Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_029134950.1 A3GO_RS0120300 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000428045.1:WP_029134950.1 Length = 480 Score = 264 bits (674), Expect = 6e-75 Identities = 157/476 (32%), Positives = 256/476 (53%), Gaps = 7/476 (1%) Query: 4 IRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKV 63 +++ + +INGEWVE++ + D +NP+T EV +V + +D+++A A+ A W K Sbjct: 1 MQEYRLFINGEWVETQDGEVLDDINPSTGEVFARVHQAGPKDVEHAITAASAASVAWGKT 60 Query: 64 AVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMM 123 R IL L E+A ++ E G +A+ E + + AAG + Sbjct: 61 QPAVREEILIKAADCLQARIHEIADVLIDEAGSTFGKAMFEASFVVNLLRSAAGEARRIF 120 Query: 124 GDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPL 183 G+++ S D+ + + R P+GV+ GIAPFNFP ++ C +AIA GN F+LKPSE T + Sbjct: 121 GETMPSDGPDIFSMSVRRPLGVIAGIAPFNFPFLLACKKVALAIAAGNAFVLKPSEETAV 180 Query: 184 LTEKLVELFEKAGLPKGVFNVVYGAHDVVNG-ILEHPEIKAISFVGSKPVGEYVYKKGSE 242 K+ E+FE+AGLPKGV NV+ G+ V G +++ P +K I+F GS VG+ + + ++ Sbjct: 181 TGLKIAEIFEQAGLPKGVLNVIPGSGPEVGGRLVDDPRVKMITFTGSTVVGKKLAVQAAQ 240 Query: 243 NLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302 LK++ G K+ IVL DA+L+ V F G+ CMA + + VE + D F Sbjct: 241 QLKKITLELGGKSPLIVLADADLDYAVDAACFGIFLHQGQVCMANSKLIVEAAVYDAFCD 300 Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGY 362 K KV +K+G+ +GP+IR + +++ L++GARL+ G S + Sbjct: 301 KFAAKVKSLKVGDPRQPNTVIGPLIRGAQCQVIDRHVQDALDKGARLLTGG----SSESN 356 Query: 363 FVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAI 422 F PT+ +V +M I+++E F PV+S+I+ + + A+ IAN SE+ + + T++ Sbjct: 357 FYQPTVMADVGPDMQIYREESFGPVVSIIKADDHEAALYIANDSEYGLSSAVITNDLQKA 416 Query: 423 RYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVT 478 ++AGM+ IN PF G K S FG G+ S++ T K +T Sbjct: 417 MELSLRLEAGMVHINDCTVFDEPHVPFGGVKKSGFG--REGGRYSMEEMTEVKWIT 470 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: 507 Number of extensions: 18 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: 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