Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_054254879.1 BN2503_RS01565 aliphatic amidase
Query= BRENDA::B3IVI7 (264 letters) >NCBI__GCF_001298675.1:WP_054254879.1 Length = 348 Score = 67.8 bits (164), Expect = 3e-16 Identities = 56/202 (27%), Positives = 87/202 (43%), Gaps = 6/202 (2%) Query: 33 GAQLLVCPEMFLTGYNIGLAQVERLAEAADGPAAMTVVEIAQAHRIAIVYGYP----ERG 88 G L++ PE G ++ A A G E + ++ V+ E Sbjct: 51 GMDLVIFPEYSTHGIMYDAKEMYDTAAAVPGEETAIFAEACRKAKVWGVFSLTGERHEEH 110 Query: 89 DDGAIYNSVQLIDAHGRSLSNYRKTHLFGELDRSMFSPGADHFPVVELEGWKVGLLICYD 148 + A YN++ L++ G + YRK + ++ + PG + +G KV L+IC D Sbjct: 111 PNKAPYNTLILMNDQGEIVQKYRKIMPWVPIEG--WYPGNCTYVSEGPKGLKVSLIICDD 168 Query: 149 IEFPENARRLALDGAELILVPTANMTPYDFTCQVTVRARAQENQCYLVYANYCGAEDEIE 208 +PE R A+ GAELI+ M P + +A A N Y+ AN G + Sbjct: 169 GNYPEIWRDCAMKGAELIVRCQGYMYPAKDQQVLMAKAMAWANNSYVAVANATGWDGVYS 228 Query: 209 YCGQSSIIGPDGSLLAMAGRDE 230 Y G S++IG DG L G +E Sbjct: 229 YFGHSALIGFDGRTLGECGEEE 250 Lambda K H 0.322 0.139 0.416 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: 226 Number of extensions: 8 Number of successful extensions: 1 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: 264 Length of database: 348 Length adjustment: 27 Effective length of query: 237 Effective length of database: 321 Effective search space: 76077 Effective search space used: 76077 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 (21.9 bits) S2: 48 (23.1 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