Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_041099671.1 SUTH_RS12545 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000828635.1:WP_041099671.1 Length = 505 Score = 203 bits (516), Expect = 1e-56 Identities = 149/471 (31%), Positives = 221/471 (46%), Gaps = 27/471 (5%) Query: 9 FRQQAYVDGAWVD--ADNGQTIKVN---NPATGEIIGSVPKMGAAETRRAIEAADKALPA 63 F A + G W++ AD G +V NPA G + V A+ RA+ AA A Sbjct: 5 FINAADLVGHWINGHADAGAGTRVGEVFNPAEGRVARQVALATRADVDRAVAAARAAFAD 64 Query: 64 WRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWF---- 119 W + + RA + ++ DL+ + D+A+L++ E GK L +A GE+ +E+ Sbjct: 65 WGSAAPQRRARVMFKFRDLVDQYSTDIAKLLSAEHGKTLPDALGEVQRGLEVIEFACGIP 124 Query: 120 ----GEEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGC 175 G+ + I G +Q + P+GVTA ITP+NFP + A ALA G Sbjct: 125 QLLKGQHSHGIGGGIDHWNQ--------RMPLGVTAGITPFNFPFMVPMWMAPMALACGN 176 Query: 176 TMVLKPASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGST 235 T +LKP+ + P +L AEL AG+P G F+V+ G V L +P V ++F GST Sbjct: 177 TFILKPSERDPSPSLFAAELLREAGLPAGAFNVIQGDKEAVDA-LLEHPFVSAVSFVGST 235 Query: 236 EIGRQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRL 295 I + + A K+V G +V DADLD A + + + Y + G+ C+ + Sbjct: 236 PIAKYIQAHGIAHGKRVQALGGAKNHMVVMPDADLDGAADALIGAAYGSAGERCMAISVA 295 Query: 296 YVQDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVV 355 D V ++ A KL +G G A V GPL+ A KV +IA V +GAK+V Sbjct: 296 VAVGSCADDLVARVLARAKKLKVGAGDAANVEMGPLVTAVHRDKVAGYIAAGVQEGAKLV 355 Query: 356 SGGKPHALG----GTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTE 411 G+ G G F PT+ +V N + ++E FGP+ V R A + + N Sbjct: 356 LDGREGLTGELAQGFFINPTLFDNVTPNMSIYQEEIFGPVLCVVRVPTFAAAVELINRHT 415 Query: 412 FGLASYFYARDLARVFRVAEQLEYGMVGINTGL-ISNEVAPFGGIKASGLG 461 F + RD +++E GMVGIN + + FGG KAS G Sbjct: 416 FANGVACFTRDGGTAQAFIQKIEVGMVGINVPIPVPMAWHSFGGWKASLFG 466 Lambda K H 0.317 0.135 0.391 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: 574 Number of extensions: 30 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: 483 Length of database: 505 Length adjustment: 34 Effective length of query: 449 Effective length of database: 471 Effective search space: 211479 Effective search space used: 211479 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