Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Marino:GFF2064 Length = 489 Score = 243 bits (621), Expect = 8e-69 Identities = 147/460 (31%), Positives = 238/460 (51%), Gaps = 6/460 (1%) Query: 3 EIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSK 62 E+ + + YING+W+ +K+ + V +PA E L VP D A + A+ A+ W Sbjct: 9 ELLREQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRS 68 Query: 63 VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122 RA IL + LL ++E+LA L+T E GK E+ GEVG G +E+ A Sbjct: 69 TPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRA 128 Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182 GD + D + P+GVV I P+NFP+ + A+A G ++KP+E TP Sbjct: 129 YGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTP 188 Query: 183 LLTEKLVELFEKAGLPKGVFNVVY----GAHDVVNGILEHPEIKAISFVGSKPVGEYVYK 238 L + L E+AG+P G+ N++ A V + + +P ++ +SF GS PVG+ + + Sbjct: 189 LSALAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGKLLMR 248 Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298 + S+ +K+V G IV +DA+L+ V ++ + + + G+ C+ V V+ G+ D Sbjct: 249 QASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQAGVYD 308 Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS 358 F KL+ V+ + +G GL+ GP+I + + +IE +GA++ GR + S Sbjct: 309 AFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGRAH-S 367 Query: 359 DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSN 418 G F PTI + T EM I ++E F PV + + + EAI +AN SEF A ++ N Sbjct: 368 LGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFYSRN 427 Query: 419 SNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 + + E +++GM+G+N G+ PF G K S G Sbjct: 428 IHRVWRVAEELESGMIGVNEGI-ISTEVAPFGGVKESGLG 466 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: 551 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: 487 Length of database: 489 Length adjustment: 34 Effective length of query: 453 Effective length of database: 455 Effective search space: 206115 Effective search space used: 206115 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 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