Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_090272720.1 BLU11_RS07260 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_900105005.1:WP_090272720.1 Length = 483 Score = 271 bits (692), Expect = 5e-77 Identities = 161/471 (34%), Positives = 260/471 (55%), Gaps = 5/471 (1%) Query: 9 NYINGEWVE--SKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66 +++NG +VE S+ D E+ +E++ + + + A A +A +W + Sbjct: 8 SFVNGVFVEADSQCDVLENRNPSNAEEIVDRFARADAALTEKAIAAARDAAGSWGRTNPQ 67 Query: 67 RRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDS 126 RA IL + + ++ELA L++ E GK +EALGEV R + +F A G+ Sbjct: 68 VRADILDRIGSEILERRQELAELLSREEGKVVREALGEVERAGRSFKFYAQEVLRANGEK 127 Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186 S+ V + PIGVVG I+P+NFP+ +P W A+A GNT ++KP+E P Sbjct: 128 YESVREGVSVDVFTQPIGVVGIISPWNFPIAIPAWKAAPALAFGNTVVMKPAELVPSSAW 187 Query: 187 KLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245 L E+ ++G+P GVFN+V G V + I+ P++ AI+F GS+ G V + ++ L Sbjct: 188 ALAEIISRSGMPAGVFNLVIGPGRTVGDTIIRSPKVDAITFTGSEGTGRQVAEIAAQRLI 247 Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305 RVQ G KN +VL+DA+L+ + + +F S G+RC A + + V GI DEF+A+L Sbjct: 248 RVQLEMGGKNPLVVLDDADLDVAIEVALNGSFYSTGQRCTASSRLIVTTGIHDEFVARLA 307 Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDG-YFV 364 E+ +++G+ L +GPV+ K+ L+YIE GL+EGA L+C G +D G Y Sbjct: 308 ERTRALRVGDPLCADTDIGPVVDPSQLKQNLAYIESGLQEGATLICGGEYLENDKGAYHF 367 Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424 P +F +V M I+++EIF PVLSV++V N +EA++ A ++++ A + T++ + Sbjct: 368 SPALFVDVQPHMRIYREEIFGPVLSVLKVANYEEALQAAEDTQYSLSAGIVTTSLKYAEH 427 Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 F+++ AGM+ +NL PF G + S G G + F+TR K Sbjct: 428 FKKHSSAGMVMVNLPTAGVDYHAPFGGNRGSSLGP-REQGTYARQFFTRVK 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: 541 Number of extensions: 22 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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 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