Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_900177295.1:WP_179243903.1 Length = 480 Score = 278 bits (710), Expect = 4e-79 Identities = 172/476 (36%), Positives = 251/476 (52%), Gaps = 8/476 (1%) Query: 9 NYINGEWVESKTDQYEDVVNPAT-KEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67 N I GEWV++ NP+ +V+ A AA AF WS+ + Sbjct: 6 NLIAGEWVDAPNASENR--NPSDLSDVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQ 63 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 R IL + KEEL L++ E GK E +GE R + +F AG + GD + Sbjct: 64 RFDILDAAGTEILARKEELGRLLSREEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRI 123 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 S V A R P+GVVG I P+NFP+ +P W A+A GN ++KP++ P Sbjct: 124 DSTRPGVIAEATREPLGVVGLITPWNFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWA 183 Query: 188 LVELFEKAGLPKGVFNVVYGAHDVV-NGILEHPEIKAISFVGSKPVGEYVYKK--GSENL 244 L ++ ++AGLPKGVFN+V G VV IL P++ AISF GS G +V ++ E + Sbjct: 184 LADILQRAGLPKGVFNLVMGRGSVVGEAILASPKVAAISFTGSVATGRHVARRCIEGEAM 243 Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 K+ Q G KN +VL+DA+LE + + AF S G+RC A + + V EGI D F+ L Sbjct: 244 KKFQLEMGGKNPFVVLDDADLEVAANSALNGAFFSTGQRCTASSRLIVTEGIHDRFVEAL 303 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYF 363 K+ +K+ N L +G +GPV+ + + L YI+ G +EGA+L G R N +G++ Sbjct: 304 TSKLKALKVDNALKEGTQIGPVVDQRQLDQDLDYIKVGQDEGAKLAWGGERLNRETEGFY 363 Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423 + P +F M I ++EIF PV SVIRVK+ A+ +AN ++F A + TS+ Sbjct: 364 LQPALFTETDNAMRINREEIFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLKHAE 423 Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTA 479 +F+ N AGM+ +NL PF G K+S +G G+ +V+FYT K A Sbjct: 424 HFKRNSQAGMVMVNLPTAGVDYHVPFGGRKNSSYGA-REQGRYAVEFYTTVKTAYA 478 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: 515 Number of extensions: 30 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: 480 Length adjustment: 34 Effective length of query: 453 Effective length of database: 446 Effective search space: 202038 Effective search space used: 202038 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 Apr 09 2024. 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