Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 218 bits (555), Expect = 4e-61 Identities = 151/465 (32%), Positives = 232/465 (49%), Gaps = 17/465 (3%) Query: 6 KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 K N+I G+WV +Y D +P + C++P S +DI+ A A A W K +V Sbjct: 18 KYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAAKDAWGKTSV 77 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMG 124 R+ IL + Q+ E LA T ENGK +E L ++ +++ + AG G Sbjct: 78 TERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137 Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184 S A I + + ++ P+GVVG I P+NFP+++ W A+A GN +LKP+E+TP+ Sbjct: 138 -SAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVS 196 Query: 185 TEKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSEN 243 L+EL E LP GV NVV G + + I ++F GS VG ++ K +E+ Sbjct: 197 ILVLLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAES 255 Query: 244 LKRVQSLTGAKNHTIVL------NDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297 L G K+ + D L+ V ++ AF + GE C + V ++E I Sbjct: 256 LIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGML-LAFFNQGEVCTCPSRVLIQESIY 314 Query: 298 DEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR--- 354 D F+ K+ + IK GN LD +G ++ + LSY+ G +EGA+++ G Sbjct: 315 DRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSLCQ 374 Query: 355 -ENVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGAC 413 E GY++ PTI +M I+++EIF PV+SV K+ EA+ IAN +E+ GA Sbjct: 375 LEGEQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAG 433 Query: 414 LFTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 ++T + N + I AG + IN P A F G+K S G Sbjct: 434 VWTRDMNRAQRMGRGIQAGRVWINCYHAYP-AHAAFGGYKKSGIG 477 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: 569 Number of extensions: 24 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: 506 Length adjustment: 34 Effective length of query: 453 Effective length of database: 472 Effective search space: 213816 Effective search space used: 213816 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