Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate GFF1961 PGA1_c19940 hippurate hydrolase HipO
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__Phaeo:GFF1961 Length = 397 Score = 232 bits (591), Expect = 2e-65 Identities = 139/367 (37%), Positives = 187/367 (50%), Gaps = 7/367 (1%) Query: 6 RRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGILVRVHG----TAPTKTIG 61 RR LHQIPEL KT ++ + L + L +G++ ++G TIG Sbjct: 18 RRHLHQIPELALDLPKTAAFVAERLREFGVDELHEGIATSGMVAIINGQGNDAGDGPTIG 77 Query: 62 YRADMDGLPIDEQTDVPFRSTHEGRMHACGHDMHMAIALGVLTHVVH-HPIRDDMLFIFQ 120 RADMD LPI E+T V + S H G MHACGHD H + LG ++ + + IFQ Sbjct: 78 LRADMDALPIPEETGVDYVSGHAGNMHACGHDGHTTMLLGAAKYLAETRNFKGRVALIFQ 137 Query: 121 PAEEGPGGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFANTSELFIDLIG 180 PAEE GGA M+E M+++ + ALH AP PVG AT G L A I++ G Sbjct: 138 PAEEAIGGARIMVEEGIMERFNIGEVYALHNAPGLPVGAFATTPGPLMAAVDTFHINIQG 197 Query: 181 KGGHAAFPHETKDMVVAASSLIMQLQTIVSRNVNPLDSAVITIGKLTSGTVQNVIAERAR 240 GGH A PHET+D V+AA + +QTIVSRN LD V+++ ++ +GTV NVI + A Sbjct: 198 VGGHGAMPHETRDPVMAACGMAQAIQTIVSRNHYALDDLVVSVTQIHTGTVDNVIPDTAY 257 Query: 241 LEGTIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYNDETLTNEFMQFV 300 + GT+RT P E V R++ IV G +Y +A +DY Y ND + T Sbjct: 258 INGTVRTFDPRVQEMVMRRMKEIVAGQAASYGVEAELDYEVGYPATINDASKTGFAASVA 317 Query: 301 EKETDVHLVRCQ--EAMTGEDFGYMLARIPGFMFWLGVQSPFGLHHAKLNPNEEAIDVAI 358 + V + M EDF YML PG +LG GLHH K + N+E + Sbjct: 318 GEVAGPENVEAEAGREMGAEDFSYMLQARPGAYLFLGQGDSAGLHHPKYDFNDEIAPIGA 377 Query: 359 QLLTRYV 365 R V Sbjct: 378 SFFARLV 384 Lambda K H 0.322 0.137 0.411 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: 384 Number of extensions: 16 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: 378 Length of database: 397 Length adjustment: 30 Effective length of query: 348 Effective length of database: 367 Effective search space: 127716 Effective search space used: 127716 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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