%), Gaps = 6/474 (1%) Query: 5 RKLKNYINGEWVESKTDQYEDVVNPAT-KEVLCQVPISTKEDIDYAAQTAAEAFKTWSKV 63 ++ NYI G+WV Y +NP+ +++ + + ++ A A AF WS Sbjct: 3 KRYDNYIGGQWVAGS--DYSRNINPSDLSDLVGEYAQADAAQVEQAIAAARAAFPAWSTS 60 Query: 64 AVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMM 123 A+ R+ L + +EEL L+ E GK EA+GEV R +F AG Sbjct: 61 AIQARSDALDKVGSEILARREELGSLLAREEGKTLAEAIGEVSRAGNIFKFFAGECLRQA 120 Query: 124 GDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPL 183 G+ LAS+ V R P+GV+G I P+NFP+ +P W A+A GN + KP++ P Sbjct: 121 GELLASVRPGVSVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAYGNCVVFKPADLVPG 180 Query: 184 LTEKLVELFEKAGLPKGVFNVVYGAHDVV-NGILEHPEIKAISFVGSKPVGEYVYKKGSE 242 + E+ +AG P GVFN+V G+ VV +++HP++ +SF GS VG + Sbjct: 181 CAWAIAEIIARAGFPAGVFNLVMGSGRVVGETLVQHPQVDGVSFTGSVGVGRSIAAVCVA 240 Query: 243 NLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302 +VQ G KN ++L+DA+L V V +AF S G+RC A + + V GI D F+ Sbjct: 241 RGAKVQLEMGGKNPQVILDDADLNTAVELSVQSAFYSTGQRCTASSRLIVTAGIHDRFVE 300 Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDG 361 + E++ +++G+ L+ GV +GPV+ + ++ L YI G +EGARLVC G R + + +G Sbjct: 301 AMAERMRSLRVGHALERGVDIGPVVSQAQLEQDLRYIGIGRDEGARLVCGGERVSCATEG 360 Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421 YF+ PT+F + T M I ++EIF PV ++++V + +EA+ +AN +EF A + T++ Sbjct: 361 YFLAPTLFADSTAAMRINREEIFGPVANILKVADYEEALAMANDTEFGLSAGICTTSLKY 420 Query: 422 IRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 +F+ + AGM+ +NL PF G K S +G+ G+ + +FYT K Sbjct: 421 ANHFKRHAQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYTTVK 473 Lambda K H 0.318 0.136 0.396 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: 555 Number of extensions: 32 Number of successful extensions: 5 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: 487 Length of database: 478 Length adjustment: 34 Effective length of query: 453 Effective length of database: 444 Effective search space: 201132 Effective search space used: 201132 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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