Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_057508189.1 ABB28_RS08325 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= BRENDA::G5CZI2 (498 letters) >NCBI__GCF_001431535.1:WP_057508189.1 Length = 892 Score = 118 bits (295), Expect = 1e-30 Identities = 93/297 (31%), Positives = 134/297 (45%), Gaps = 8/297 (2%) Query: 3 TIGHLINGQLVTENTRSQNVFNPA-TGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPP 61 T L+ G VT S V NPA T ++ A TV++A++ A A P W TP Sbjct: 586 TAAPLVPGATVTG--ASLPVTNPADTRQVVGHWQAADAATVQKALANAVAAQPAWNRTPA 643 Query: 62 LKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEY-ACGAPELLKG 120 RA ++ + LE E L +E GK D + E++ ++ + Y A A E Sbjct: 644 TSRAAILEHAADQLEARIAEFMALCVKEAGKSLPDGVAEVREAVDFLRYYAKQAREQFAH 703 Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180 G + + GV I+P+NFP+ + L A+ GN + KP+E+ Sbjct: 704 AEKLPSPTGESNELQLHGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTNLI 763 Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVD-ALLHDDRVKAVSFVGSTPIAEYIYRTASAN 239 Y +LL +AG+P+GV+ + GD V AL D RV V+F GST A I R +A Sbjct: 764 GYYAVKLLLDAGVPEGVLQFLPGDGATVGAALTADPRVAGVAFTGSTDTARAINRAMAAR 823 Query: 240 GKRCQAL---GGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAA 293 L G +N I A + V +G+AF S+G+RC A V D A Sbjct: 824 DAAIGVLIAETGGQNAFIADSSALPEQLVKDAIGSAFTSAGQRCSAARVLFVQDDIA 880 Lambda K H 0.319 0.135 0.405 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: 891 Number of extensions: 52 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: 498 Length of database: 892 Length adjustment: 38 Effective length of query: 460 Effective length of database: 854 Effective search space: 392840 Effective search space used: 392840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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