Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PP_2694 PP_2694 Aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Putida:PP_2694 Length = 480 Score = 255 bits (651), Expect = 3e-72 Identities = 156/475 (32%), Positives = 245/475 (51%), Gaps = 6/475 (1%) Query: 9 NYINGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67 NYI+G+W E +P+ T +++ Q ++ E A Q A A W+ + Sbjct: 8 NYIDGQWCEGHATLGN--YSPSDTGDLIGQYHQASAEQARQAIQAARAAQPLWAASGLES 65 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 R ++L L KEEL L++ E GK E +GEV R + + A MG++ Sbjct: 66 RQQVLMAIGDELIARKEELGELLSREEGKPLAEGIGEVNRSGQFFHYYAAEVLRQMGETA 125 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 AS+ V+ +R P+GVVG I P+NFPM W A+A GN + KP+ P Sbjct: 126 ASVRPGVDIEVHREPVGVVGIITPWNFPMATAAWKIAPALAFGNAVVFKPANLVPASAWA 185 Query: 188 LVELFEKAGLPKGVFNVVYGA-HDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 L E+ + GLP G FN+V G+ DV +++ EI A++F GS G V + NL R Sbjct: 186 LTEIISRQGLPSGTFNLVMGSGADVGEALIQSAEIDALTFTGSLQTGRRVAVATAGNLVR 245 Query: 247 VQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQE 306 Q G+KN +V++DA+LE V + AF G++C A + + V +GI D F+ L+ Sbjct: 246 CQLEMGSKNALVVMDDADLELAVECALNGAFFGTGQKCTASSRLIVCDGIHDRFVEALRL 305 Query: 307 KVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVG 365 ++ +K+G+ L+ GV +GPV ++ L+Y++ EGA L+ G R ++ DGY++ Sbjct: 306 RMRQLKVGHALEAGVQIGPVADARQLEQNLAYLQLAQAEGATLIEGGERLQLACDGYYMR 365 Query: 366 PTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYF 425 P +F N +M I ++E+F P+ VIRV++ +EA+ N +E+ A + T + +F Sbjct: 366 PALFINSRNDMRINREEVFGPIACVIRVRDFEEALATLNDTEYGLTAGIITQSLRHASHF 425 Query: 426 RENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTAR 480 + G + +NL PF G K+S FG G+ + DFYT K R Sbjct: 426 KRRAQTGCVMVNLPTAGTDYHVPFGGRKASSFGP-REQGQYARDFYTVVKTTYLR 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: 541 Number of extensions: 19 Number of successful extensions: 4 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 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