Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_1083 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1083 Length = 490 Score = 266 bits (679), Expect = 2e-75 Identities = 170/484 (35%), Positives = 262/484 (54%), Gaps = 12/484 (2%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 MA K YI+G + ++ +D + +NPA EVL +V +TKED++ A +A + K W Sbjct: 1 MARFELQKLYIDGAYSDASSDATFEAINPANGEVLAKVQRATKEDVERAVVSAEKGQKIW 60 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAP 119 + + R+RIL ++L + +ELA L T++ GK E ++ G + +E+ AG Sbjct: 61 AAMTAMERSRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLV 120 Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 + G+ + + T R P+GVV GI +N+P+ + W A+A GN I KPSE Sbjct: 121 PAIEGEQIP-LRTTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSE 179 Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVY- 237 T L T KL E++ +AG+P GVFNV+ G+ +V + EHP I+ +SF G G+ V Sbjct: 180 VTSLTTLKLAEIYTEAGVPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMA 239 Query: 238 KKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297 S +LK V G K+ I+ +DA+L+ + A F S+G+ C V V + Sbjct: 240 SASSSSLKDVTMELGGKSPLIICDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPAHLK 299 Query: 298 DEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENV 357 F AK+ E+VA I+IGN D+ GP++ + + L YI KG EEGARL+C G E + Sbjct: 300 AAFEAKIAERVARIRIGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGG-ERL 358 Query: 358 SD----DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGAC 413 +D G FV PT+F + T +MTI ++EIF PV++++ + +E I AN ++F A Sbjct: 359 TDGEFAKGAFVAPTVFTDCTDDMTIVREEIFGPVMAILSYETEEEVIRRANDTDFGLAAG 418 Query: 414 LFTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTR 473 + T + N ++AG+ IN + A P G+K S G NG S++ +TR Sbjct: 419 IVTKDLNRAHRVIHQLEAGICWINAWGESD-AKMPVGGYKQS--GVGRENGISSLNNFTR 475 Query: 474 KKVV 477 K V Sbjct: 476 IKSV 479 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: 575 Number of extensions: 23 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: 490 Length adjustment: 34 Effective length of query: 453 Effective length of database: 456 Effective search space: 206568 Effective search space used: 206568 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