Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_110207251.1 DNK54_RS12190 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_003194585.1:WP_110207251.1 Length = 474 Score = 239 bits (609), Expect = 2e-67 Identities = 147/468 (31%), Positives = 234/468 (50%), Gaps = 6/468 (1%) Query: 6 KLKNYINGEWVESKTDQYEDVVNPATK-EVLCQVPISTKEDIDYAAQTAAEAFKTWSKVA 64 K++ ++ GEW + T + NPA EV+ +T +D+ A A +A + W + Sbjct: 4 KIRQFVGGEW-RAGTGSAIESRNPARPHEVVASGHAATPDDVTEAVAAATKAAQAWRRTL 62 Query: 65 VPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMG 124 + RA +L +LL + + L +T+E GK E +GEV R E F AG +G Sbjct: 63 MHERAAVLRRTAELLEERADALGLELTLEEGKTLVEGIGEVRRAAEIFRFNAGQADREVG 122 Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184 + AS R PIGVV I P+NFP+ +P W A+ GN + KP+ PLL Sbjct: 123 EVFASPRRGERIVVTRKPIGVVAVITPWNFPIAIPAWKIAPALIHGNAVVWKPASIVPLL 182 Query: 185 TEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244 +L E AGLP GV +++ G + + I P + A++F GS +G + + + Sbjct: 183 AVRLAEALHDAGLPAGVLSLIIGPGALGSQIASAPGVHAVTFTGSTGIGTGLLQLCAPLR 242 Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 + VQ+ G KN +V DA+LE IV A S G++C A + + VE+ +A++ L Sbjct: 243 RPVQAEMGGKNAAVVFADADLELAADQIVLGAMRSTGQKCTATSRLVVEDSVAEDLRTLL 302 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364 +++ + +G+G V +GPV + S I+ L GAR+V + DDG++V Sbjct: 303 VQRIEALVVGDGTRSDVTVGPVSSGGAQAEITSMIDDALRGGARVV--AQAEAPDDGHYV 360 Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424 PTI + V IW++E+F PVL++ + +E+AN SEF A +FTS+ + Sbjct: 361 PPTILE-VDVRQPIWREEVFGPVLAMTTGADEDRVLELANASEFGLSAAVFTSDLSRTLR 419 Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYT 472 + ++ G+L +N PF G K S G G+ S +F+T Sbjct: 420 IMDELEVGVLHVNSESAGADPHVPFGGVKDSGIGP-KEQGRASREFFT 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: 502 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: 474 Length adjustment: 34 Effective length of query: 453 Effective length of database: 440 Effective search space: 199320 Effective search space used: 199320 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: 51 (24.3 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