Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate H281DRAFT_06224 H281DRAFT_06224 hippurate hydrolase
Query= curated2:Q04FS2 (382 letters) >FitnessBrowser__Burk376:H281DRAFT_06224 Length = 326 Score = 182 bits (462), Expect = 1e-50 Identities = 104/282 (36%), Positives = 151/282 (53%), Gaps = 7/282 (2%) Query: 74 MDALPIQEETGLDFASKNDHVMHACGHDIHMTVALGILSYFAKHQPKDNLLVF-FQPAEE 132 MDALPIQE + SKND MHACGHD H + LG + AKH D +VF FQPAEE Sbjct: 1 MDALPIQELNSFEHKSKNDGKMHACGHDGHTAMLLGAARHLAKHGEFDGTIVFIFQPAEE 60 Query: 133 NEFGGKRFYDAGGFQGEYLPDEFYALHVNPQLPAGQIASRKGTLFAGSNELRISFIGKSG 192 G + D G F+ ++ D + +H P +PAG+ +G + A SNE RI G Sbjct: 61 GGAGAQAMIDDGLFE-KFPVDAVFGIHNWPGMPAGKFGVTEGPIMASSNEFRIEIKGVGS 119 Query: 193 HAAYPQNAKDSIVAAANFVTNVQTVVSRNVDPIEGGVVTIGKFNAGKAMNIIAGKADIEG 252 HAA P N +D + A +Q++++RN P++ V++I + +AG A+N++ A + G Sbjct: 120 HAALPHNGRDPVFTAVQIANGLQSIITRNKKPLDTAVLSITQIHAGDAVNVVPNDAWLAG 179 Query: 253 TIRSFTQSGMEIMTKHIRMIAEGIAGAFGQELKINFRQGGYMPVVNDERTTNFFIDYMK- 311 T+R+FT ++++ +R I E A A+ K++F + Y P +N F MK Sbjct: 180 TVRTFTTETLDLIEARMRKIVENTAEAYDCSAKVHFHR-NYPPTINSGDEARFAASVMKE 238 Query: 312 --NADGVDFKIVQPAMIAEDFGFLSNQFEGTMCWLGVNDPKH 351 A+ VD V+P M AEDF F+ G +LG D H Sbjct: 239 IVGAENVD-DSVEPTMGAEDFSFMLLAKPGCYAFLGNGDGGH 279 Lambda K H 0.320 0.137 0.397 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: 315 Number of extensions: 16 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: 382 Length of database: 326 Length adjustment: 29 Effective length of query: 353 Effective length of database: 297 Effective search space: 104841 Effective search space used: 104841 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 (21.8 bits) S2: 49 (23.5 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